AU2012200711B2 - "Method and apparatus for orientating sperm in a fluid stream" - Google Patents

Abstract

The present application provides a flow cytometry apparatus nozzle to sort sperm cells in a fluid stream by chromosome content, as well as a method of orientating sperm cells in a flow cytometry apparatus and an apparatus for classifying and supporting sperm cells according to chromosomal DNA characteristics of the cells.

Description

AUSTRALIA PATENTS ACT 1990 REGULATION 3.2 Name of Applicant: INGURAN, LLC Actual Inventor/s: Gary Durack; Jeffrey D. Wallace; Gary P. Vandre; Lon A. Westfall; Jeremy T. Hatcher; and Niraj V. Nayak. Address for Service: E. F. WELLINGTON & CO., Patent and Trade Mark Attorneys, 312 St. Kilda Road, Melbourne, Southbank, Victoria, 3006. Invention Title: "METHOD AND APPARATUS FOR ORIENTATING SPERM IN A FLUID STREAM" The following statement is a full description of this invention including the best method of performing it known to us. This application is a 'divisional' application derived from Australian Patent Application No. 2010200961, which in turn is a 'divisional' application derived from Australian Patent Application No. 2004225436 (PCT/US2004/009646 : WO 2004/088283), claiming priority of US Application Nos. 60/458607 and 60/458731, the entire text of which are hereby incorporated herein by reference. 1 ' A Background of the Invention 5 This invention relates generally to apparatus and methods for animal semen collection, and more particularly to apparatus and methods using various techniques, including flow cytometry, to yield sperm populations that are enriched with sperm cells having one or more desired characteristics, such as viable populations of sperm cells sorted according to DNA characteristics for use by the animal production industry to preselect the sex of animal offspring. 10 The fertilization of animals by artificial insemination (Al) and embryo transplant following in vitro fertilization is an established practice. In the livestock production industry, the ability to influence the reproductive outcome toward offspring having one or more desired characteristics has obvious advantages. By way of example, there would be an economic benefit in the dairy industry to preselect offspring in favor of the female sex to ensure the production of dairy cows. 15 Efforts have been made toward achieving this goal by using flow cytometry to sort X and Y sperm cells, as evidenced by the disclosures in US Patents Nos. 6,357,307 (Buchanan, et al.), 5,985,216 (Rens, et al.), and 5,135,759 (Johnson). However, none of these efforts has resulted in the introduction of a commercially successful high-throughput system capable of producing production volumes of relatively pure sexed sperm cells having a motility sufficient for effective 20 fertilization. Accordingly, there is a current need in the animal production industry for a viable high speed system for efficiently isolating sperm cells based on a specified DNA characteristic (or other characteristics) to produce quantities of such cells, which can be used on a commercial scale. Also needed is a sperm handling system that preserves the viability of such isolated 25 sperm as it is processed by the isolating system and that allows for preservation of such isolated sperm until such time that it is ready for use. The present invention addresses these needs. This invention also has application to improvements in the field of flow cytometry on a more general basis. Flow cytometry may broadly be defined as measuring characteristics of individual particles as they pass generally single file in a fluid stream through a measuring device 30 which, typically, provides information for classifying the particles according to selected characteristics. Optionally, the particles may then be separated into populations using any number of techniques, including droplet sorting, droplet interference sorting, and fluid switching. Another option is to selectively destroy unwanted particles, for example by photo ablation. In an optically-based flow cytometry system, optics are used to direct and focus a beam 35 of light (e.g., visible light or UV light) on the stream containing the particles, and to collect emissions from the particles, including scattered light and/or fluorescence emissions from the particles. In one common optic system, for example, a beam of light (e.g., a laser beam) is focused on the stream and emissions are collected by a pair of collection units, one positioned forward of the laser for collecting scattered light emissions and another positioned orthoganally to 40 both stream and the laser for collecting fluorescence emissions. Each collection unit includes a separate photodetector, which increases the cost of the system. Further, in traditional optic 2 systems the photodetectors translate the collected emissions into electrical signals, which are analyzed using analog systems to classify the particles according to selected characteristics of the particles. Analog systems are relatively inexpensive, but only limited information can be derived from the signals. 5 Others have tried to develop technology that can be used to process sperm cells to obtain populations of sperm cells that are enriched with sperm that have a desired sex chromosome. However, the existing technology falls short of the inventive technologies described herein. For example, Johnson et al. (U.S. Patent No. 5,135,759) describe the separation of 10 intact X and Y chromosome-bearing sperm populations according to DNA content using a flow cytometer/cell sorter into X and Y chromosome-bearing sperm enriched populations. As described, the sperm is combined with a DNA selective dye at a temperature of 30 to 39*C for a period of 1 hour (39'C) to 1.5 hours (30*C). A flow cytometer is then used to measure the amount of fluorescent light emitted as the sperm passes through a laser beam that excites the 15 dye. Because the X chromosome-bearing sperm contains more DNA than the Y chromosome bearing sperm, with most species of mammal having about 3 to 5% difference, the X chromosome-bearing sperm emits more fluorescent light than the Y chromosome-bearing sperm. In order to account for the fact that the fluorescence measurement may vary depending on the rotational orientation of the sperm cells, two photo detectors are used. The first determines 20 whether the sperm cells are properly oriented, while the second takes a measurement that is used to classify the sperm as having an X or Y chromosome. An oscillator is used to cause the stream containing the sperm to break into droplets downstream of the place where the sperm pass through the laser beam. Droplets containing single sperm of a predetermined fluorescent intensity are given a charge and electrostatically deflected into collection vessels. The collected, 25 gender enriched sperm population, is then used for microinjection, in vitro fertilization, or artificial insemination. Seidel et al. (WO 02/43574) also describe separation of sperm into gender enriched populations of X and Y chromosome-bearing cells using flow cytometry. Seidel et al. describe staining the cells at a temperature between 30 0 C and 40 0 C. 30 United States Patent Application Pub. No. 2003/0157475 Al (Schenk, August 21, 2003) describes a method of cryopreserving sperm cells that have been sorted according to X or Y chromosome content. As noted therein, it is desirable to add a cryoprotectant to sperm cells before they are cryopreserved to protect the sperm cells during the cryopreservation process. For example, glycerol is one cryoprotectant that is commonly added to bovine sperm cells prior 35 to cryopreservation. However, in order to obtain better protection from the cryoprotectant, it is desirable to wait for the cryoprotectant to equilibrate with the sperm cells before subjecting the sperm cells to temperatures below 0*C. During the equilibration period, the cryoprotectant penetrates the cell membrane to provide intra-cellular protection in addition to any extra-cellular protection provided by the cryoprotectant. Thus, the cryopreservation methods described in 40 United States Patent Application Pub. No. 2003/0157475 Al specify that an extender containing 3 glycerol is added to the sperm cells after they have been cooled to about 50C. Then the sperm cells and glycerol are allowed to equilibrate at 5*C for anywhere between 1 and 18 hours before the sperm cells are subjected to lower temperatures. The disclosure recommends an equilibration period of between three and six hours in order to obtain the best results. 5 Unfortunately, the time and expense involved in a 3 to 6 hour equilibration period will have a negative impact on profitability of a commercial sperm sorting process. Furthermore, in the context of a commercial sperm sorting process, it is believed that the health of the sperm is generally improved by reducing the time between collection of the sperm and cryopreservation (other factors being equal). From this standpoint as well, it would be desirable to have access to 10 cryopreservation technology that does not require a long equilibration period to obtain the optimal benefits of a cryoprotectant. Moreover, the known cryopreservation technology is reported to have a detrimental impact on sperm motility, which is indicative of decreased sperm fertility. Thus, there is a need for cryopreservation techniques that preserves sperm health compared to conventional techniques. 15 Summary of the Invention This invention is directed to an improved system (methods and apparatus) for analyzing, classifying-and sorting particles based on one or more desired characteristics; the provision of such a system which, in one embodiment, uses flow cytometry to accurately isolate and sort cells 20 'by DNA content; the provision of such a system which, in certain embodiments, incorporates sorting protocols which enable the output of the system to be controlled as a function of one or more factors, including the purity of the desired sorted population of particles, the rate at which the desired particle population is collected, the loss of desired particles not sorted into the desired population, and other factors; the provision of such a system which, in one embodiment, 25 operates at high-speed to provide sex sorted sperm for commercial use by the animal production industry; the provision of such a system which can be used to sort cells without significant detrimental effect on the cells, including the motility of sperm cells; the provision of a system that can be used to preserve sorted sperm cells until they are needed with minimal detrimental effect on the cells, including, the motility of the cells, the provision of such a system which, as it relates 30 to the production of sexed sperm, incorporates techniques which increase the speed and accuracy of the classification and sorting of the sperm cells; the provision of a flow cytometry system which uses epi-illumination optics to detect various characteristics of particles to be analyzed and, optionally, sorted; the provision of such an epi-illumination flow cytometry system which is economical to manufacture; the provision of a system which, in one embodiment, 35 incorporates multiple flow cytometry units which share an integrated platform for classifying and (optionally) sorting particles, such as cells in general and sperm cells in particular, at high rates of production; the provision of such a multi-channel system which share common components and systems to reduce variations between the channels for more efficient operation; and the provision of such a sorting system which, in one embodiment, incorporates protocols which 4 enable a sample to be quickly tested to determine the quality of the sample so that the profitability of further sorting can be evaluated. In addition, this invention is directed to an improved system (methods and apparatus) for digitally processing signals representing fluorescence; the provision for such a digital system, in 5 one embodiment, for detecting analog to digital converted-pulses as a function of background characteristics; the provision for such a digital system, in one embodiment, for initializing discrimination parameters; the provision for such a digital system, in one embodiment, for detecting digital information corresponding to waveform pulses; the provision for such a digital system, in one embodiment, for digital information analysis including feature extraction; the 10 provision for such a digital system, in one embodiment, for classifying pulses and defining decisions boundaries; the provision for such a digital system, in one embodiment, employing a droplet break-off sensor to control transducer amplitude; and the provision for using such a digital system, in one embodiment, to distribute and collect cells for commercial distribution. Further, this invention is directed an improved comprehensive system (apparatus and 15 methods) for commercial processing of animal semen from the time a semen sample is collected from a male animal through cryopreservation of a sperm sample containing a greater percentage of a sperm having a desired chromosome characteristic than exists in the collected semen; the provision of such a system, in one embodiment, that allows efficient processing of commercial quantities of viable gender enriched sperm; the provision of such a system that allows, in one 20 embodiment, adjustment of the system to counter day-to-day and animal-to-animal variations in the semen characteristics; the provision of such a system that, In one embodiment, allows production of about 18,000,000 gender enriched sperm per hour by a single flow cytometry unit at 85% purity; and the provision of such a system that allows, in one embodiment, complete processing of a batch of semen (e.g., the amount of semen collected from a male animal) to yield 25 viable sperm samples having a desired gender characteristic at 85% purity with less than 10% loss of collected sperm having the desired gender characteristic in about 1 hour of processing time. In general, this invention is directed to the apparatus and methods set forth in the claims of this application. 30 Other objects and features of this invention will be in part apparent and in part pointed out hereinafter. Brief Description of the Drawings Fig. 1 is a work flow diagram for an exemplary sperm sorting process of the present 35 invention; Fig. 2 is a schematic diagram of a one embodiment of a flow cytometry droplet sorting system of the present invention; Fig. 3 is a side view of a portion of one embodiment of a flow cytometry apparatus of the present invention for droplet sorting showing an epi-illumination optic assembly focusing an 40 excitation beam on an upward moving fluid stream generated by a nozzle system; 5 Fig. 4 is an end view of one embodiment of a nozzle and nozzle holder of the present invention; Fig. 5 is a sectional view of the nozzle and nozzle holder of Fig. 4 taken through cutting plane 5--5 on Fig. 4; 5 Fig. 6 is a schematic diagram of a sperm cell entrained in a fluid stream being interrogated by an elliptically shaped beam spot according to one embodiment of the present invention; Fig. 7 is a schematic diagram showing the angular envelope for the desired orientation of a sperm cell in which the light beam from the optics system will strike a wide face of the cell 10 generally broadside; Fig. 8 is a cross sectional view of one embodiment of a nozzle body of the present invention; Fig. 9 is a side view of the nozzle body shown in Fig. 8 showing a series of cutting planes (A-A through H-H and J-J through K-K) through the nozzle body; 15 Figs. 9A-9H and 9J-9K are sectional views of the nozzle body shown in Figs. 8 and 9 along the corresponding planes (A-A through H-H and J-J through K-K) of Fig. 9; Fig. 10 is a perspective view of a cross section of one embodiment of a nozzle system having an orienting baffle in the nozzle; Fig. 11 is a cross sectional view of the nozzle system shown in Fig. 10; 20 Fig. 12 is an enlarged partial cross sectional view of a portion of the nozzle system shown in Figs. 10 and 11; Fig. 13 is an enlarged partial cross sectional view similar to the view shown in Fig. 12, but taken from a direction that is perpendicular to the viewing direction in Fig. 12; Fig. 14 is a side view of one embodiment of baffle holder holding a baffle plate; 25 Fig. 15 is a top view of the baffle holder and baffle plate shown in Fig. 14; Fig. 16 is a top view of one embodiment of a baffle holder rotationally oriented in a nozzle so that the legs of the baffle plate intersect in a line that is parallel to the major axis of ellipse D in the nozzle; Fig. 17 is a top view of one embodiment of a baffle holder rotationally oriented in a 30 nozzle so that the legs of the baffle plate intersect in a line that is perpendicular to the major axis of the ellipse D in the nozzle; Fig. 18 is a side cross sectional view of one embodiment of a nozzle system including a baffle showing a series of cutting planes (A-A through E-E) through the nozzle and baffle; Figs. 18A-18E show the cross sectional flow areas at various points in the nozzle system 35 shown in Fig. 18; Fig. 19 is a cross sectional view similar to Fig. 12 taken through a nozzle having a baffle plate that is perpendicular to the longitudinal axis of the nozzle; Fig. 20 is a cross sectional view of the nozzle shown in Fig. 19 taken through the cutting plane 20-20 shown on Fig. 19; 6 Fig. 21 is a cross sectional view similar to the cross sectional view of Fig. 18 showing a nozzle system having a sample introduction conduit at an offset location; Fig. 22 is a perspective view of one embodiment of a nozzle system mounted on a nozzle mount of the present invention; 5 Fig. 23 is schematic diagram of a plurality of aligned sperm cells being rotationally oriented as they pass through an orifice member of the present invention toward the interrogation location; Fig. 24 is a schematic diagram showing the droplet break-off location downstream from the nozzle according to one embodiment of the present invention; 10 Fig. 25 is a schematic diagram of one embodiment of a break-off sensor system of the present invention; Fig. 26 is a front elevation of one flow cytometry system of the present invention; Fig. 27 is an enlarged perspective view of a portion of the system shown in Fig. 26 with parts of the system removed for clarity; 15 Fig. 28 is a schematic diagram of one embodiment of an epi-illumination optics system of the present invention; Fig. 29 is a perspective view of one embodiment of an epi-illumination optics system of the present invention; Fig. 30 is a side view of the epi-illumination optics system shown in Fig. 29; 20 Fig. 31 is a top view of the epi-illumination optics system shown in Figs. 29 and 30; Fig. 32 is a sectional view of the epi-illumination optics system along the plane 32-32 of Fig. 30; Fig. 33 is a sectional view of a portion of the epi-illumination optics system along the plane 23-33 of Fig. 31; 25 Fig. 34 is a perspective view showing only elements of the optical filtering system that are rearward of the dichroic filter of the epi-illumination optics system shown in Fig. 29; Fig. 35 is a perspective view of another epi-illumination optics system of the present invention including translational adjustment of the cylindrical lens; Fig. 36 is a schematic diagram of an interrogation location of one embodiment of the 30 present invention showing a laser beam focused on a fluid stream downstream of the nozzle at a skewed angle of incidence; Fig. 37 is a schematic diagram of one embodiment of a sort calibration system of the present invention; Fig. 38 is a schematic diagram of one embodiment of an epi-illumination sensor for use 35 with the sort calibration shown in Fig. 37; Fig. 39 is a block diagram of one embodiment of a digital cell analyzer (DCA) and processor controller according to the invention. Fig. 40 is a schematic diagram of one embodiment of a multi-channel sorter of the present invention showing two channels; 7 Fig. 41 is a work flow diagram of one embodiment of a multi-channel sorter of the present invention showing four channels; Fig. 42 is block diagram of one embodiment of an analog cell analyzer (ACA) according to the invention; 5 Fig. 43 is a graph illustrating a stream of waveform pulses from a photodetector output detecting fluorescent pulses from cells streaming at an average rate of 10,000 cells/second; Fig. 44 is an exploded view of Fig. 43 illustrating the stream from a photodetector output detecting three fluorescent pulses from three cells streaming at an average rate of 10,000 cells/second; a square wave of a 100MHz droplet clock has been superimposed on the 10 illustration to show the synchronization between the three pulses and the square wave pulses of the droplet clock; Figs. 45 illustrates movement of a sperm cell relative to a laser beam spot having a narrow width; Fig. 49 is an exemplary illustration of the digital information corresponding to a time 15 varying analog output from a photodetector detecting a single fluorescence pulse based on 122 samples at a 105MHz continuous sampling rate; Fig. 50 is a schematic diagram illustrating the timing relationship between laser pulses, fluorescence emissions from a cell resulting from the laser pulses and the digital samples of the photodetector output in one embodiment of the invention; 20 Fig. 51 is a schematic diagram Illustrating how the digital samples shown in Fig. 50 form a pulse waveform; Fig. 52 is a schematic diagram of a pulse waveform from and X sperm cell synchronized with the pulse waveform of a Y sperm cell showing higher peak intensity in the pulse waveform for the X sperm cell; 25 Fig. 53 is a schematic diagram of a pulse waveform showing a threshold and integration window that can be used for pulse analysis; Fig. 54 Is a histogram of a sample containing X and Y sperm cells showing the high resolution attainable with slit scanning techniques; Fig. 55 is histogram of a sample containing X and Y sperm cells showing the relatively 30 poor resolution attained with standard illumination; Figs. 56-59 show fluorescence histograms and scatter plots of peak vs. area for sperm nuclei and live sperm cells; Figs. 60-61 illustrate a four-component model of a fluorescence intensity histogram for sperm cells - Fig. 60 shows raw data and Fig. 61 shows model curves generated by one 35 embodiment of an iterative algorithm of the present invention based on the data shown in Fig. 60; Figs. 62-63 illustrate a three-component model of a fluorescence intensity histogram for sperm cells - Fig. 62 shows raw data and Fig. 63 shows model curves generated by one embodiment of an iterative algorithm of the present invention based on the data shown in Fig. 62; Fig. 64 illustrates the non-linear nature of the CSD feature; the top panel shows average 40 M plots for X-bearing and Y-bearing sperm cells; the middle panel shows a graph of the first 8 derivatives of these average M plots (i.e. M') for signal amplitude values less than the peak height of the average Y-bearing fluorescence emission pulse; and the bottom panel shows the difference between the first derivatives (M'x - M'y) as a function of signal amplitude; Fig. 65 illustrates one embodiment in which the CSD feature is the computed slope of a 5 line that passes through two points on the fluorescence emission pulse; Figs. 66-69 illustrate improved discrimination achieved by use of CSD feature extraction; Fig. 70 illustrates a bi-variate sort region set on a scatter plot of CSD vs. pulse area scatter; Fig. 71 illustrates one embodiment of flow cytometry re-analyses for a test in which the 10 left panel corresponds to the high recovery/coincident accept sort strategy (no coincidence abort strategy) and the right panel corresponds to the high purity/coincident reject sort strategy (coincident abort strategy); Fig. 72 is a work flow diagram of one embodiment of digital signal processing of the present invention; 15 Fig. 73 Is an example of a k-Means clustering strategy that may be employed according to one embodiment of the present invention; Fig. 74 is a conceptual illustration and graphical representation of application of a Bayes Minimum Error decision rule to pulse feature data as may be employed according to one embodiment of the present invention; 20 Fig. 75 is graphical representation of results obtained using a Bayes Minimum Error decision rule and Mahalonobis distance thresh holding as may be employed according to one embodiment of the present invention; Fig. 76 is a conceptual illustration of moving window statistics to provide "forgetting" as may be employed according to one embodiment of the present invention; 25 Fig. 77 Is a graphical representation drift compensation as may be employed according to one embodiment of the present invention; Fig. 78 illustrates a fluid stream containing an exemplary distribution of particles; Fig. 79 is a graph showing purity as a function of fluid delivery rate with a coincident accept sort strategy; 30 Fig. 80 is a graph showing the percentage of desired particles successfully sorted into the usable population as a function of fluid delivery rate with a coincident reject sort strategy; Fig. 81 is a graph showing the inverse relationship between the percentage of coincident droplets accepted for sorting into a population of desired particles compared to the percentage of coincident droplets rejected for sorting into that population; 35 Fig. 82 is a decision flow diagram showing the overall operation of one embodiment of a sorting apparatus of the present invention; Fig. 83 is a side elevation of a cytometer oriented to produce a stream of droplets having a horizontal velocity component and a collection system to collect the droplets; Fig. 84 is an enlarged perspective view of the collection system shown in Fig. 83 shown 40 relative to the nozzle system and deflector plates; 9 Fig. 85 is a schematic diagram of one embodiment of a collection system of the present invention; Fig. 86 is a front elevation of an intercepting device of the collection system shown in Fig. 83; 5 Fig. 87 is a side elevation of an intercepting device of the collection system shown in Fig. 83; Figs. 88-95 show graphical results of several sperm centrifugation experiments; Fig. 96-98 are schematic diagrams illustrating the steps in one embodiment of a filtration method of the present invention; 10 Fig. 99 is a schematic diagram of one embodiment of a filtration system used to filter sperm cells; Fig. 100 is a schematic diagram of another filtration system used to filter sperm cells; Figs. 101 and 102 show graphical results of sperm cell filtration experiments; Fig. 103 is a work flow diagram for one embodiment of a cryopreservation method of the 15 present invention; Fig. 104 shows graphical results for a sperm cell cryopreservation experiment; Fig. 105 is a work flow diagram for one embodiment of a method of processing sperm cells according to the present invention; Fig. 106 is a perspective view of one embodiment of a multi-channel particle sorter of the 20 present invention with parts broken away to show internal features of the sorter; Fig. 107 is a perspective view of a manifold system that may be used for fluid delivery in the multi-channel particle sorter of Fig. 106; Fig. 108 Is a perspective view of the manifold system of Fig. 107 showing internal fluid connections of the manifold system; 25 Fig. 109 is a perspective view of the particle sorter shown in Fig. 106 with additional elements removed or partially removed to better show internal features of the sorter; Fig. 110 is a front elevation of the particle sorter shown in Fig. 106; Fig. 111 is a side elevation of the particle sorter shown in Fig. 106 with the side wall of the housing removed to show intemal features of the sorter; 30 Fig. 112 is a side elevation of the particle sorter shown in Figs. 106 (taken from the side opposite the side from which Fig. 107 was taken) with the side wall removed to show internal features of the sorter; Fig. 113 is a perspective view of the particle sorter shown in Figs. 106 taken from an angle behind the sorter and with the back cover removed to show internal features of the sorter; 35 Fig. 114 is a perspective view of a portion of the particle sorter shown in Fig. 106 showing the mounting of multiple nozzle systems to a cross bar; Fig. 115 is a perspective view of a portion of the particle sorter shown in Figs. 106 showing the relative positions of the collection system and other parts of the particle sorter; Fig. 116 is a schematic diagram of one embodiment of a fluid delivery system for a multi 40 channel sorter of the present invention; 10 Figs. 117 and 118 are schematic diagrams of two different laser beamsplitting systems; Figs. 119 and 120 are perspective views of another multi-channel system of the present invention; Figs. 121-134 show graphical results of various experiments; 5 Fig. 135 is a schematic diagram of one alternative embodiment for a nozzle system of the present invention wherein the nozzle directs the fluid stream through a capillary tube; Fig. 136 is a schematic diagram of one embodiment of a photo damage sorting system of the present invention; Fig. 137 is a schematic diagram of an alternative sorting system based on fluidic 10 switching that may be used in an apparatus employing the technology of the present invention; and Fig. 138 is a schematic diagram of an alternative sorting system based on a high-speed droplet interference stream that diverts selected discrete segments of the fluid stream carrying the analyzed particles. 15 Corresponding parts are designated by corresponding reference numbers throughout the drawings. A parts list with associated reference numerals for each part follows. The parts list is provided with section headings generally corresponding to section headings in the specification to facilitate use of the parts list. Generally, each section of the parts list provides a reference 20 numeral for the parts that are introduced for the first time in the corresponding section of the Detailed Description. Parts List with Associated Reference Numerals for Each Part 25 General Overview 39 Semen Collection 41 Label Semen 41A Add Buffer 43 Quality Control 30 47 Washing 48 Staining Fluid 49 Staining 51 Incubation 53 Load into Sample Introduction Device of Flow Cytometer 35 54 Add Sheath Fluid Through Flow Cytometry 55 Sorting 57 Collecting Sorted Sperm 58A Add Collection Fluid 58B Concentrate Sperm Cells 40 58C Add Cryoextender 59 Load Sorted Sperm into Straws 61 Cryopreservation 63 Packing in Liquid Nitrogen 65 Distribution 45 67 Sales 69 Storage 71 Artificial Insemination 11 Flow Cvtometry 1 System (Overall) 3 Supply of Carrier Fluid 7 Supply of Sheath Fluid 5 9 Flow Cytometry Apparatus Having Sorting Capabilities 15 Fluid Delivery System 17 Carrier Fluid 19 Sheath Fluid 21 Stream of Fluid 10 23 Stream of Particles 25 Beam of Electromagnetic Radiation 31 Electromagnetic Radiation Emission from Particles 33 Droplets 35 Particles Contained in Droplets 15 Flow Ctometry Apparatus (Single Channel) 101 Nozzle System 103 Nozzle Orifice 105 Transducer 20 107 Droplet Break-off 109 Optics System 115 Interrogation Location 117 Photodetector 119 Sorting System 25 123 First Different Group or Population of Droplets 125 Second Different Group or Population of Droplets 2201 Collection System 131 Processor 30 Nozzle System 133 Cylindrical Flow Body 135 Central Longitudinal Bore 137 Nozzle 139 Funnel-shaped Nozzle Body 35 141 Passage Through Nozzle Body 145 Internally Threaded Counterbore 149 Threaded Projection or Stud 155 O-ring Seal 157 Conduit (Tubular Needle) 40 167 Annular Space (Gap) 173 Radial Bore in Flow Body (Sheath Fluid) 183 Second Radial Bore (Additional Sheath Fluid) 189 Central Core of Carrier Fluid 191 Outer Co-axial Sheath of Fluid 45 Cell Orientation 201 Bovine Sperm Cell 205 Paddle-shaped Head 207 Flat Wide Opposite Faces 50 209 Narrow Edges 211 Sperm Equator 213 Nucleus 215 Tail 217 Nucleus Length 55 219 Head Length 221 Head Width 223 Overall Length 225 Localized Region Within Nucleus 227 Direction of Stream Flow 60 229 Angular Envelope in Which Light Beam Strikes Wide Face 12 R1 Angular Range P Plane Nozzle Design 5 231 Interior of Nozzle Body 233 Interior Surface of Nozzle Body 235 First Axially Tapered Region 237 Second Axially Tapered Region 239 Third Axially Tapered Region 10 247 Longitudinal Axis of Nozzle 249 Fourth Region Interior of Nozzle 251 Axial Length of Fourth Region 255 Orifice Member 257 Counterbore at Front End of Nozzle 15 259 First Torsional Zone 261 Second Torsional Zone 263 Surface of First Torsional Zone 267 Surface of Second Torsional Zone 271 Torsional Forces 20 273 Axial Length of First Torsional Zone 275 Axial Length of First Tapered Region 277 Axial Length of Second Tapered Region 279 Axial Length of Second Torsional Zone 309 Conical Upstream Surface of Orifice Member 25 315 Cylindrical Downstream Surface of Orifice Member 317 Axial Length of Conical Upstream Surface 327 Axial Length of Downstream Surface Orienting Baffle 30 2001 Orienting Baffle 2003 Baffle Plate 2005 Baffle Holder 2007 Upstream Leg 2009 Downstream Leg 35 2015 Line of Intersection 2017 Central Axis of Nozzle Body 2019 Curved Edge of Upstream Leg 2025 Distance Lower Leg Extends Downstream 2027 Overall Length of Baffle Holder 40 2029 Exterior Diameter of Baffle Holder 2031 Interior Diameter of Baffle Holder 2033 Distance Between Line of Intersection and Center of Nozzle 2035 Upstream End of Baffle 2037 Inclined Surface of Baffle Holder 45 2039 Side Edges of Downstream Leg 2041 Downstream Edge of Downstream Leg 2049 Gap Between Baffle Plate and Baffle Holder 2051 Inside surface of Baffle Holder 2053 Volume Behind Baffle Plate 50 2055 Interior Volume of Nozzle 2057 Longitudinal Axis of Cylindrical Baffle Holder 2059 Line Through Major Axis of Ellipse D 2061 Distance Between Injection Needle and Baffle 2067 Downstream End of Baffle Holder 55 2069 Contact Points Between Baffle Holder and Nozzle 2071 0-Rings 2077 Downstream End of Nozzle Holder (Boss) 2079 Interior Diameter of Boss 2081 Portion of Sheath Fluid Between Core Stream and Nozzle Surface 60 2087 Cross Section Upstream (A) 13 2089 Cross Section at Baffle (B) 2091 Cross Section at Baffle (C) 2093 Cross Section at Baffle (D) 2094 Cross Section Downstream of Baffle (E) 5 2097 Perpendicular Baffle System 2095 Air Bubble 2099 Perpendicular Baffle Plate 2101 Curved Edge of Perpendicular Baffle Plate 2103 Straight Edge of Perpendicular Baffle Plate 10 2105 0-ring 2107 Annular Shoulder (Shelf) in Nozzle 2109 Outer Diameter of Sample Injection Needle (Conduit) 2151 Nozzle System Having an Offset Sample Introduction Conduit 15 Nozzle Mounting and Adlustment 331 Nozzle Mount 333 First Linear Stage 337 Second Linear Stage 339 X Axis 20 341 Y Axis 343 Third Rotational Stage 345 Z Axis 347 Fixed First Stage Member (Not Shown) 349 Frame for First Fixed Stage Member 25 355 Movable First Stage Member 357 Actuator (Micrometer) for First Stage 359 Fixed Second Stage Member 361 Movable Second Stage Member 363 Actuator (Micrometer) for Second Stage 30 365 Fixed Third Stage Member 371 Movable Third Stage Member 373 Actuator (Micrometer) for Third Stage 375 Generally Upward Direction of Stream Containing Cells 377 Angle of Upward Direction 35 Transducer and Droplet Formation 379 Collar 381 Piezoelectric Element (Not Shown) 383 Terminals 40 D Diameter of Stream Break-off Sensor 389 Break-off Sensor 391 Microprocessor 45 393 Light Source 395 Linear Photoarray (Photodlodes) 401 Lens for Droplet Break-off Sensor 405 Current to Voltage Op-amp Circuits 407 Track/hold Amplifiers 50 409 Sinewave Generator (Track/hold Signal) 411 AD Converter 412 Camera System 413 Strobe 414A Mask 55 414B Slit-Shaped Opening in Mask Epi-illumination Optics System 415 Epi-illumination System 60 417 Epi-illumination Instrument 14 419 Longitudinal Optical Axis 425 Beam Spot 427 Axis of Focused Illumination Beam 429 Rectangular Base 5 431 Reflecting Filter 435 Laser or Arc-lamp 437 Conditioning Lens Assembly 439 Opening in 441 Side Wall of a Dichroic Chamber 10 443 Dichroic Chamber 445 Retaining Ring 447 Neutral Density Filter 449 Cylindrical Lens 455 Lens Holder 15 457 Jam Nut 459 Elliptical Cross Section of Beam Spot 461 Clips for Reflecting Filter 463 Filter Holder 465 Angular Face of Filter Holder 20 467 Openings in Filter Holder 469 Linear Stage for Filter Holder 471 X Axis 473 Outrigger 475 Actuator for Linear Stage 25 477 Dichroic Filter 479 Clips for Dichroic Filter 485 Frame for Dichroic Filter 487 Forward Direction 489 Longitudinal Optical Axis of the Optical Instrument 30 491 Focusing Lens Assembly 497 Fluorescent Pulse Waveform or Signal Emitted by Cell 498 Excitation Spatial Function 501 Microscope Adapter 503 Opening in Front Wall of Dichroic Chamber 35 505 Front Wall of Dichroic Chamber 507 Focusing Barrel 509 Lens Mount Barrels 511 Focusing Lens 513 Rearward Direction 40 515 Telescoping Focus Adjustment 517 Collimated Emitted Light 519 Filtering System 521 Emission Filter 523 Emission Filter Holder 45 525 Opening in Back Wall of Dichroic Chamber 527 Back Wall of Dichroic Chamber 529 Alignment Pellicle Assembly 531 Slider of Alignment Pellicle 533 Rail for Filter Assembly Components 50 535 Filter Holder for Alignment Pellicle 539 Pellicle Filter Element 541 Clips for Securing Filter Element to Filter Holder 543 Angle for Alignment Pellicle Relative to Optical Axis 545 Fasteners for Securing Slider to Base 55 547 Parallel Slots in Base 549 Aspheric Lens 551 Holder for Aspheric Lens 553 Frame for Aspheric Lens 557 Fasteners for Aspheric Lens 60 559 Spatial Filter 561 Aperture Plates 563 Frame for Spatial Filter Plates 567 Vertical Slit 571 Horizontal Slit 5 573 Aperture 575 Vertical Dimension 577 Horizontal Dimension 579 Collection Volume 583 Plate Holder 10 587 Fasteners for Plate Holder 589 Backing Member for Aperture Plates 449A Adjustable Mounting Assembly 449B Slots 449C Slots 15 450 Epi-illumination that Reflects Fluorescence Emissions 451 Dichroic Filter Photodetector 20 591 Mounting Plate for Photodetector 595 Fasteners for Photodetector Angle of Beam Incidence 605 Distance Between Interrogation Location and Nozzle Orifice 25 609 Beam Axis A Angle of Incidence Focused Beam Spot LI Length along Major Axis 30 W1 Width along Minor Axis Sorting System 627 Charging Device 629 Charged Deflector Plates 35 631 Charging Element 633 Opening in Charging Element 635 Power Supply for Deflector Plates 5001 Adjustable Mounting Assembly 5003 Mounting Assembly Adjustment Board 40 5005 Mounting Assembly Backing 5007 Fasteners 5009 Slots 5011 Translation Axis 5013 Translation Axis 45 5015 Mounting Assembly Adjustment Board 5017 Fasteners 5019 Slots 5021 Fixed Support 5023 Fasteners 50 5025 Spring Automat Sort Calibration 4201 Calibration System 4203 Epi-Illumination Sensor 55 4205 Fiber Optic Cable 4207 Dichroic Filter 4209 Lens System 4211 Fluorescent Emission from Particle in Droplet 4213 Photodetector 60 4215 Beam Stop 16 Sort System Fault Correction 5047 Debris Removal System for Charging Element 5 5049 Debris Removal System for Deflector Plates 5051 Support for Charging Element 5053 Vacuum Passage 5055 Vacuum Line 5057 Opening Adjacent Charging Element 10 5058 Fitting 5059 Compressed Gas Line 5061 Manifold 5063 Air Passages 5064 Openings 15 5065 Fitting 5066 Side of Deflector Plate Protection of Sorted Sample 20 4033 Collection Vessel 4041 Contamination Prevention Mechanism 4043 Pneumatic Actuator 4045 Swing Arm 25 4047 End of Swing Arm Fluid Delivery System 645 Syringe Pump 647 Flow Line from Pump to Carrier Supply 30 649 Vessel for Containing Supply of Carrier Fluid 651 Line from Pump to Injection Needle 657 Supply Line from Syringe Pump to Needle 659 Variable Speed Motor 661 Second Vessel - for Supply of Sheath Fluid 35 667 Supply Line for Connecting Sheath Fluid to Radial Bore in Nozzle 669 Control Valve in Supply Line 671 Gas Pressure System for Sheath Fluid 675 Source of Pressurized Gas 679 Air Line for Pressurized Gas 40 681 Regulator for Controlling Pressure Supplied to Sheath Fluid Tank 683 Two-way Valve in Air Line Control 689 A/D Converter 45 693 Relative Beam Intensity Experienced by Point Moving Through Beam Spot 695 Relative Emitted Pulse Intensity From Sperm Traversing Beam Spot d Distance Between Nozzle and Droplet Break-off Location Signal Processing 50 701 Output Signal From Photodetector 703 Droplet Generation Clock Signals 705 Digital Signal Processing (Digital Cell Analyzer) 707 Digital Signal from A/D 735 PC/Computer Terminal 55 737 Master Clock (128 x Clock Signal) 739 Data Acquisition (HH1') 741 Initializing Detection Parameters (HH1) 745 Initializing Discrimination Parameters (HH2) 747 Digital Pulse Detection (HH3) 60 749 Digital Pulse Analysis - Feature Extraction (HH4) 17 753 Pulse Area (HHS) 755 Pulse Peak (HH6) 757 Pulse Discrimination (HH7) 759 Sorting (HH8) 5 761 Drift Analysis (HH9) 763 Decision Boundary for Bayes Rules 769 Initialize 771 System Check 773 User Interaction 10 775 Retry (Up to Three Times) 777 Flush 779 Bead Quality Control 781 Aspirate Sample 783 Sample Quality Control 15 785 Start Sample 787 Sort On 789 Sample Complete 791 Continue Sample 793 Sort Off 20 795 X/Y Discrimination Optimum 797 Set X/Y Discrimination 799 Discrimination OK 801 Rate Optimum 803 Set Syringe Rate 25 805 Rate OK 807 System Check 809 System Reset 811 System OK 813 Exemplary Overall Operational Flow 30 825 Integrator 827 Width/Area Comparator 829 Dynamic Threshold Calculator 831 Pulse Discrimination 833 JTAG Port 1/O 35 837 Window Comparator (Area) 839 Pulse Width and Trigger Logic 841 Sort Decision 843 i/O Controllers 845 Slave Controllers 40 847 Sort Controller Board 849 USB 851 DSP Board SDRAM 853 Sort Signal 854 Low-Pass Filter 45 855 I/O Board SDRAM 857 Processor i/O 859 Peripheral I/O Bus 861 Sort Pulse Generator 863 Data Management Processor 50 865 Pulse Detection Processor 867 Feature Extraction Processor 873 Sort Processor 875 DSP Board RAM OL Inverse Relationship Between Coincident Droplets in Usable Population Compared to 55 Coincident Droplets in Unusable Population P1 Point on Line OL Corresponding to 85% Purity LL Point on Line OL Corresponding to 60% Collection of Desired Particles OR Operating Range (Segment of OL Between P1 and LL) 6000 Raw Data 60 6001 1st Population of Non-aligned Cells 181 6003 2nd Population of Non-aligned Cells 6005 Aligned Y Population 6007 Aligned X Population 6010 Raw Data 5 6011 Population of Non-aligned Cells 6015 Aligned Y Population 6017 Aligned X Population Multi-channel System 10 1001 Multi-channel System 1003 Flow Cytometry Units 1005 Common Particle Supply 1007 Common Source of Electromagnetic Radiation 1009 Common Housing 15 1011 Common Input for Control 1019 Common Output 1021 Common Fluid Delivery System 1023 Common Temperature Control System 1025 Common Power Source 20 1027 Common Waste Recovery System 1029 Common Deflector Plate System 1031 Common Cleaning System Common Housing 25 1069 Base 1071 Two Side Walls 1073 Lower Pair of Shoulders 1075 Lower Cover Panel 1077 Front of Housing 30 1081 Upper Pair of Shoulders 1083 Upper Cover Panel 1085 Rear of Housing 1087 Framework for Mounting Multiple Cytometry Units 1089 Cross Bar Affixed to Side Walls of Housing (For Attaching Nozzle Mounts) 35 1093 Angled Mounting Plate Extending Between Side Walls Common Fluid Supply 1105 Pump for Carrier Fluid 1107 Common Supply of Carrier Fluid 40 1115 Gas Pressure System for Sheath Fluid 1117 Common Supply of Sheath Fluid 1121 Manifold System 1123 Vessel Containing Common Supply of Carrier Fluid 1125 Holder for Vessel 45 1133 Holding Block 1135 Cavity for Receiving Vessel 1137 Second Cavity for Buffer Material 1139 Vessel for Buffer Material 1141 Syringe Pump 50 1147 Supply Line from Syringe Pump to Manifold 1149 Three-way Valve Controlling Carrier and Buffer Fluid 1155 Vessel for Common Supply of Sheath Fluid 1157 Supply Line from Sheath Fluid Vessel to Manifold 1161 Source of Pressurized Gas 55 1163 Gas Line 1165 Regulator in Gas Line 1167 Two-way Valve for Gas Line Between Gas Source and Sheath Fluid Tank 1169 Gas Line for Pressurizing a Supply of Cleaning Solution 1173 Tank for Cleaning Solution 60 1175 Two-way Valve for Gas Line for Cleaning Solution 19 1177 Manifold 1179 Laminated Block 1181 Passages 1185 Fluid Flow Circuit 5 1189 Inlets Connected to Syringe Pump 1191 Inlets Connected to Supply of Sheath Fluid 1193 Outlets for Carrier Fluid and Sheath Fluid V1-V6 Valves for Controlling Flow Through Manifold Passages 1203 Frame Member (For Attaching Manifold Block) 10 1205 Fittings Threaded into Block 1207 Sample Reservoir VI A-V1 D Two-way Valves (For Controlling Flow of Sample Fluid to Nozzles) 1217 Needle of Sample Reservoir 1221 Waste System 15 1223 Waste Tank (Receptacle) 1225 Mechanism Such as Vacuum Pump (For Generating Vacuum) 1227 Waste Lines (Connecting Valves VIA-V1 D to Waste Tank) 1233 Hydrophobic Filter (in Line Connecting Waste Tank and Vacuum Pump) 1235 Fluid Circuit for Sheath Fluid 20 V2A-V2D Two-Way Valves (For Controlling Flow of Sheath Fluid to Nozzles) 1241 Sheath Supply Line 1247 Waste Lines Connecting Sheath Fluid Flow Circuitry to Waste Tank Common Power Supply and Controls 25 1249 Common Power Supply 1251 Common Power Delivery Systems 1253 Common Input (GUI) 1255 Common Output (To Microprocessor) 30 Common Temperature Control 1257 Temperature Control System 1259 Fluid Flow Circuit (For Temperature Control) 1263 Fluid Passages (For Temperature Control in Holding Block) 1265 Control Unit 35 1269 Fluid Passages (For Temperature Control in Manifold) V6 Shut off Valve Common Light Beam and Beam Splitting System 1270 Beamsplitter 40 1270A First Beam from Beamsplitter 1270B Second Beam from Beamsplitter 1271 Second Beamsplitter 1271A First Beam from Second Beamsplitter 1271B Second Beam from Second Beamsplitter 45 1272 Third Beamsplitter 1272A First Beam from Third BeamSplitter 1272B Second Beam from Third Beamsplitter 1273 Beam Guidance System 1279 Lower Filter Assembly 50 1281 Upper Mirror Assembly 1285 Base (For Lower Filter Assembly) 1289 Stage (For Lower Filter Assembly) 1291 Mechanism for Moving Stage (Micrometer) 1293 Tiltable Platform on the Stage 55 1295 Mirror (On Platform) 1297 Base (For Upper Mirror Assembly) 1299 Stage (For Upper Mirror Assembly) 1301 Tiltable Platform (For Upper Mirror Assembly) 1303 Mirror (For Upper Mirror Assembly) 60 1305 Mechanism for Moving Upper Stage 20 1309 Target Plates (Affixed to Side Wall of Housing) 1311 Vertically Aligned Holes (In the Target Plates) 1315 1st Reflecting Filter 1317 2nd Reflecting Filter 5 1319 3rd Reflecting Filter 1321 4th Reflecting Filter Common Deflector Plates 1331 Two Common Deflector Plates 10 1333 Frame (For Mounting Common Deflector Plates on Housing) Modular Multi-Channel System 4001 Multi-Channel System 4009 Modular Cytometry Unit 15 4011 Housing for Modular Unit 4013 Common Housing 4015 Laser 4017 Beam Splitting and Guidance System 4021 Hole for Laser to Enter Modular Housing 20 4023 Plate to Cover Exit Hole 4025 Collection System for System Capillary Tube Nozzle System 1335 Capillary Tube Nozzle System 25 1337 Capillary Tube 1341 Chamber Filled with Light-transmitting Medium Alternative Sorting Systems 1351 Photodamage Sorting System 30 1353 Second Laser 1355 Collection Receptacle 1357 Fluid Switching System 1359 Fluid Switching Device 1361 Capillary Branch to First Collection Vessel 35 1365 Capillary Branch to Second Collection Vessel 1367 Transducer (For Creating Pressure Waves for Selectively Controlling Direction of Fluid Flow) 1369 Capillary Tube on End of Nozzle 40 1371 Droplet Interference Stream Sorting System 1373 High-Speed Droplet Interference Stream 1375 Droplet Generation System for High-Speed Droplet Stream 1377 High-Speed Nozzle System 1379 High-Speed Fluid Stream 45 1381 Transducer for Droplet Interference Stream Generation 1383 High-Speed Droplets 1387 Electric Deflection Plate for High-Speed Droplet Deflection 1389 Uncharged Droplets 1391 Charged Droplets 50 1397 Diverted Segment of Fluid Stream 1399 Intersection of High-Speed Droplet Stream with Coaxial Fluid Stream 1403 Collection Capillaries Collection System 55 2201 Collection System 2203 Intercepting Device 2205 Impact Surface 2207 Collection Vessel 2211 Droplet Entryway 60 2213 Bulb of Pipette 21 2215 Pipette 2217 Inside Wall of Pipette 2225 Guide Tube 2227 Collection System Frame 5 2229 Circular Holder 2231 Set Screw for Intercepting Device Height 2233 Mounting Plate 2235 Set Screws for Lateral Adjustment 2241 Lateral Slot 10 2243 Tray for Holding Collection Vessels 2245 Exit Window 2247 First Intercepting Device 2249 Second Intercepting Device 2265 Stray Droplets 15 Collection Fluid 2301 Collection Fluid Filtration 20 2401 Filter 2403 Collection Vessel for Filtration 2405 Concentrated Slurry Containing Sperm Cells 2409 Syringe Mechanism 2411 Cannula Filter 25 2413 Resuspension fluid 2419 Second Container 2421 Syringe for Filtration Experiment 2423 Sample for Filtration Experiment 2425 Filter for Filtration Experiment 30 2427 Vacuum Pump for Filtration Experiment 2431 Syringe for Filtration Experiment Il 2433 Sample for Filtration Experiment i 2435 Filter for Filtration Experiment Il 2437 Filter Holder for Filtration Experiment Il 35 Cryopreservation 2501 Adjust Concentration 2503 Add Cryoprotectant 2505 Add Protein Source 40 2507 Load in Straws 2509 Cool to Holding Temperature 2511 Maintain at Holding Temperature 2513 Cool to Temperature Approaching Critical Zone 2515 Cool Through Range of Ice Crystal Formation 45 2517 Immerse in Liquid Nitrogen Common Collection System 2801 Common Collection System 2803 Common Frame for Intercepting Devices 50 2805 Waste Trough 2807 Tray for Collection Vessels Pulsed Laser System 3001 Pulsed Laser 55 3003 Laser Pulse Sensor 3005 Laser Pulse 3007 Fluorescence Pulse Lifetime Decay 3009 Digital Sample 60 22 Detailed Description of Embodiments The embodiments described below relate to collection and processing of animal semen, particularly to processing semen from a domestic animal to sort the sperm cells according to a specified DNA characteristic (e.g., X/Y chromosome content to preselect the gender of offspring). 5 A number of inventive technologies are combined to achieve the results described below. However, it will be understood that the inventive technologies described herein may be applied to other applications without deviating from the scope of this invention. General Overview 10 Figure 1 is a work flow diagram providing an overview of the steps in one exemplary process of the present invention. The process starts with collection of neat semen samples from one or more male animals (e.g., bulls) at step 39. The semen samples are labeled for identification at step 41 , contacted with a buffer, at step 41A and transported to a processing facility. In addition to the buffer, additives may also be added at step 41A, including, for example, 15 an energy source, a protein source, an antibiotic, and/or a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly. An optional quality control test may be performed at step 43 to insure that the quality of each sample (e.g., sperm motility) is sufficient to indicate that the final product is likely to meet minimal quality criteria. An optional washing step may be performed at step 47. At step 47A the staining protocol that will be used 20 for processing is selected by using various staining protocols to stain aliquots of the sample and then analyzing the sortability of each aliquot to identify a desired staining protocol for that particular sample. Staining according to the selected staining protocol is performed at step 49 by adding a staining fluid 48 containing a chemical dye (e.g., a DNA selective fluorescent dye) to each sample. In addition to the staining fluid, additives may also be added at step 48, including, 25 for example, an energy source, a protein source, an antibiotic, and/or a composition which regulates oxidation/reduction reactions Intracellularly and/or extracellularly. The samples are incubated at step 51 to allow for uptake of the dye by the sperm. Then a sample is loaded into the sample introduction device of a flow cytometer at step 53. The sample fluid is introduced into the flow cytometer along with a sheath fluid at step 54. In addition to the sheath fluid, additives 30 may also be added at step 54, including, for example, an energy source, a protein source, an antibiotic, and/or a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly. At step 55 the flow cytometer sorts the sperm cells according to a specified DNA characteristic, as will be described below. As the sorted sperm cells are collected by the collection system of the flow cytometer at step 57, they are added to a collection vessel 35 that contains a collection fluid or cryoextender at step 58A. In addition to the collection fluid, additives may also be added at step 58A, including, for example, an energy source, a protein source, an antibiotic, and/or a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly. By this time the sperm cells are in a solution that has been diluted by the various fluids added throughout the process. Accordingly, the population of sperm 40 cells having the desired DNA characteristic are concentrated at step 58B for use in commercial 23 artificial insemination. A cryoextender is added to the concentrated sorted sperm cells at step 58C. In addition to the cryoextender, additives may also be added at step 58C, including, for example, an energy source, a protein source, an antibiotic, and/or a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly. The sperm cells are then 5 packed in tubular containers (referred to in the breeding Industry as "straws") at step 59 and cryopreserved at step 61. The cryopreserved sperm are packed for storage in liquid nitrogen at step 63. The cryopreserved sperm are then distributed through a commercial distribution system at step 65 and sold to animal breeders at step 67. The animal breeders may store the cryopreserved sperm at step 69 until they are ready to use the sperm to artificially inseminate a 10 female animal (e.g., cow) at step 71. As will be discussed below, one embodiment of the present invention involves temperature control through substantially the entire process. Likewise, completion of the various steps within defined time limits is one aspect of another embodiment of the present invention. This overall process is only one example of how the present invention can be used, and it will be understood that some of the aforementioned steps can be deleted and/or 15 others added. The sorted sperm cells can also be used for microinjection or other In vitro fertilization, followed by embryo transplant Into a recipient female animal. The steps of the overall process incorporating advances of the present invention are described in detail below. While a particular process described is in the context of sorting animal sperm (e.g., bovine sperm), it will be understood that the various aspects of this Invention are 20 more generally applicable to any type of sperm (equine, porcine, and others), even more generally to any type of cells, and even more generally to any type of particles, organic and inorganic, including latex particles, magnetic particles, chromosomes, sub-cellular elements, protoplasts, and starch particles. These particles generally fall within a size range of 0.5 to 200 microns, but the technology of this invention is not limited to this range. 25 Sample Collection and Dilution Sample Collection The sperm sample to be sorted may be a freshly collected sample from a source animal, such as bovine, equine, porcine, or other mammalian source, or a thawed, previously 30 cryopreserved sample. Moreover, the sample may be a single ejaculate, multiple pooled ejaculates from the same mammal, or multiple pooled ejaculates from two or more animals. Various collection methods are known and include the gloved-hand method, use of an artificial vagina, and electro-ejaculation. The sperm are preferably collected or quickly transferred into an insulated container to avoid a rapid temperature change from physiological 35 temperatures (typically about 35'C to about 390C). The ejaculate typically contains about 0.5 to 15 billion sperm per milliliter, depending upon the species and particular animal. Regardless of the method of collection, an aliquot may be drawn from the sperm sample and evaluated for various characteristics, such as for example, sperm concentration, sperm motility, sperm progressive motility, sample pH, sperm membrane Integrity, and sperm 40 morphology. This data may be obtained by examination of the sperm using, for example, the Hamilton-Thorn Motility Analyzer (IVOS), according to standard and well known procedures (see, 24 for example, Farrell et al. Theriogenology (1998) 49(4): 871-9; and U.S. Patent Nos. 4,896,966 and 4,896,967). Dilution 5 The sperm sample may be combined with a buffer (in the form of a solid or solution) to form a sperm suspension. Among other things, the buffer may enhance sperm viability by buffering the suspension against significant changes in pH or osmotic pressure. Generally, a buffer is non-toxic to the cells and is compatible with the dye used to stain the cells. Exemplary buffers include phosphates, diphosphates, citrates, acetates, lactates, and combinations thereof. 10 Presently preferred buffers include TCA, TEST, sodium citrate, HEPES, TL, TES, citric acid monohydrate, HEPEST (Gradipore, St. Louis, MO), PBS (Johnson et al., Gamete Research, 17:203-212 (1987)), and Dulbecco's PBS (Invitrogen Corp., Carlsbad, CA). One or more buffers may be combined together or with additives as discussed below to form a buffered solution, and the buffered solution combined with the sperm sample to form a 15 sperm suspension. A buffered solution may also contain one or more additives, as described in greater detail below. Exemplary buffered solutions are described in Table 1. Preferred buffered solutions include a solution comprising 3% TRIS base, 2% citric acid monohydrate, and 1% fructose (w/v) in water at a pH of about 7.0, a solution designated as TCA #1 in Table I, and a solution designated as TCA #2 in Table 1. 20 [rest of page blank) 25 Table 1. Buffered Solutions COMPONENTS TCA#1 TCA#2 TEST Na Citrate HEPES TL Sodium chloride (NaCI) Potassium chloride (KCI) 5.8, Sodium bicarbonate (NaHCO3) 0. 0.2: odium phosphate monobasic 2.1 NaH2PO4-H20) 0.0, +)-2-hydroxyproprionic acid (Na Lactate) 3.68 agnesium chloride (MgCl2) N-(2-hydroxyethyl)piperazine-N'-(2- 0.19 0.01 ethansulfonic acid) (HEPES) ris(hydroxymethyl) amimonethane (TRIS Citric Acid Monohydrate 32.02g 10.289 Na Citrate Dihydrate 57 86 2-[(2-hydroxy-1,1-bis[hydroxyethyl] 29g Athyl) aminoethanesulfonic acid (TES) .m 43.25g Fructose Meaoi iniitr cas t D-Glucose - 12.5gi2.679o10 n 2.52g Steptamycin 2 P"enicillin-G 0.25g atr0.15g -7 Tare pHI liter 1 liter 1 liter 1 liter 1 iter 1 lit Fargt pH7.35 7.35 7.35 7.35 7.35 7.3 Target osmolality (milliosmols/kg H2O) ~3-14 ~ 300 ~302 ~316 ~298 -2 Alternatively, the sperm may be combined with a metabolic inhibitor to form an inhibited sperm suspension. Metabolic inhibitors cause the sperm cells to emulate sperm cells of the 5 epididymis of a mammal, such as for example a bull, by simulating the fluid environment of the epididymis or epididymal tract of the mammal. Such an inhibitor would reduce or inhibit the motility and metabolic activity of the sperm. Exemplary inhibitors of this class include carbonate based inhibitors, such as for example those disclosed in Salisbury & Graves, J. Reprod. Fertil., 6:351-359 (1963). A preferred inhibitor of this type comprises NaHCO 3 , KHCO 3 , and 10 C 6

H

8

O

7

H

2 0. A more preferred inhibitor of this type comprises 0.204g NaHCO 3 , 0.433g KHCO 3 , and 0.473g C 6 HaOr1H 2 0 per 25mL of purified water (0.097 moles/L of NaHCO 3 , 0.173 moles/L of

KHCO

3 , 0.090 moles/L C 6

H

8

O

7

H

2 0 in water). In addition to a buffer, the sperm suspension may also contain a range of additives to enhance sperm viability or motility. Exemplary additives include energy sources, protein 15 sources, antibiotics, and compositions which regulate oxidation/reduction reactions intracellularly and/or extracellularly. One or more of these additives may be introduced into the buffer or buffered solution before the formation of the sperm suspension or, alternatively, may be separately introduced into the sperm suspension.

26 One or more energy sources may be added to minimize or inhibit the sperm cells from oxidizing intracellular phospholipids and other cellular components. Exemplary energy sources include monosaccharides, such as fructose, glucose, galactose and mannose, and disaccharides, such as sucrose, lactose, maltose, and trehalose, as well as other 5 polysaccharides. For example, the resulting sperm suspension may include about 1% (w/v) to about 4% (w/v) of the energy source(s). If included, the energy source is preferably fructose and the sperm suspension contains about 2.5% (w/v). To minimize dilution shock, provide support to the cells, or disperse the cells throughout the suspension, a protein source may also be included in the buffer, buffered solution, or sperm 10 suspension. Exemplary protein sources include egg yolk, egg yolk extract, milk (including heat homogenized and skim), milk extract, soy protein, soy protein extract, serum albumin, bovine serum albumin, human serum substitute supplement, and combinations thereof. Albumin, and more particularly bovine serum albumin (BSA), is a preferred protein source. For example, if included, BSA may be present in the sperm suspension in an amount of less than about 15 5.0% (w/v), preferably less than about 2% (w/v), more preferably less than about 1% (w/v), and most preferably in an amount of about 0.1% (w/v). The use of a protein source, such BSA, alone may initiate the process of capacitation in a percentage of the sperm cells in the suspension. It is preferred that this process take place in the female reproductive tract. Therefore, in order to inhibit the initiation of capacitation during 20 dilution, as well as during the subsequent staining and sorting, an alternative protein source or a protein substitute may be included in the sperm suspension. The alternative protein source or protein substitute possess the advantageous effects of a typical protein source, such as BSA, in addition to the ability to inhibit the initiation of capacitation in a larger percentage of the cells in the sperm suspension. Examples of alternative protein sources include human serum substitute 25 supplement (SSS) (Irvine Scientific, Santa Ana, CA) and cholesterol enhancer BSA, while an example of a protein substitute includes a polyvinyl alcohol, such as for example, a low to medium viscosity polyvinyl alcohol generally of a molecular weight of about 30,000 to about 60,000. Generally, if included, these compositions will be present in the same amounts as disclosed above with respect to BSA, with the total albumin content of the buffer or buffered 30 solution generally not exceeding about 5.0% (w/v). An antibiotic may be added to the sperm suspension in order to inhibit bacterial growth. Exemplary antibiotics include, for example, tylosin, gentamicin, lincomycin, spectinomycin, Linco Spectino) (lincomycin hydrochloride-spectinomycin), penicillin, streptomycin, ticarcillin, or any combination thereof. The antibiotics may be present in a concentration of about 5og to about 35 800og per ml of semen, regardless of whether the semen is neat, buffered, or contains additional substances, such as for example, any of the additives mentioned herein. The Certified Semen Services (CSS) and National Association of Animal Breeders (NAAB) have promulgated guidelines regarding the use of antibiotics with respect to sperm collection and use. A composition which regulates oxidation/reduction reactions intracellularly and/or 40 extracellularly may also be included in the sperm suspension. Such a composition may provide 27 a protective effect to the sperm cells, such as for example by maintaining sperm viability or progressive motility. Examples of such a composition include, for example, pyruvate, vitamin K, lipoic acid, glutathione, flavins, quinones, superoxide dismutase (SOD), and SOD mimics. If included in the sperm suspension, such a composition may be present in a concentration 5 sufficient to effect the protective effect without detrimentally affecting sperm health. Exemplary concentration ranges Include from about 100M to about 50mM depending upon such factors as the particular composition being used or the concentration of sperm in the suspension. For example, pyruvate may be present in the sperm suspension in a concentration from about 1mM to about 50mM, preferably from about 2.5mM to about 40mM, more preferably from about 5mM 10 to 25mM, even more preferably from about 10mM to 15mM, still more preferably about 15mM, and most preferably about 10mM. Vitamin K may be present in the sperm suspension in a concentration from about 10M to about 1000M, preferably from about 100M to about 1000M, and more preferably about 1000M. Lipoic acid may be present in the sperm suspension in a concentration from about 0.1mM to about 1mM, preferably from about 0.5mM to about 1mM, and 15 more preferably about 1mM. Staining of the Cells to be Sorted Generally, sperm cells may be stained by forming a staining mixture comprising sperm cells, a buffer, and a dye. The sperm cells may be derived from a freshly obtained semen 20 sample, as discussed above with respect to sample collection and dilution, or from a thawed cryopreserved semen sample. If the semen sample is a thawed, previously cryopreserved sample, the sperm are preferably thawed immediately prior to staining. Generally, a straw or other cryopreservation vessel containing the frozen sperm may be placed in a water bath, the temperature of which is 25 preferably in excess of the glass transition temperature of the sperm cell membrane (i.e., about 17 0 C), but not so great as to adversely impact sperm health. For example, frozen sperm may be thawed by immersing the cryopreservation vessel In a water bath maintained at a temperature of about 17 0 C to about 40*C for a period of about 30 seconds to about 90 seconds. Once obtained, the sperm cells may be introduced into the staining mixture in the form of 30 neat semen or in the form of a suspension derived therefrom, e.g., a sperm suspension as discussed above with respect to sample collection and dilution. The dye may be in the form of a neat solid or a liquid composition. The dye may also be dissolved or dispersed in an unbuffered liquid to form a dye solution. Alternatively, the dye may be in the form of a dye suspension comprising a dye and a buffer or buffered solution that is 35 biologically compatible with sperm cells. A range exemplary buffers and buffered solutions are discussed above with respect to sample collection and dilution. For example, among the buffers which may be used is a TCA buffer solution comprising 3% TRIS base, 2% citric acid monohydrate, and 1% fructose in water at a pH of about 7.0, or a carbonate-based inhibitor solution comprising 0.204g NaHCO 3 , 0.433g KHCO 3 , and 0.473g C 8 H0 7

-H

2 0 per 25mL of 40 purified water (0.097 moles/L of NaHCO 3 . 0.173 moles/L of KHCO 3 , 0.090 moles/L C 6

H

8 0rH 2 0 28 in water). Thus, for example, a staining mixture may be formed by combining neat semen with a dye. Alternatively, the staining mixture may be formed by combining neat semen with a buffer or buffered solution and a dye. Additionally, the staining mixture may be formed by combining a sperm suspension with a dye. 5 The staining mixture may be formed by using one or more UV or visible light excitable, DNA selective dyes as previously described in U.S. Patent No. 5,135,759 and WO 02/41906. Exemplary UV light excitable, selective dyes include Hoechst 33342 and Hoechst 33258, each of which is commercially available from Sigma-Aldrich (St. Louis, MO). Exemplary visible light excitable dyes include SYBR-14, commercially available from Molecular Probes, Inc. (Eugene, 10 OR) and bisbenzimide-BODIPY* conjugate 6 -{[3-((2Z)-2-{[1-(difluoroboryl)-3,5-dimethyl-1H pyrrol-2-yl]methylene}-2H-pyrrol-5-yl)propanoyl]amino}-N-[3-(methyi{3-[({4-[6-(4-methylpiperazin 1 -yI)-1H,3'H-2,5'-bibenzimidazol-2'-yl phenoxy}acetyl)aminolpropyi~amino)propyl]hexanamide ("BBC") described in WO 02/41906. Each of these dyes may be used alone or in combination; alternatively, other cell permeant UV and visible light excitable dyes may be used, alone or in 15 combination with the aforementioned dyes, provided the dye does not detrimentally affect the viability of the sperm cells to an unacceptable degree when used in concentrations which enable sorting as described elsewhere. The preferred concentration of the DNA selective dye in the staining mixture is a function of a range of variables which include the permeability of the cells to the selected dye, the 20 temperature of the staining mixture, the amount of time allowed for staining to occur, and the degree of enrichment desired in the subsequent sorting step. In general, the dye concentration is preferably sufficient to achieve the desired degree of staining in a reasonably short period of time without substantially detrimentally affecting sperm viability. For example, the concentration of Hoechst 33342, Hoechst 33258, SYBR-14, or BBC in the staining mixture will generally be 25 between about 0.1pM and about 1.OM, preferably from about 0.1pM to about 700pM, and more preferably from about 1 00pM to about 200pM. Accordingly, under one set of staining conditions, the concentration of Hoechst 33342 is preferably about 100pM. Under another set of staining conditions, the concentration of Hoechst 33342 is about 150pM. Under still another set of staining conditions the concentration is preferably about 200pM. 30 In addition to buffer, other additives may be included in the staining mixture to enhance the viability or motility of the sperm; these additives may be provided as part of the sperm source, the dye source, or separately to the staining mixture. Such additives include energy sources, antibiotics, compositions which regulate oxidation/reduction reactions intracellularly and/or extracellularly, and seminal plasma, the first three of which are discussed above with respect to 35 sample collection and dilution, and the last of which is discussed below with respect to collection fluids. Such additives may be added during the staining techniques in accordance therewith. In particular, it has been observed that the inclusion of a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly in the staining mixture may help to maintain sperm viability at elevated staining temperatures, at elevated dye concentrations, at 40 increased staining 'eriods, or any combination thereof. Examples of these compositions and the 29 use of the same are discussed above with respect to buffers and diluents. Such compositions may be added during the staining techniques in accordance therewith. The staining mixture may be maintained at any of a range of temperatures; typically, this will be within a range of about 4 0 C to about 50*C. For example, the staining mixture may be 5 maintained at a "relatively low" temperature, i.e., a temperature of about 4*0 to about 300C; in this embodiment, the temperature is preferably from about 200C to about 300C, more preferably from about 25*C to about 300C, and most preferable at about 280C. Alternatively, the staining mixture may be maintained within an "intermediate" temperature range, i.e., a temperature of about 300C to about 39*C; in this embodiment, the temperature is preferably at about 34*C to 10 about 39 0 C, and more preferably about 37 0 C. In addition, the staining mixture may be maintained within a "relatively high" temperature range, i.e., a temperature of about 400C to about 500C; in this embodiment, the temperature is preferably from about 400C to about 45*C, more preferably from about 40'C to about 430C, and most preferably at about 41*C. Selection of a preferred temperature generally depends upon a range of variables, including for example, the 15 permeability of the cells to the dye(s) being used, the concentration of the dye(s) in the staining mixture, the amount of time the cells will be maintained in the staining mixture, and the degree of enrichment desired in the sorting step. Uptake of dye by the sperm cells in the staining mixture is allowed to continue for a period of time sufficient to obtain the desired degree of DNA staining. That period is typically a 20 period sufficient for the dye to bind to the DNA of the sperm cells such that X and Y chromosome-bearing sperm cells may be sorted based upon the differing and measurable fluorescence intensity between the two. Generally, this will be no more than about 160 minutes, preferably no more than about 90 minutes, still more preferably no more than about 60 minutes, and most preferably from about 5 minutes to about 40 minutes. 25 Accordingly, in one embodiment, a staining mixture is formed comprising sperm cells and a dye in a concentration from about 100pM to about 200pM, and the staining mixture is held for a period of time at a temperature of about 410C. In another embodiment, the staining mixture further comprises pyruvate in a concentration of about 10mM, vitamin K in a concentration of about 100pM, or lipoic acid in a concentration of about 1mM. 30 In still another embodiment, a staining mixture is formed comprising sperm cells and a dye in a concentration from about 100pM to about 200pM, and the staining mixture is held for a period of time at a temperature of about 280C. In another embodiment, the staining mixture comprises pyruvate in a concentration of about 10mM, vitamin K in a concentration of about 100pM, or lipoic acid in a concentration of about 1mM. 35 In yet another example, a staining mixture is formed comprising sperm cells, a metabolic inhibitor comprising 0.204g NaHCO 3 , 0.433g KHCO 3 , and 0.473g C 6

H

8

O

7

H

2 0 per 25mL of purified water (0.097 moles/L of NaHCO 3 . 0.173 moles/L of KHCO 3 , 0.090 moles/L C 6

H

8

O

7

H

2 O in water), and a dye in a concentration from about 100pM to about 200pM, and the staining mixture is held for a period of time at a temperature of about 28*C. In another embodiment, the 40 staining mixture is held for a period of time at a temperature of about 41*C.

30 Sheath Fluid To sort the sperms cells, the stained cells are introduced as a sample fluid into the nozzle of a flow cytometer as described below. As part of the process, the sample fluid is 5 typically surrounded by a sheath fluid. The sheath fluid permits the sperm cells in the sample fluid to be drawn out into a single file line as discussed below. The sheath fluid is collected along with the sperm cells by the collection system of the flow cytometer and therefore forms part of the post-sort environment for the sperm cells. Thus, it Is desirable that the sheath fluid provides a protective effect to the cells upon contact of cells by the sheath fluid. 10 The sheath fluid generally comprises a buffer or buffered solution. Examples of buffers and buffered solutions and illustrative concentrations of the same that may be used in the sheath fluid are disclosed above with respect to sample collection and dilution. In a particular embodiment, the sheath fluid comprises 0.96% Dulbecco's phosphate buffered saline (w/v), 0.1% BSA (w/v), in water at a pH of about 7.0. 15 Optionally, the sheath fluid may also contain a range of additives that are beneficial to sperm viability or motility. Such additives include, for example, an energy source, a protein source, an antibiotic, a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly, an alternative protein source, and polyvinyl alcohol. Each of these additives, and examples of the same, is discussed above with respect to sample collection and 20 dilution. Such additives may be added to the sheath fluid in accordance therewith. The sheath fluid may optionally be filtered prior to the sorting step. Contaminants that may be present in the sheath fluid, such as non-soluble particulates, may interfere with sorting. Therefore, the sheath fluid may be filtered prior to its introduction into a flow cytometer. Such filters and methods of using the same are well known in the art. Generally, the filter is a 25 membrane of about 0.1 microns to about 0.5 microns, preferably about 0.2 microns to about 0.3 microns, and more preferably about 0.2 microns. The stained cells may be introduced into the sheath fluid at any time subsequent to staining. Typically, a stream of the stained cells in the sample fluid is injected into a stream of sheath fluid within the nozzle of the flow cytometer. Initially, there is substantially no contacting 30 of the sample fluid and the sheath fluid due to laminar flow of the fluids as discussed in more detail below. It is desirable that the sample fluid and the sheath fluid remain as substantially discrete flowing streams until after the particles (e.g., the stained sperm cells) in the sample fluid have been analyzed. At some point, however, the sheath fluid and the cells of the sample fluid come in contact with one another. For instance in a droplet sorting flow cytometer (discussed 35 below) the sheath fluid and sample fluid begin contacting one another as droplets are being formed downstream of the interrogation location. At the time of the introduction of the stained cells and the sheath fluid, both the stained cells and the sheath fluid may be at a temperature from about 4 0 C to about 50 0 C. The sheath fluid and the stained cells may be at the same or at different temperatures, with either being at a 40 higher temperature than the other. Accordingly, in one embodiment, at the time of the 31 introduction of the stained cells and the sheath fluid, both the cells and the sheath fluid are at the same temperature; for example, at a "relatively low" temperature, such as for example at about 5 0 C to about 80C; at an "intermediate" temperature, such as for example at about 25*C to about 30*C; or at a "relatively high" temperature, such as for example at about 400C to about 430C. In 5 another embodiment, the stained cells are at a higher temperature than the sheath fluid, such as for example, the cells being at about 40*C to about 43 0 C and the sheath fluid being at about room temperature or at about 5*C. In yet another embodiment, the stained cells are at a lower temperature than the sheath fluid. 10 FLOW CYTOMETRY One embodiment of the present invention employs inventive technologies in flow cytometry to analyze and sort the sperm cells. Referring now to Figs. 2 and 3, one embodiment of a flow cytometry system of the present invention is designated in its entirety by the reference numeral 1. As will appear, the flow cytometry system 1 is useful for classifying and sorting 15 particles, such as sperm cells, according to selected characteristics. In general, the system I comprises a supply 3 of carrier fluid 17 containing particles to be sorted, a supply 7 of sheath fluid 19, flow cytometry apparatus having sorting capabilities, generally designated 9, and a fluid delivery system 15 for delivering the carrier 17 and sheath fluids 19 from respective supplies 3, 7 under pressure to the flow cytometry apparatus 9. The flow cytometry apparatus 9 is adapted for 20 receiving the carrier 17 and sheath 19 fluids, for combining the fluids 17, 19 to create a stream of pressurized fluid 21, for directing the stream 21 carrying the particles through a focused beam of electromagnetic radiation 25 (e.g., UV laser light), and for analyzing the electromagnetic radiation 31 (e.g., fluorescent light) emitted by particles passing through the focused beam 25. The apparatus 9 also functions to break the stream 21 up into droplets 33 containing particles to be 25 evaluated, and to sort the droplets 33 based on the aforesaid measurements according to one or more characteristics of the particles contained in the droplets 33. While this invention may be used to analyze and preferably sort any type of particle, it has particular application to sorting cells according to one or more desired characteristics of the cells (e.g., size, DNA content, shape, density, gene sequence, etc.). This invention is especially suited for sorting animal sperm 30 cells for commercial use by the animal production industry for in vivo or in vitro artificial insemination, as discussed in more detail below. SINGLE-CHANNEL SORTING APPARATUS AND METHOD 35 Flow Cytometry Apparatus The flow cytometry apparatus 9 shown in Fig. 3 comprises a nozzle system, generally designated 101, for delivering a fluid stream 21 containing particles (e.g., stained sperm cells) through a nozzle orifice 103 under pressure with the cells substantially in single file and, in the case of sperm cells, with asymmetric heads of the sperm cells substantially in a desired 40 orientation which will be described. As in conventional flow cytometry droplet sorting systems, a 32 transducer 105 is provided opposite the nozzle orifice 103 for introducing acoustical energy into the fluid stream 21 which causes the stream 21 to break into droplets 33 containing individual cells at a "droplet break-off' location 107 spaced from the nozzle orifice 103. The system I also includes an optics system, generally designated 109, for focusing a beam of electromagnetic 5 radiation 25 (e.g., 350-700 nm UV or visible laser light) on the fluid stream 21 at an "interrogation" location 115 which, in the described embodiment, is between the nozzle orifice 103 and the droplet break-off location 107. Thus, the described embodiment is a jet-in-air system. In other embodiments, the interrogation location 107 could be inside the nozzle orifice 103 or upstream from the orifice 103. In any event, the cells are adapted to pass through the 10 beam of light 25 at the interrogation location 107, resulting in excitation of a chemical stain (or other reporting medium) in the cells to cause fluorescence emissions 31 having a wavelength different from that of the beam 25 (e.g., If the illumination light 25 has a wavelength of about 350 to 370 nm, the fluorescent emissions 31 may have a wavelength of about 460 nm). A photodetector 117 is operable to detect these emissions 31 and to convert them into electrical 15 signals which are processed and used to classify the cells according to selected characteristics, such as the X/Y chromosome content of sperm cells. The flow cytometry apparatus 9 further comprises a sorting system, generally designated 119, for sorting the droplets 33 into different groups or populations (e.g., two populations 123, 125) according to the classification of the cells contained in the droplets 33 and a collection system, generally designated 2201 (Fig. 2), for 20 collecting the droplets 33 and maintaining the segregation of the different populations 123, 125. Operation of the system 1 is controlled by a processor 131, such as microprocessor or other digital or analog control and/or processor, or combinations thereof, which controls the various functions of the components of the system 1 In a manner to be described. Significantly, the processor 131 is also responsive to particle analysis information to control the output of the 25 system I based on selected control and sorting strategies involving different parameters, including the desired purity of one of the sorted populations of particles, the acceptable quantity (or percentage) of desired particles one of the populations as compared to the quantity (or percentage) of desired particles in one or more of the other populations, and other parameters, as will be discussed later. 30 The various components of the system 1 are described in detail below. Nozzle System Referring to Figs. 4 and 5, the nozzle system 101 comprises, in one exemplary embodiment, a generally cylindrical flow body 133 having a central longitudinal bore 135 through 35 it, and a nozzle 137 on the flow body 133 having a funnel-shaped nozzle body 139. A passage 141 extends through the nozzle body 139 co-axial with the bore 135 in the flow body 133 and terminates in the aforementioned nozzle orifice 103 at the forward end of the nozzle 137. The nozzle body 139 has an internally threaded counterbore 145 at its rearward end for threadably receiving a threaded projection or stud 149 at the forward end of the flow body 133 to removably 40 connect the nozzle 137 to the flow body 133, the connection being sealed by an O-ring seal 155.

33 It will be understood that the nozzle can be removably connected to the flow body in other ways or, alternatively, the parts could be integrally formed as one piece. Particles are delivered to the nozzle 137 by means of a conduit 157 positioned co-axially in the bore 135 of the flow body 133. The outside diameter of the conduit 157 is less than the 5 inside diameter of the bore 135 so that an annular space 167 is formed around the conduit 157. In one particular embodiment, the conduit 157 is a tubular needle (e.g., a 16-ga. needle having an inside diameter of 0.01 in.) having a front end which extends into the counterbore 145 at the back of the nozzle 137. The back end of the conduit 157 is connected to the fluid delivery system 15 for delivery of carrier fluid 15 (e.g., a staining mixture containing sperm cells) to the 10 conduit 157. The annular space 167 surrounding the conduit 157 is connected by means of a radial bore 173 in the flow body 133 to the fluid delivery system 15 for delivery of sheath fluid 19 into the annular space 167. As shown in Figs. 3 and 5, an optional second radial bore 183 may be provided in the flow body 133 connecting the annular space 167 to another line (not shown) for supply of additional sheath fluid 19 to the nozzle 137. 15 As in conventional flow cytometry systems, sheath fluid 19 Is introduced into the annular space 167 surrounding the conduit 157. The velocity of the sheath fluid 19 as it flows past the tip of the conduit 157 is much higher that the velocity of the carrier fluid 17 exiting the conduit 157, so that the carrier fluid 17 and cells (e.g., sperm cells) contained therein are accelerated by the sheath fluid 19 toward the orifice 103 of the nozzle 137. This acceleration functions to space the 20 cells out generally in a single file arrangement for separate analysis by the optics system 109. The sheath fluid 19 surrounds the carrier fluid 17, resulting in the fluid stream 21 having a central core 189 of carrier fluid 17 and an outer co-axial sheath 191 of sheath fluid 19 surrounding the central core 189 (see Fig. 6). As will be understood by those skilled in flow cytometry, the laminar flow and hydrodynamic focusing of the central core 189 tends to confine the particles to 25 the core 189, with little mixing of the sheath 19 and carrier fluids 17 in the nozzle 137. Further, the central core 189 remains essentially intact within the sheath 191 as the stream 21 moves through the nozzle system 101, until such time as droplets 33 are formed at the break-off location 107. This type of co-axial flow is particularly suited for flow cytometry, because the particles to be analyzed are confined within the relatively narrow core 189 of the stream. As a result, a beam 30 of light 25 focused on the center or core 189 of the stream 21 will illuminate the particles so that they may be analyzed substantially one at a time. By confining the core 189 within a sufficiently narrow diameter, one can obtain more uniform illumination of the particles in the core fluid 189. For good analytical results, the diameter of the core containing the particles should desirably be within a range of 7 to 20 microns, and more desirably within a range of 7 to 14 microns. The 35 diameter of the core stream 189 can be increased or decreased by adjusting the rate of delivery of the carrier fluid 17 relative to the rate of delivery of the sheath fluid 19. Cell Orientation For optimizing analytical results, it is desirable that particles having asymmetric shapes 40 be in a desired orientation when they pass through the light beam from the optics system. As is 34 known to those skilled in the art, fluorescence emissions from asymmetric particles tend to anisotropic (i.e., the intensity of the emissions are not uniform in all directions). As used herein, the term "desired orientation" means an orientation which allows the processing system to discriminate between cells having different characteristics with an accuracy in a range of 70% to 5 100%, more desirably in a range of 80% to 100%, still more desirably in a range of 90% to 100%, and most desirably 95% or greater. To illustrate the point, a bovine sperm cell 201 is illustrated in Figs. 6 and 7. Typically, the cell has a paddle-shaped head 205 with relatively flat wide opposite faces 207 and narrow edges 209, a nucleus 213 in the head 205 containing the chromatic DNA mass of the cell, and a 10 tail 215 extending from the head 205 providing the motility necessary for effective fertilization. The average bovine sperm cell 201 has a head length 219 of about 8 pm, a head width 221 of about 4 pm, and an overall length 223 from the front of the head to the end of the tail of about 100pm. In the average bovine sperm cell 201, the nucleus 213 occupies most of the head volume and is only slightly smaller than the sperm head 205. Thus, the nucleus length 217 Is 15 almost equal to the head length 219, again being about 8.pm in length. It has been observed that in the bovine the X/Y chromosomes of the sperm cells 201 are localized in a region of the nucleus 225 (Fig. 6) below and immediately adjacent the longitudinal midline or equator 211 or center of the head 205. More specifically, this sub-equatorial region 225 extends no more than about 20% of the nucleus length 217 on the lower half (toward the tail 215) of the nucleus 213, 20 even more specifically no more than about 10-15% of the nucleus length 217 on the lower half of the nucleus 213, and still more specifically no more than about 1.0-1.5 pm below the equator 211 of the nucleus 213. When sperm cells pass through the excitation beam 25, it is desirable that the cells be substantially in single file and that the head 205 of the each cell 201 be substantially similarly 25 oriented to reduce orientation variability from cell to cell and thus provide for a more uniform measurement of the cells. It is also desired that the cells have an orientation which will enable accurate discrimination between X and Y cells. Desirably, this orientation is one where the length of the sperm cell 201 is generally aligned with the direction of stream flow 227 (either head leading (shown Fig. 6) or head trailing) and where the head 205 of the sperm cell 201 is rotated 30 on its longitudinal axis so that the head 205 falls within an angular envelope 229 in which the light beam 25 from the optics system 109 will strike a wide face 207 of the cell 201 generally broadside, as shown schematically in Fig. 7, rather than a narrow edge 209 of the cell. Preferably, the envelope 229 defining the desired orientation is generated by rotation of a sperm cell 201 through an angular range of R1 relative to a plane P which is generally perpendicular to 35 the incoming light beam 25, as viewed in a cross section taken transversely through the stream 21. The range R1 is preferably 0 to 90 degrees, more preferably 0 to 60 degrees, and even more preferably 0 to 30 degrees. The nozzle of the present invention is configured to achieve this desired orientation with an accuracy of up to 90% or more. The tolerance for sperm orientation (i.e., the size of the envelope 229 defined by angular 40 range RI) is related to the numerical aperture of the lens used to collect fluorescence emissions 35 31 from the sperm cells. In the embodiment shown Fig. 7, for example, the optics system 109 has a fluorescence emission 31 detection volume 579 defined by a solid angle of 55 degrees. When the rotational orientation of a sperm head 205 is outside the envelope 229 defined by R1 as the sperm moves through the beam 25, a relatively stronger fluorescence emission 31 from 5 an edge 209 of the sperm head 205 will be collected by the optic system 109, preventing the processor 131 from correlating the intensity of the fluorescence emission 31 with the X/Y chromosome content of the sperm cell 201. However, the optics system 109 does not collect the relatively stronger fluorescence emissions 31 from the narrow edge 209 of the sperm heads 205 as long as the rotational orientation of a sperm head 205 is within the envelope 229 as it passes 10 through the interrogation location 115. Thus, in the embodiment shown Fig. 7, the orientation of the sperm cell does not result in collection of the relatively stronger edge-wise fluorescence emissions as long as the narrow edges 209 of the sperm head 205 are confined within angle R1. The solid angle of the collection volume 579 can be decreased by using a lens with a smaller numerical aperture, thereby increasing angle RI and the tolerance for poorly oriented sperm. 15 However, this also decreases the number of photons that can be collected by the optics system 109, which can impact the measurement of fluorescence emissions 31 by reducing the intensity of the emissions 31 detected by the photodetector. Likewise, if the optics system 109 collects fluorescence emissions 31 with a high numerical aperture lens to obtain a stronger intensity of the fluorescence emissions detected by the photodetector, then the tolerance for sperm 20 orientation decreases. Thus, in designing a system of the present invention, one needs to strike a balance between the tolerance for sperm orientation and the numerical lens aperture. The optimal balance will depend on the orienting capabilities and optical sensitivity of the system. In one desirable embodiment, for example, a lens having a numerical aperture 0.65 is used. 25 Nozzle Design In one embodiment, as shown in Figs. 8 and 9, the interior 231 of the nozzle body 139 downstream from the counterbore 145 has an interior surface 233 comprising first, second and third axially tapered regions 235, 237, 239 for progressively accelerating the speed of the fluid stream 21 in a downstream direction toward the nozzle orifice 103. As noted previously, this 30 acceleration functions to space the particles (e.g., cells) in the stream 21 so they assume a generally single file formation so they can be analyzed substantially one particle at a time. At least two of these regions, and preferably all three 235, 237, 239, have generally elliptical (oval) shapes in cross sections taken at right angles to the longitudinal axis 247 of the nozzle 137, as is shown in Figs. 9A-9H and Figs. 9J-9K. The interior surface 233 of the nozzle body 139 also has 35 a fourth region 249, not tapered, downstream from the first three regions 235, 237, 239 and immediately upstream of the nozzle orifice 103 which, in one embodiment, is formed in a separate orifice member 255 secured in a counterbore 257 at the front of the nozzle body 139. In one embodiment, the generally elliptical cross sectional shapes of the first 235 and second 237 regions are oriented in substantially the same direction to define a first torsional zone 259, 40 and the generally elliptical cross sectional shape of the third region 239, constituting a second 36 torsional zone 261, is oriented at an angle (e.g., about 90 degrees) relative to the generally elliptical cross sectional shapes of the first 235 and second 237 regions. The orientation is such that the interior surface 233 of the nozzle body 139 applies torsional forces to the fluid stream 21 and thereby tends to orient the sperm cells 201 in the aforestated desired orientation as they 5 pass through the nozzle orifice 103. Preferably, the first torsional zone 259 has an axial length 273 of 3.0-4.5 mm, preferably about 3.6 mm, and the first 235 and second 237 tapered regions making up the zone 259 have approximately equal axial lengths 275, 277 (e.g., about 1.8 mm). The second torsional zone 261 has an axial length 279 of 3.5-5.0 mm, preferably about 4.45 mm. The fourth region 249 is preferably generally cylindrical in shape. Each generally cross-sectional 10 elliptical shape A-D (Fig. 8) at the boundaries of the first 235, second 237 and third 239 regions has a major axis diameter and a minor axis diameter, exemplary dimensions of which are shown in Fig. 8 and Table 1 below. Table 1 15 Ellipse Major Axis Minor Axis Ratio Diameter Diameter (mm) (mm) A 7.0 6.0 1.2 B 6.1 5.3 1.15 C 2.1 2.1 1 D 0.9 0.2 1.45 It will be understood that the above dimensions are exemplary, and that other dimensions and shapes may also be suitable. Functionally, the changes in the ratios between the major and minor diameters, and the different orientations of the elliptical shapes of the 20 regions, create side forces which act on each cell 201 and apply a torsional force 271 tending to rotate the cell 201 on its longitudinal axis so that its wide faces 207 align with the minor axis in the first torsional zone 259 and as the cell is gently twisted (e.g., 90 degrees) to align with the minor axis of the second torsional zone 261. Each of the tapered surfaces 235, 237, 239 also serves to accelerate the stream 21 (and cells) flowing through the nozzle 101. In one 25 embodiment, the acceleration increases more gradually in the first 235 and third 239 regions and more rapidly in the second region 237. Again by way of example, the taper of the first region 235 may range from about 11-14 degrees; the taper in the second region 237 may range from about 42-48 degrees; and the taper in the third region 239 may vary from about 8-12 degrees. The nozzle body 139 is formed from a suitable material such as molded plastic (ABS) or metal. 30 The orifice member 255 (Fig. 8) is preferably formed from a hard, wear resistant material, such as sapphire, which is capable of being machined or otherwise formed with precise dimensions. The orifice member 255 itself has, in one embodiment, a conical upstream surface 309 of generally circular cross section which decreases in diameter from about 0.92 mm to about 0.060 mm and has an axial length 317 of about 0.54 mm and a taper angle of about 39 degrees.

37 The orifice member 255 also has a generally cylindrical downstream surface 315 with a diameter of about 0.060 mm and an axial length 327 of about 0.36 mm. These dimensions are exemplary only, and it will be understood that the orifice member 255 may have other sizes and shapes. For example, the shape of the upstream surface 309 may be generally elliptical (oval) in cross 5 section, and the diameter of the orifice 103 at the downstream end of the nozzle 137 may range from 40 to 100 microns or more. It is desirable that the size of the orifice 103 be such that the cells exiting the nozzle 101 are substantially in single file formation within the core 189 of the stream 21 and substantially in the desired orientation, as described previously. For example, in the case of sperm cells an orifice 103 having a diameter of about 60-62 microns at the 10 downstream end has been found to be suitable. Preferably, the nozzle orifice 103 serves to further accelerate the stream 21 and to shape and size the stream 21 for optimum cell spacing, cell orientation and droplet 33 formation, as will be described. The velocity of the cells as they exit the nozzle 137 will depend on various factors, including the pressure at which sheath fluid 19 is introduced into the nozzle system 101. At a 15 pressure of 20 psi, the cells will exit the nozzle orifice 103 of the above embodiment at a velocity of about 16.6 m/s as a generally cylindrical stream 21 containing cells which are substantially similarly oriented at the core 189 of the stream 21. At a sheath pressure of 30 psi, the cell velocity will be about 20.3 m/s. At different sheath fluid 19 pressures, the velocity of the stream 21 will vary. 20 Introduction of Core Stream to Torsional Zone Improved orientation of particles may be obtained by altering the flow of the fluid stream 21 through an orienting nozzle so that the core stream 189 containing the particles to be oriented (e.g., sperm cells) is directed along a flow path, at least a portion of which is offset from the 25 center of the nozzle so that the particles are subjected to the hydrodynamic orienting forces generated by a nozzle while they are at a location that is offset from the center of the nozzle. Directing the core stream 189 along an offset flow path may also improve orientation of particles in a traditional nozzle (i.e., one that does not have any torsional zones). In many nozzles, one can determine that a given position is offset from the center of the nozzle because it is displaced 30 from a longitudinal axis of the nozzle. One can also recognize that a particular position is offset from the center of a nozzle because it is displaced from the geometric center of a cross sectional area of the nozzle through which the fluid stream flows. A number of techniques may be used to direct the core stream 189 along a flow path that is offset from the center of the nozzle. For example, an orienting baffle may be positioned in the 35 nozzle to deflect the core stream to one side of the nozzle. Similarly, the conduit 157 for introducing the core stream 189 containing the sample particles may be relocated from the traditional center of the nozzle to an offset location. Furthermore, it is contemplated that an offset sample introduction conduit 157 may be used in combination with an orienting baffle. Exemplary embodiments of use of an orienting baffle and use of an offset sample introduction 40 conduit are discussed below.

38 The improved orientation of particles (e.g., sperm cells) achieved by use of an orienting baffle and/or offset sample introduction conduit 157 may be due to a number of factors. One factor is that the deflection of the core stream 189 and/or a change in the size and shape of the cross sectional flow area results in application of hydrodynamic forces that tend to orient 5 asymmetric particles. (Kachel, et al., Histochemistry and Cytochemistry, 25(7): 774-80 (1977)). Another factor is that it has been found that asymmetric particles (in particular sperm cells) tend to orient as they flow in a fluid stream in close proximity to a solid surface. Thus, by directing the core stream 189 so that it is in close proximity to the interior surface of a nozzle or a baffle surface one can obtain improved orientation of the particles. Furthermore, a baffle and/or offset 10 sample introduction conduit can be used in conjunction with an orienting nozzle which applies additional orienting forces (e.g., torsional forces) to the asymmetric particles. In that case, the baffle can operate to direct the fluid stream so that the core stream containing the particles to be oriented flows along a path that is offset from the center of the nozzle while the particles are subjected to the torsional forces generated by one or more of the torsional zones. 15 Orienting Baffle Figs. 10-13 show one exemplary orienting baffle, generally designated 2001, positioned in the orienting nozzle 137 described above. However, the baffle 2001 could be used in conjunction with a different nozzle, including a non-orienting nozzle, without departing from the 20 scope of this invention. The baffle 2001 is positioned in the nozzle upstream from the orifice 103 and downstream from the sample injection needle 157. Referring to Figs. 14 and 15, the baffle comprises a baffle plate 2003 that is held in place by a baffle holder 2005. In the embodiment shown, the baffle plate 2003 is generally L-shaped and constructed of a substantially rigid, durable and corrosion-resistant material (e.g., stainless steel). The L-shaped plate 2003 has an 25 upstream leg 2007 and a downstream leg 2009, which are desirably substantially perpendicular to each other (e.g., within about 5 degrees of being perpendicular). In the exemplary embodiment shown in the drawings, the two legs 2007, 2009 of the L-shaped plate 2003 intersect at a line 2015 that is perpendicular to the longitudinal axis 2017 of the nozzle 137 (Fig. 11). As shown in Fig. 14, the line of intersection 2015 is also spaced a short distance 2033 (e.g., 30 about 0.3 mm) away from the longitudinal axis 2057 of the baffle holder 2005. The upstream leg 2007 of the L-shaped plate 2003 extends from the line of intersection 2015 away from the longitudinal axis 2017 of the nozzle 137 all the way to the edge of the baffle holder 2005, as shown in Fig. 15. Thus, the upstream leg 2007 is formed with a curved edge 2019 that closely matches the shape of the baffle holder 2005. As shown in Fig. 14, the upstream leg 2007 is 35 inclined at an angle AA of about 15-25 degrees from perpendicular to the longitudinal axis 2057 of the baffle holder 2005. The downstream leg 2009 of the L-shaped plate 2007 extends downstream from the line of intersection 2015 of the two legs 2007, 2009 a distance 2025 of about 2.0-2.5 mm at an angle BB that is in the range of about 60-80 degrees from perpendicular to the longitudinal axis 2057 of the baffle holder 2005.

39 The baffle holder 2005 is sized and shaped to fit inside the nozzle 137, as shown in Figs. 10-13. The baffle holder 2005 is preferably made of a moldable material (e-g., polypropylene) although the baffle holder 2005 may be constructed from other materials without departing from the scope of the present invention. The baffle holder 2005 used in the exemplary embodiment, 5 shown in Figs. 14 and 15, is generally shaped as a hollow cylindrical shell about 4.0-4.5 mm in overall length 2027. The baffle holder 2005 has an exterior diameter 2029 of about 5-6 mm and an interior diameter 2031 of about 2.5-3.5 mm. If the baffle holder 2005 is to be molded, a minor draft (not shown) can be provided on the surfaces of the holder 2005 (e.g., to allow the baffle holder to be easily removed from an injection molding machine). The upstream end 2035 of the 10 exemplary baffle holder 2005 has an inclined surface 2037 which is inclined at the same angle AA as the upstream leg 2007 of the L-shaped plate 2003. The upstream leg 2007 of the L shaped plate 2003 abuts against and is supported by the inclined surface 2037 of the baffle holder 2005. The side edges 2039 (Fig. 15) of the downstream leg 2009 of the L-shaped plate 2003 are partially embedded (e.g., received in slots) in the baffle holder 2005 to hold the baffle 15 plate 2003 in a position in which the downstream leg 2009 spans generally from one side of the baffle holder 2005 to the other. The downstream edge 2041 of the downstream leg 2009 in the exemplary embodiment forms a straight line which is generally perpendicular to the longitudinal axis 2057 of the baffle holder 2057. There is a gap 2049 (Fig. 14) between the downstream edge 2041 of the downstream leg 2009 and the interior cylindrical surface 2051 of the baffle 20 holder 2005. The gap 2049 provides fluid communication between a volume 2053 defined by the legs 2007, 2009 of the L-shaped plate 2003 and the interior cylindrical surface 2051 of the baffle holder 2003 and the rest of the interior volume 2055 of the nozzle 137. The baffle holder 2005 is desirably positioned inside the nozzle with the longitudinal axis 2057 of the baffle holder 2005 generally aligned with the longitudinal axis 2017 of the nozzle 137 25 so that it holds the L-shaped plate 2003 in the position described above. Desirably, the exemplary baffle plate 2003 is rotationally oriented so that the line of intersection 2015 of the two legs 2007, 2009 of the plate 2003 is parallel to a line 2059 running through the major axis of ellipse D, as shown in Fig. 16. However, the exemplary baffle 2001 also performs well when the intersection 2015 of the two legs 2007, 2009 of the L-shaped plate 2003 is perpendicular to the 30 line 2059 running through the major axis of ellipse D, as shown in Fig. 17. Furthermore, the baffle may have any rotational orientation without departing from the scope of this invention. As shown In Fig. 12, the sample injection needle 157 in the exemplary embodiment is desirably a distance 2061 of about 0.25 - 1.0 mm upstream from the most upstream portion 2035'of the baffle 2001. More desirably, the sample injection needle 157 Is about 0.55 - 0.65 mm upstream 35 from the most upstream portion 2035 of the baffle 2001. The baffle holder 2005 may be held in a desired position relative to the nozzle in any number of ways. Referring to Fig. 14, the downstream end 2067 of the baffle holder 2005 is stepped so that it fits farther downstream in the nozzle 137. The stepped downstream end 2067 of the holder 2005 is circular in shape and abuts against the elliptically shaped interior surface 40 233 of the nozzle 137. Thus, the contact between the interior surface 233 of the nozzle 137 and 40 the baffle holder 2005 is generally limited to two points 2069, as shown in Fig. 13. A pair of 0 rings 2071 are positioned around the baffle holder 2005 between the nozzle 137 and the threaded projection 149 of the flow body 133 (Figs. 11-13) and seal the nozzle system 101 against leakage. The O-rings 2071 may be made of Viton@, or any other similar materials. The 5 two 0-rings 2071 are compressed as the nozzle 137 is screwed onto the threaded projection 149 to provide a fluid-tight seal. Two O-rings 2071 are used in the exemplary embodiment because a single 0-ring cannot be compressed within the space between the nozzle 137 and the flow body 133 due to the length 2027 of the baffle holder 2005. Any number of 0-rings or a different type of seal could be used without departing from the scope of the present invention, provided that the 10 number of O-rings or other type of seal is selected so that there will be a fluid-tight seal when the nozzle 137 is screwed onto the flow body 133. This will depend on a number of factors, including the size and shape of the nozzle 137, flow body 133, baffle holder 2005, and O-rings 2071 as well as the type of seal. The O-rings 2071 also help hold the baffle holder 2005 in the desired position. The O-rings 2071 occupy the space around the baffle holder 2005, thereby restricting 15 side-to-side movement of the baffle holder 2005 inside the nozzle 137. Frictional forces between the 0-rings 2071 and the baffle holder 2005 also resist rotational movement of the baffle holder 2005. When the nozzle 137 is tightened on the flow body 133 as shown in Fig. 12, the downstream end 2077 of the threaded projection 149 from the flow body 133, in the form of a 20 boss in this embodiment, is approximately even with the most upstream portion 2035 of the baffle 2001. As a result, the baffle holder 2005 is held axially captive between the flow body 133 (at the upstream end 2035 of the baffle holder 2005) and the interior surface 233 of the nozzle 137 (at the downstream end 2067 of the baffle holder 2005). Other retaining mechanisms may be used. In the embodiment shown in the drawings, the interior diameter of the boss 2079 (Fig. 12) 25 at the downstream end of the threaded projection 149 is roughly equal to the internal diameter 2031 of the baffle holder 2005. Those skilled in the art will recognize that the flow through the nozzle system 101 remains laminar notwithstanding the baffle 2001 because the small cross sectional area through which the fluids must flow results in a low Reynolds number for the flow. As is shown in Fig. 11, 30 the baffle deflects the core stream 189 and sheath stream 191 away from the central longitudinal axis 2017 of the nozzle 137 and toward an interior surface 233 of the nozzle 137. In one embodiment, the core stream 189 also flows very close to the interior surface 233 of the nozzle 137 as the core stream 189 passes between the transition between the first 259 and second 261 torsional zones. However, a portion 2081 of the sheath fluid stream 191 remains between the 35 core stream 189 and the interior surface 233 of the nozzle 137 so the particles in the core stream 189 do not actually impact or contact the interior surface 233 of the nozzle 137. Farther downstream in the nozzle 137, the hydrodynamic forces push the core stream 189 back toward the center of the nozzle 137 (e.g., in alignment with the longitudinal axis 2017 of the nozzle 137). Referring to Figs. 18A-18E, the baffle 2001 changes the shape and reduces the size of 40 the cross sectional flow area in the nozzle 137. (For the sake of clarity, Figs. 18A-18E do not 41 show any nozzle structure downstream from the baffle. The flow area in each of the Figs. 18A 18E is outlined in bold for clarity.) Upstream from the baffle 2001 (Fig. 18A), the cross sectional flow area 2087 is generally circular or elliptical. At the upstream end 2035 of the baffle 2001, the flow area begins to change from a circular shape to a generally semi-circular shape 2089 at the 5 intersection 2015 of the legs 2007, 2009 of the baffle plate 2003 (Fig. 18B), although other shapes may be suitable. There the cross sectional flow area 2089 is smaller than the flow area 2087 upstream from the baffle. Fig. 18C illustrates the flow area 2091 as fluid flows through a part of the baffle holder 2005, and Fig. 18D illustrates the flow area 2093 farther downstream at the downstream end 2041 of the downstream leg 2009 of the baffle plate 2003. It will be 10 observed that flow area 2093 is somewhat larger than flow area 2091 due to the angular orientation of the downstream leg 2009 of the baffle plate 2003. Downstream from the baffle plate 2003 (Fig. 18E) the flow area 2094 through the baffle corresponds the shape of the interior surface 2051 of the baffle holder 2005, which Is circular in the illustrated embodiment. (Other shapes may be suitable.) Downstream from the baffle holder 2005 the torsional zones 259, 261 15 of the nozzle 137 desirably provide torsional forces as discussed above. As shown in Fig. 11, it has been observed that one or more air bubbles 2095 may become trapped in the volume 2053 between the downstream leg 2009 of the L-shaped plate 2003 and the baffle holder 2005. Furthermore, a portion of a bubble 2095 may extend through the gap 2049 between the edge 2041 of the downstream leg 2009 and the baffle holder 2005. 20 Thus, the air bubble(s) 2095 can occupy a portion of the cross sectional flow area downstream of the downstream leg 2009 of the L-shaped plate 2003, perhaps affecting the flow of fluid through the nozzle 137. The exemplary baffle 2001 has been found to work well both with and without the air bubble(s) 2095. Thus, a baffle can be used to orient sperm cells without involvement of any bubbles without departing from the scope of the present invention. 25 Another exemplary orienting baffle, generally designated 2097, is shown in Figs. 19 and 20. The baffle 2097 comprises a flat generally semi-circular baffle plate 2099 in the orienting nozzle 137 discussed above. The baffle plate 2099 is positioned in the nozzle 137 downstream of the sample introduction conduit 157 and generally perpendicular to the longitudinal axis 2017 of the nozzle 137. The baffle plate 2099 has a curved edge 2101 that generally matches the 30 curvature of the interior surface 233 of the nozzle 137 so that there are no large gaps between the curved edge 2101 of the baffle plate 2099 and the interior surface 233 of the nozzle 137. The baffle plate 2099 also has a straight edge 2103 that extends a short distance past longitudinal axis 2017 of the nozzle 137 so that it is approximately aligned with the outer diameter 2109 of the sample introduction conduit 157. The baffle plate 2099 is held in position 35 by friction resulting from compression of the baffle plate 2099 between an o-ring seal 2105, which is similar to the o-ring seals 2071 described in connection with the L-shaped baffle 2001 above, and an annular shoulder or shelf 2107 formed on the interior of the nozzle 137. As shown in Fig. 19 the orienting baffle 2099 operates by deflecting the fluid stream so that the core stream 189 containing the particles to be analyzed Is offset from the central longitudinal axis 2017 of the 40 nozzle 137 along a portion of its flow path. For example, the core stream 189 may be directed 42 along a flow path that is offset from the longitudinal axis 2017 of the nozzle 137 as it flows through the first torsional zone 259, as well as at least a portion of the second torsional zone 261. Consequently, the particles (e.g., sperm cells) are subjected to the torsional forces generated by the torsional zones 259, 261 while they are in a position that is offset from the 5 central longitudinal axis 2017 of the nozzle 137. Those skilled in the art will recognize that substantial changes may be made to the exemplary baffles 2001, 2097 described above without departing from the scope of the present invention. All that is required is that the baffle be configured to deflect the core stream 189 and sheath stream 191 toward an interior surface of the nozzle or to cause the core 189 and sheath 10 stream 191 to flow through a cross sectional area that changes in size and/or shape. Further, it is understood that the orienting baffle structure may be integrally formed with the nozzle or integrally formed with the nozzle and flow body without departing from the scope of the present invention. 15 Offset Sample Introduction Conduit The core stream 189 may be directed along a flow path that is offset from the central longitudinal axis 2017 of the nozzle 137 by repositioning the sample introduction conduit 157 from its traditional position at the center of the nozzle 137 to an offset position. For example, Fig. 21 shows an exemplary offset sample introducing nozzle system 2151 having an offset sample 20 introduction conduit 157. Except as noted, the nozzle system 2151 is substantially the same as the nozzle system 101 shown in Figs. 4 and 5. The significant difference is that the sample introduction conduit 157 has been moved away from the center of the nozzle 137 so that it is no longer aligned with the nozzle's longitudinal axis 2017. Thus, the core stream 189 is directed into the torsional zones 259, 261 of the orienting nozzle 137 along a flow path that is offset from 25 the longitudinal axis 2017. Although the exemplary nozzle system 2151 shown in Fig. 21 uses the exemplary orienting nozzle 137 describe above, It Is contemplated that offset sample introduction conduit 157 could be used with a different orienting nozzle or a non-orienting nozzle to orient particles in the core stream 189. 30 Nozzle Mounting and AdJustment The flow body 133 and nozzle 137 are mounted in a selected orientation and position by means of a nozzle mount, generally designated 331. In one embodiment (Fig. 22), the mount 331 comprises a plurality of stages, including first and second linear stages 333, 337 providing linear adjustment of the flow body 133 and nozzle 137 along X and Y axes 339, 341, 35 respectively, and a third rotational stage 343 providing rotational adjustment about a Z axis 345 corresponding to the longitudinal axis 2017 of the flow body 133 and nozzle 137. These stages 333, 337, 343 may be conventional in design, suitable stages being commercially available, for example, from Newport Corporation of Irvine CA. In particular, the first linear motion stage 333 comprises a fixed first stage member (not shown) mounted on a frame 349, a movable first stage 40 member 355 slidable on the fixed first stage member along the X axis 339, and an actuator 357, 43 e.g., a micrometer, for precisely moving the movable first stage 355 member to a selected X-axis position. The second linear motion stage 337 comprises a fixed second stage member 359 mounted on the movable first stage member 355, a movable second stage member 361 slidable on the fixed second stage member 359 along the Y axis 341, and an actuator 363, e.g., a 5 micrometer, for precisely moving the movable second stage member 361 to a selected Y-axis position. The rotational (third) stage 343 comprises a fixed third stage member 365 mounted on the movable second stage member 316, a movable third stage member 371 rotatably mounted on the fixed third stage member 365 for rotation about the Z-axis 345, and an actuator 373, e.g., a micrometer, for precisely rotating the movable third stage member 371 to a selected angular 10 position relative to the Z-axis 345. The three-axis adjustment provided by these stages 333, 337 343 allows the nozzle 137 and the fluid stream 21 exiting the nozzle orifice 103 to be precisely positioned relative to the optics system 109. Rotation of the nozzle 137 about the Z-axis 345 is particularly helpful because it enables the stream 21 exiting the nozzle 137 to be rotated to bring the cells (e.g., sperm cells) oriented by the nozzle 137 into a position in which the light beam 25 15 from the optics system 109 will fall on the desired surfaces of the cells (e.g., the flat faces 207 of sperm heads 205), as illustrated schematically in Fig. 23. Other nozzle mounts may be suitable. For example, a 4-axis nozzle mounting system can also be used, providing linear adjustment along X, Y and Z axes and rotational adjustment along the Z axis. Further, it may be desirable to use one or more stages having an automated alignment feature, such as a servo or stepper 20 motor controlled microtranslation stage (e.g., part number M-1 10.2DG from Polytech PI, Inc. of Auburn, Michigan). In one embodiment shown schematically in Fig. 36, for example, the nozzle 137 is oriented to direct a stream 21 containing cells to be analyzed in a generally upward direction. The angle 377 between the direction of the fluid stream 21 and horizontal is preferably in the 25 range of 5 to 85 degrees, more preferably in the range of 15 to 75 degrees, even more preferably about 30 to 65 degrees, still more preferably about 45 to 60 degrees, and most preferably about 50 to 55 degrees. This orientation is advantageous in that any air trapped in the nozzle system 101 is readily removed. Also, the velocity of the fluid stream 21 decreases gradually under the force of gravity prior to collection of the droplets 33. A more gradual deceleration of the droplets 30 33 is believed to be less stressful to the cells being analyzed which, in the case of sperm cells, can result in higher motility of the sorted sperm after collection. Of course, in other embodiments of the present invention, the nozzle 101 is positioned so that the fluid stream 21 has a substantially downward velocity when it exits the orifice 103 as is conventional for jet-in-air cytometers. 35 Optionally, components of the nozzle system 101 such as the flow body 133 and nozzle 137 are coated with a non-reflective, non-emissive material (e.g., a dull dark paint or epoxy which does not emit light when subjected to UV laser light) to reduce any reflected and/or emitted light off these elements 133, 137 which might otherwise cause signal noise or have other adverse effects on the optics system 109. 40 44 Transducer and Droplet Formation The transducer 105 for introducing energy into the fluid stream 21 comprises, in one embodiment, a collar 379 containing a piezoelectric element (not shown) secured around the flow body 133 of the nozzle system 101 (Figs. 3 -5 ). The transducer is of conventional design, 5 such as is available from Beckman Coulter, Inc. as part No. 6858368. The transducer has terminals 383 for connection to a suitable source of acoustical energy so that energy can be delivered to the fluid stream 21 at a frequency which will cause it to break into droplets 33 at the droplet break-off location 107 downstream from the nozzle 137 a distance d (Fig. 24). As will understood by those skilled in flow cytometry, the characteristics of the droplet formation are 10 governed by the following Equation 1: (V = fA) Equation 1 where V is the velocity of the stream 21; f is the frequency applied to the fluid stream 21 through 15 the nozzle 137; and A is the "wave length" or distance between the droplets 33. It is a known principle of flow cytometry that droplets 33 will form in a regular pattern with the distance between droplets 33 being 4.54 times the diameter of the stream 21. Since the diameter D of the stream 21 close to the nozzle 137 generally corresponds to the diameter of the nozzle orifice 103 at its downstream end, the frequency at which the stream 21 (and nozzle 137) must be 20 vibrated to form the droplets 33 can be easily calculated using the following Equation 2: (f = V/4.54D) Equation 2 The transducer 105 may be operated to generate in the range of 30,000 - 100,000 droplets 33 25 per second. For example, the transducer 105 may generate 50,000 - 55,000 droplets per second. Assuming the frequency is 55,000 cycles per second (55 kHz), and further assuming that the concentration of cells in the stream 21 is such that cells exit the nozzle 137 at a substantially matching rate of 55,000 cells per second, then there will be, on average, one cell per droplet 33. (In reality, some droplets 33 will contain no cells, some will contain one cell, and 30 some will contain more than one cell.) Of course, any of various factors can be changed to vary this average, including a change in frequency (f), stream 21 (orifice 103) size (D) and stream 21 velocity (V). Ideally, these factors should be such as to reduce the amount of stress imparted to the cells during the course of the process, especially In the case of sperm cells where the preservation of motility is important. 35 Break-off Sensor Referring to Fig. 2, a break-off sensor 389 may be employed to determine the location (e.g., break-off location 107) at which the stream 21 begins to form free droplets 33. The break off location 107 will vary depending on several factors including stream 21 viscosity, surface 40 tension of the fluid and the amplitude of vibration of the transducer 105. By monitoring the break- 45 off location 107, the amplitude of the transducer 105 may be varied to maintain the break-off location 107 within a given range so that the time at which each droplet 33 breaks off can be more accurately predicted by the microprocessor 131. This allows the microprocessor 131 to accurately control the electrical charge of the droplet 33 which is accomplished by selectively 5 controlling the charge of the stream 21. Since the charge of the droplet 33 will be the same as the charge of the stream 21 immediately before droplet 33 formation, the microprocessor 131 controls the sorting of the droplets 33 by selectively charging the stream 21, as noted below. In general, a break-off sensor is for use with any continuous stream of fluid which is breaking into droplets at a break-off location. (in the embodiment of Fig. 2, the break-off sensor 10 389 is located downstream from the nozzle 137 and interrogation location 115.) One exemplary break-off sensor 389 is shown schematically in Fig. 25. A light source 393 Is positioned on one side of the stream 21 to illuminate the stream 21 within the given range at which the break-off location 107 will be maintained. A linear photoarray 395 positioned on the other side of the stream 21 is adapted to be oriented along an axis substantially parallel to the stream 21. As a 15 result, the photoarray 395 detects light from the light source 393 which passes through the droplets 33 and provides output signals corresponding to the detected light. The output signals are processed to determine the position of the break-off location 107. For example, the output signals may be digitized and provided to the processor 131 for processing. Alternatively, as shown in Fig. 25, the light source 393 may be an LED or other 20 source which generates a near-infrared portion of the visible spectrum. The light passing between the droplets 33 is magnified by a lens 401 and directed toward an 8 by 1 linear array of photodiodes 395. Each photodiode generates a current that is proportional to the light intensity impinging thereon. This current is fed into 8 current to voltage op-amp circuits 405. The output voltage from the op-amps is AC coupled into 8 track/hold amplifiers 407. The track/hold signal 25 409 used by the amplifiers is taken from the transducer 105. The output from the track/hold amplifier is fed Into the A/D converter 411 of a microprocessor unit (MPU) 391. The digital values computed by the MPU 391 will be provided to the system control microprocessor 131. A lookup table and/or algorithm may be used by the system control microprocessor 131 to convert between break-off location 107 drift and voltage adjustment to the transducer 105. Alternatively, 30 the output from the MPU 391 may be an analog signal such as a DC voltage having an amplitude corresponding to a change in the amplitude of vibration of the transducer 105. The dc voltage can be applied to the high voltage amplifier input driving the droplet transducer 105 to vary the amplitude of vibration. Thus, such a processor 391 would constitute a control for receiving the output signal from the photoarray 395 and providing a location signal corresponding to a location 35 of the break-off location 107. Such a processor 391 would also constitute a control for receiving the output signal indicative of the position of the break-off location 107 of the droplets 33 and varying operation of the transducer 105 as a function of the position of the location 107. Alternatively, as is well known to those skilled in the art, a video camera and strobe light may be used to monitor and control the droplet break-off location. Thus, as shown in Figs. 26 40 27, a video camera system 412 and strobe 413 may be provided to monitor the break-off location 46 107. It is desirable to place the strobe 413 behind a mask 414A (e.g., a cover with a small slit shaped opening 414B) to limit the amount of light produced by the strobe 413 that enters the optics system 109 (Fig. 27). 5 Epi-Illumination Optics System The optics system 109 is adapted for focusing a beam of electromagnetic radiation 25 (e.g., a laser beam) on the fluid stream 21 as a beam spot, so that the cells to be analyzed pass through the spot. The beam 25 may be laser light in the visible or ultraviolet portion of the 10 spectrum, for example, having a wavelength of about 350-700 nm, although other wavelengths may be used. The wavelength of the laser light may be selected so that It is capable of exciting a particular fluorochrome used to analyze particles. If the optics system 109 is used to analyze sperm cells stained with Hoechst 33342, for instance, the wavelength may be selected to be in the range of about 350-370 nm. The power output of the laser may vary between 50 and 300 15 mW. Sperm cells may be analyzed using a 200 mW laser, for example. Referring to Figs. 28 34, the system 109 is an epi-illumination system 415 comprising an instrument, generally designated 417, having a longitudinal optical axis 419. As used herein, the term "epi illumination" means an optics system where at least some of the fluorescence emissions from cells passing through the beam spot are directed back through the optical instrument along the 20 same axis as the focused beam 25, but in the opposite direction. This type of system is advantageous in that only one set of optics is required, including only one photodetector 117, unlike conventional systems which detect forward and side fluorescence and which use two or more photodetectors. However, it will be understood that while an epi-illumination system is preferred, many of the aspects of this invention can be applied regardless of the type of optics 25 system used. In one embodiment, the epi-illumination instrument 417 comprises a rectangular base 429 supporting a plurality of optical elements. These optical elements are described below, with specific examples of relevant dimensions, focal lengths, and part numbers. As will be understood by those skilled in the art, this information is exemplary only, and alternative optical 30 elements can be used without departing from the scope of this invention. Referring to Figs. 28-34, the optical elements include a reflecting filter 431 which reflects a collimated beam 25 of light from a laser or arc lamp 435, for example, through a conditioning lens assembly 437 mounted in an opening 439 in a side wall 441 of a dichroic chamber 443 extending up from the base 429. In this particular embodiment, the conditioning lens assembly 35 437 comprises a retaining ring 445, neutral density filter 447, cylindrical lens 449, lens holder 455 and jam nut 457. The cylindrical lens 449 introduces a one-dimensional divergence into the beam 225 and directs it toward optical elements (described below) which shape the beam to have a desired cross sectional shape 459, preferably generally elliptical. By way of example, the cylindrical lens 449 may be a plano-convex lens having a focal length of 16 mm. A beam 47 expander (not shown) can optionally be installed in the instrument 417 to allow adjustments to be made to the shape of the elliptical beam spot 459. The reflecting filter 431 is mounted by clips 461 on the angular face 465 of a filter holder 463 which has openings 467 in it to permit the beam 25 to reflect off the filter 431 toward the 5 optics of the instrument 417. The holder 463 is fastened to a linear stage 469 movable along an X-axis 471 relative to an outrigger 473 secured to the base 429 and dichroic chamber 443, the stage 469 being movable by suitable means 475 (e.g., a micrometer) to precisely locate the holder 463 and reflecting filter 431 to reflect the beam 25 into the instrument 417 at the proper location. A dichroic filter 477 is held by clips 479 on a frame 485 mounted in the dichroic 10 chamber 443 and functions to reflect the shaped beam 25 in a forward direction 487 along an axis 489 which, in this particular embodiment, corresponds to the longitudinal optical axis 419 of the instrument. The beam 25 passes through a focusing lens assembly 491 which focuses the beam 25 on the fluid stream 21 as a beam spot having the aforementioned generally elliptical shape 459 (Fig. 6) with the major axis of the ellipse extending generally perpendicular to the 15 direction of flow 227 of the stream 21. As each cell passes through the beam spot 459, the fluorescing dye (or other reporting agent) in the cell is activated to emit fluorescent light 31 (Fig. 23). In the case of sperm cells stained with a DNA selective fluorescing dye, X cells have more DNA than Y cells, include more fluorescing dye, and emit a stronger signal than Y cells (e.g., 3.8%), which provides a basis for discriminating and sorting cells, as will be described. The 20 focusing lens assembly 491 includes, in one embodiment, a microscope adapter 501 mounted in an opening 503 in a front wall 505 of the dichroic chamber 443, a focusing barrel 507, a pair of lens mount barrels 509, and the lens 511 itself, which may be a 12.5 mm diameter, pIano-convex lens with a focal length of 16 mm, available from Oriel Corporation as part number 41209, and is anti-reflective coated for light having a wavelength in the range of 340-550 nm. The lens 511 25 may be made of fused silica. Other focusing lenses may also be suitable, such as an infinity corrected fluorescence microscope objective. The focusing lens assembly 491 has a conventional telescoping focus adjustment 515 to focus the elliptically-shaped beam spot 459 on the core 189 of the stream 21. The outgoing fluorescent light 31 emitted by the cells as they pass through the beam 30 spot 459 is of a different (longer, due to the Stoke's shift principle) wavelength than the incoming laser light 25. Some of the fluorescence emissions 31 are transmitted in a rearward direction 513 along the incoming beam axis back through the focusing lens 511 which collects and collimates the fluorescence emission 31. The collimated fluorescence emissions 517 pass in a rearward direction from the lens 511 to the dichroic filter 477, which transmits the fluorescence 35 emission 517. By way of example, the dichroic filter 477 may be a filter available from Omega Optical as part number XF2001, 400DCLP. The optics system 415 includes a filtering system 519 positioned rearward of the dichroic filter 477 along the optical axis 419 of the instrument 417. In one embodiment, the filtering system 519 includes an emission filter 521 In a holder 523 mounted in an opening 525 in a back 40 wall 527 of the dichroic chamber 443. The emission filter 521 attenuates any laser light scatter 48 or other undesired electromagnetic radiation that is transmitted through the dichroic filter 477. By way of example and not limitation, the emission filter 521 can be a thin film, long-pass filter adapted to transmit more than 90% of light having a wavelength greater than 408 nm, as is available from Omega Optical as part number XF3097. An alignment pellicle assembly 529 is 5 spaced rearwardly along the optical axis 419 from the emission filter. This assembly includes a slider 531 movable on a rail 533 extending longitudinally of the base 429 parallel to the longitudinal optical axis 419 of the instrument 417, a filter holder 535 secured to the slider 531, a pellicle filter element 539, and clips 541 for securing the pellicle filter element 539 to the filter holder 535 at an angle 543 relative to the optical axis 419 of the instrument 417. The pellicle 10 filter element 539 has the same thickness as the dichroic filter 477 and functions to translate the collimated fluorescence emission 517 back onto the optical axis 419 of the instrument 417. Fasteners 545 extending up through parallel slots 547 in the base 429 on opposite sides of the rail 533 secure the slider 531 to the base 429 in the desired position along the optical axis 419. Spaced to the rear of the alignment pellicle assembly 529 is an aspheric lens 549 held by a 15 holder 551 mounted in a frame 553 which is also slidable on the rail 533 and secured in selected position by suitable fasteners 557. The aspheric lens 549 focuses the collimated fluorescence emission 517 onto a spatial filter, generally designated 559, which filters out reflection or emission from sources other than the cells to be analyzed. The aspheric lens 549 may be, for example, an 12.5 mm diameter aspheric lens having a focal length of 15 mm, as is available from 20 Oriel Corporation. The lens 549 is preferably anti-reflective coated for visible emission wavelengths but made of a material (e.g., flint glass) which further attenuates transmission of laser light scatter. As shown in Fig. 34, the spatial filter 559 comprises, in one embodiment, a pair of aperture plates 561 releasably held by a frame 563 mounted on the base 429 of the instrument 25 417. Each of the plates 561 has a slit 567, 571 therein, one slit 567 preferably being generally vertical and the other 571 preferably generally horizontal, the arrangement being such that the slits 567, 571 intersect to form an aperture 573. In one embodiment, the aperture 573 is generally rectangular in shape and has a vertical dimension 575 of 100 microns and a horizontal dimension 577 of 500 microns. The size and shape of the aperture 573 may vary (or even be 30 adjusted by changing aperture plates), so long as it functions to remove reflections and light from any source other than the collection volume 579. The frame 563 holding the aperture plates 561 preferably has two parts, namely, a plate holder 583 slidable on the rail 533 of the base 429 and secured in selected position by fasteners 587, and a backing member 589 for securing the aperture plates 461 in position on the plate holder 583. 35 In one embodiment, the smaller (vertical) dimension 575 of the aperture 573 in the spatial filter 559 is sized (or adjusted) to enable use of a "slit scanning" technique to evaluate the cell. This technique is described in more detail in the "Focused Beam Spot" section of this specification. Another embodiment of an epi-illumination optics system, generally designated 450, is 40 shown in Fig. 35. This embodiment is substantially the same as the embodiment shown in Figs.

49 28-34, except as noted. One significant difference is that the dichroic filter 477 has been replaced with a different dichroic filter 451 that transmits (rather than reflects) the illumination beam 25 and reflects (rather than transmits) the fluorescent emissions 31. Also, because the fluorescence emissions 31 are reflected by the dichroic filter 451 rather than transmitted, there is 5 no need for an alignment pellicle 539 in this embodiment of an epi-illumination optics system 450. Thus, the epi-illumination system 450 is just one example of how the optics system can be reconfigured if desired without departing from the scope of this invention. Further, the cylindrical lens 449 is mounted on an adjustable mounting assembly 449A. The mounting assembly 449A allows two-axis translational movement of the cylindrical lens 449 10 in a plane perpendicular to the illumination beam 25. Releasable fasteners (e.g., screws (not shown)) extend through slot-shaped holes 449B (only one of which is visible on Fig. 35). Release of the fasteners allows translational movement of the lens 449 in a first direction perpendicular to the beam 25. Similar fasteners (not shown) extend through slot-shaped holes 449C, allowing translational movement of the lens 449 in a second direction perpendicular to the 15 first direction. This allows minor adjustment of the relative positions of the cylindrical lens 449 and beam 25 so that the intersection of the beam 25 and lens 449 can be moved across the surface of the lens 449, thereby causing slight changes to the focusing provided by the cylindrical lens 449. Once the lens 449 is in the desired position, the fasteners can be tightened to hold it there. 20 Photodetector The emitted fluorescence passing though the spatial filter 559 falls upon a photodetector 117 fastened to a mounting plate 591 slidable on the rail 533 of the base 429 at the rear of the epl-illumination instrument 417 and securable in fixed position by fasteners 595 (Fig. 32). The 25 photodetector 117 detects the fluorescent emissions 31 and converts them into electrical signals which can be processed to analyze the desired characteristics of the cells, as will be described in more detail later. The photodetector 117 may be a conventional device, such as a photodetector available from Hammamtsu. The photodetector 117 preferably includes a preamplifier and PMT gain which is optimized for emission Intensity produced by the epi-illumination system for the 30 particular stained cells being analyzed. In general, the PMT gain is optimized when between about 200 and 2000 volts are applied to the vacuum tube. In the case of detecting fluorescent emissions from Hoechst 33342, for instance, the PMT gain is optimized when between about 400-800 volts are applied to the vacuum tube. One particularly desirable photodetector includes a PMT having a spectral range 35 of 185-830 nm (530 nm peak), a 0.01 mA maximum average anode current, a cathode radiant sensitivity of 70 mA/W typical, a cathode luminous sensitivity of 140 pAlm, anode luminous sensitivity of 300 A/Im, max anode dark current of 1 nA (0.1 nA typical), and a 1.4 nanosecond risetime. The PMT is DC coupled amplifier demonstrating a fiat gain to > 37 MHz, having a 1 V peak output into a 50 D load and a recovery time of less than 400 nanoseconds. It is also 50 desirable for the amplifier to allow high voltage adjustment for compensation of PMT efficiency variations without decreasing the signal-to-noise ratio to less than 800 dB. Angle of Beam incidence 5 Fig. 36 schematically illustrates one desirable orientation of the intersection of the light beam and the fluid stream. Several points are of note. As shown, the light beam 25 is focused on the stream 21 at a location 115 that is only a short distance 605 from the exit orifice 103 of the nozzle 137, preferably less than 1.0 mm, or even inside the nozzle 137, so that the cells pass through the spot 459 while they are still substantially in desired orientation, as previously 10 described. This is particularly important for cells which are mobile in the fluid stream 21, including sperm cells. Another point of note is that the beam 25 of this embodiment may be directed toward the fluid stream 21 along a beam axis 609 which intersects the fluid stream 21 at an angle of incidence A which is skewed (off 90 degrees) relative to a longitudinal axis of the fluid stream 21, 15 as viewed from a side of the stream 21 (see Fig. 36). When sorting certain particles, it has been found that better discrimination of the different types of particles may be obtained by illuminating the stream 21 at an angle of incidence other than 0*. Sperm nuclei, for instance, are desirably illuminated at an angle of incidence A that is in the range of 5 to 45 degrees, more preferably in the range of 15 to 30 degrees, and even more preferably in the range of 18 to 24 degrees. Other 20 particles (e.g., live sperm cells) are easier to Interrogate when the light beam 25 is generally perpendicular to the fluid stream 21 (i.e., when angle A is about 0*). Thus, it is contemplated that angle A may be any angle without departing from the scope of this invention. The proper selection of angle A results in improved signal to noise discrimination in certain particles and thus more accurate discrimination based on different characteristics of those 25 particles (e.g., sperm nuclei with X and Y chromosomes sperm cells). This improvement may be due to a number of factors, including reduced laser light scatter entering the focusing lens 511. Because the focused beam spot 459 is preferably wider than the stream 21, a diffraction pattern is created at the intersection 115 of the beam 25 and the stream 21. When angle A is greater than about 12 degrees, the reflected diffraction pattern does not fall on the lens 511. Another 30 factor may be that the skewed angle A allows the beam 25 to be focused very close to the nozzle orifice 103, so that the nozzle body 139 does not interfere with the lens 511. Relatedly, the cells are more uniformly aligned closer to the nozzle 137, so that focusing the beam spot 459 closer to the nozzle 137 results in an improved signal. Further, the more "head on" profile of the cell presented to the lens 511 (beam 25) at the skewed angle A reduces the variation of total 35 fluorescence intensity caused by any misalignment of the cells. In this regard, in the case of sperm cells it is preferable that the beam 25 fall on one of the wide faces 207 of each sperm cell 201, as discussed above, and that the nozzle 101 and optics system 109 be positioned to achieve this result. While a skewed angle of incidence A is believed to be beneficial in sorting some 40 particles, it is contemplated that the angle of intersection between the beam axis and the stream 51 may be 90 degrees or any skewed angle without departing from the scope of this invention. It is also expected that the optimal angle of incidence may vary widely depending on the properties of the particular particles being analyzed. 5 Focused Beam Spot Referring to Fig. 6, the focused beam spot of one embodiment is shown as having a generally elliptical (oval) shape 459 with a length Li along a major axis extending generally at right angles to the direction of fluid stream flow 227 and a width WI along a minor axis extending generally parallel to the direction of fluid stream flow 227. In one embodiment, the width WI is 10 less than the length of the head of the sperm cell 219, and even more preferably less than the length of the region 225 containing the chromatic DNA mass of the cell, which in the case of a bovine sperm cell 201 has a length of less than about 1 pm. For a stream 21 having sheath stream 191 that is about 60 pm in diameter and a core stream 189 containing bovine sperm cells 201, an exemplary length Li is about 80 pm and an exemplary width W1 is about 1.5 pm. By 15 focusing the beam spot 459 to a width W1 which is less than the length of the head 205 of the sperm cell 201, or any other cell or particle being analyzed, and even more preferably less than the diameter of the DNA region 225 of the head 205 of the sperm cell 201, greater signal resolution is achieved, as will be understood by those familiar with "slit scanning" techniques. This is a technique by which a beam 25 is narrowed to have a width less than the length of a cell 20 (i.e., the dimension of the cell in the direction of stream flow) so that as the cell moves through the narrow beam, photon emissions 31 from the cell are measured over the length of the cell, as will be discussed later. In this way, information can be obtained about variations in structure, including DNA material, along the length of the cell. The slit-scanning technique is also helpful in identifying "coincident" cells, that is, cells which are overlapping or very close together. 25 As mentioned previously, slit scanning can also be carried out by sizing the aperture 573 of the spatial filter 559 to have a vertical dimension 575 such that only a portion of the light emitted from a cell, corresponding to a fraction of the cell length in the direction of stream flow, passes through the aperture to the photodetector 117. Further, signal resolution can be optimized by adjusting the width of the beam and/or the size of the aperture of the spatial filter to 30 work together to provide a beam spot that is suitably shaped for slit scanning. One way to adjust the shape of the beam spot 459 is by changing to a different cylindrical lens and/or by making an adjustment to a beam expander in the optics system 109. Further any method of shaping the beam 25 to form an elliptically shaped beam spot 459 is contemplated as being within the scope of the present invention. Beam spots of other shapes 35 and sizes may also be used and are contemplated as falling within the scope of this invention. Sorting System Fig. 2 illustrates an exemplary embodiment of the sorting system 119. The sorting system 119 comprises an electrostatic charging device 627 for charging and/or not charging the 40 droplets 33 depending on the classification of the particles contained in the droplets 33 (e.g., the 52 X/Y chromosome content of sperm cells), and a pair of electrostatic charged deflector plates 629 for sorting the droplets 33 into different groups 123, 125, according to their charge. It is desirable to coat the deflector plates 629 with a dull, low-emissive coating (e.g., epoxy or paint) to limit light reflected or emitted by the deflector plates 629. The deflector plates 629 may be charged by any 5 suitable power supply 635. It is generally desirable for the electrical potential between the two fully charged deflector plates 629 to be in the range of 2000 - 4000 volts. However, the electrical potential between the deflector plates 629 may be anywhere between about 1000 and 6000 volts. The charging device 627 comprises a charging element 631 having an opening 633 10 therein through which the stream 21 passes at a location near the droplet break-off location 107 (e.g., within five droplet lengths or closer). It is desirable to mount the charging element 631 with a mechanism that facilitates adjustment of the position of the charging element 631 with respect to the droplet break-off location 107. As shown in Figs. 26 and 27, for example, the charging element 631 and deflector plates 629 may be attached to an adjustable mounting assembly 5001 15 that allows three-axis translation and tilt adjustment of the charging element 631 and deflector plates 629 with respect to the nozzle system 101. For translation along an axis 5011 parallel to the stream 21, the mounting assembly 5001 includes a board 5003 fastened to a backing 5005 by releasable fasteners 5007 passing through slots 5009 in the board 5003, the slots 5009 being oriented generally parallel to axis 5011. For translation in an axis 5013 perpendicular to the 20 stream 21, a second adjustment board 5015 is fastened to the first board 5003 by releasable fasteners 5017 passing through slots 5019 in the second adjustment board 5015, the slots 5019 being oriented generally parallel to axis 5013. The charging element 631 and deflector plates 629 are secured to the second adjustment board 5015. Thus, by releasing the fasteners 5007 and/or 5017, one can adjust the position of the charging element 631 and deflector plates relative to the 25 nozzle system 101 in a plane parallel to the fluid stream 21 and then tighten the fasteners 5007 and/or 5017 to secure the mounting assembly 5001. For translation along a third axis perpendicular to the first two axes 5011, 5013, the backing 5005 is fastened to a fixed support 5021 by adjustable fasteners 5023 (e.g., threaded bolts screwed into tapped holes in the fixed support 5021). In one embodiment, each adjustable 30 fastener 5023 passes through a spring 5025 positioned between the backing 5005 and the fixed support 5021. The amount of compression of any spring 5025 can be adjusted by tightening or loosening the respective fastener 5023. Adjusting the compression of all springs 5025 in the same amount results in translation along the third axis. The mounting assembly 5001 can be tilted in virtually any direction by changing the relative compression of one or more of the springs 35 5025 with respect to one or more other springs 5025. In this exemplary embodiment, the relative positions of the charging element 631 and deflector plates 629 remain fixed with respect to one another because they are all fastened to the same adjustment board 5015. This prevents adjustment of the mounting assembly 5001 from affecting alignment of the changing element 631 with respect to the deflector plates 629.

53 The charging element 631 is connected to a suitable electrical circuit (e.g., a 90 volt selectively charging circuit) under the control of the processor 131 and coupled to a power supply for applying an electrical charge to the charging element 631. The circuit is used to charge or not charge the stream 21 immediately prior to the formation of a droplet 33 at the break-off location 5 107 depending on whether the droplet 33 contains a particle having the desired characteristics (e.g., at least one live X-chromosome sperm cell). The charging element 631 is positioned electrostatically near the stream 21 or near the droplets 33 formed from the stream 21 for providing an electrical reference with respect to the electrostatic polarity of the stream 21. The droplets 33 carry the same charge as the stream 21 at the instant the droplet 33 breaks from the 10 stream 21. The charged or uncharged droplets 33 then pass between the deflector plates 629 and are sorted by charge into collection vessels 2207 of the collection system 2201. While sorting produces two groups or populations of droplets 123, 125 in Fig. 2, the particles may be separated into any number of populations from 1 to N sorted by placing different charges on the droplets 33 in respective groups, any by supplying the appropriate number of collection vessels, 15 each being positioned to collect a different population of droplets. Automated Drop Delay Calibration In the sorting system 119 described above, the processor 131 must estimate the time it takes for a particle to move from the interrogation location 115 to the droplet break-off location 20 107 so that the charge (or lack of charge) to be applied to the droplet 33 containing that particle is applied when the particle is in the last attached droplet 33 at the break-off location 107. If the delay setting used by the processor 131 is wrong, the droplets 33 will not be sorted according to their contents. Similarly, if the application of electrical charges to the droplets 33 is even slightly out of phase with droplet 33 formation this can degrade sorting because none of the droplets 33 25 will be fully charged and droplets 33 that are supposed to have neutral charge will carry a small positive or negative electrical charge. This will alter the paths of the droplets 33 through the electric field between the deflection plates 629. The best way to verify that the processor 131 is using the appropriate delay setting or to adjust the drop delay setting (i.e., calibrate the system's 9 drop delay setting), is to sort a number 30 of droplets 33 and examine the results. By incrementally varying the delay setting and monitoring the results, one can select the optimal delay setting. Traditionally, this sort calibration Is performed manually. Recently, automated calibration systems have been designed to sample or examine the contents of the droplets in the sorted droplet streams and automatically adjust the delay setting without human intervention. For example U.S. Patent Nos. 6,372,506 (Norton) and 35 5,643,796 (van den Engh), which are hereby incorporated by reference, both disclose automated sort calibration systems. The purported advantages of these systems are that they are less labor intensive and are capable of verifying the delay setting throughout the sorting process rather than just during initial set up. The drawbacks are that they are cumbersome and take up valuable space unnecessarily. 40 54 (i) Epi-illumination Sensors Referring to Fig. 37, an automated continuous calibration system 4201 of the present invention for a fluorescence activated droplet sorting cytometry system comprises one or more epi-illumination sensors 4203 positioned to sense the contents of droplets 33 to verify the delay 5 setting for droplet charging. Referring to Fig. 38, each epi-illumination sensor includes a light source (not shown), a fiber optic cable 4205, a dichroic filter 4207, a lens system 4209, a photodetector 4213, and a control system. In one exemplary embodiment, the processor 131 serves as the control system, but other processors or controls could be used instead. The light source may be a low-power solid state laser dedicated solely to the automated 10 calibration system 4201. Alternatively, a beamsplitter (not shown) may be used to divert a portion (e.g., about 5%) of the energy in the beam 25 used for interrogation of particles in the fluid stream 21 to one or more epi-illumination sensors 4203. Similarly, the fiber optic cable 4209 can be positioned in a beam stop 4215 (Fig. 26) to gather light from beam 25 after It passes through the interrogation location 115. The light from the light source must include light having a 15 wavelength capable of exciting fluorescent molecules in the particles being sorted, thereby causing fluorescence emissions 4211 from the particles. If the particles are stained with Hoechst 33342, for instance, the light source can provide light having a wavelength of about 350 nm, about 407 nm or any other wavelength capable of exciting the Hoechst 33342 molecules. The fiber optic cable 4205 extends from the light source to a location downstream of the 20 interrogation location 115. For example, in the exemplary embodiment the fiber optic cable 4205 leads to a location adjacent the trajectory of one of the droplet streams as it moves through the electric field between the deflector plates 629. The dichroic filter 4207 is positioned in front of the end of the fiber optic cable 4205. The dichroic filter 4207 transmits light having the spectral characteristics of the light conducted by fiber optic cable 4205, but reflects light having the 25 spectral characteristics of the fluorescence emissions 4211. Thus, the dichroic filter 4207 may have the same specifications as the dichroic filter 477 describe above in connection with the epi illumination optics instrument 417. The focal length of the lens system 4209 is selected based on the expected distance of the sensor 4203 from the droplets 33 so that the illumination/detection volume of each sensor 4203 is about equal to the volume of the droplets 33. 30 Referring to the exemplary embodiment shown in Fig. 37, an epi-illumination sensor 4203 is positioned adjacent the trajectory of each of the three sorted droplet streams 4225, 4227, 4229 to sense the contents of droplets 33 in a respective stream. The cytometer system 9 includes an electrically Insulated support 4221 for mounting the two deflection plates 629. The support has three holes 4223, one adjacent the trajectory of each sorted droplet stream 4225, 35 4227, 4229. An epi-illumination sensor 4203 is positioned at each hole 4223 to observe droplets 33 in one of the droplet streams 4225, 4227, 4229 through the respective hole 4223. This compact configuration takes up relatively little space and keeps components of the calibration system 4201 out of the way, providing better access to other parts of the cytometer 9. If a droplet containing a fluorescent particle passes through the illumination/detection 40 volume of the sensor 4203, this will result in a flash of fluorescence emissions 4211, some of 55 which will be collected by the lens system 4209 and reflected off from the dichroic filter 4207 to the photodetector 4213. Signals from the photodetector 4213 are provided to the processor 131. Based on the signals received from the photodetectors 4213, the processor 131 can determine the contents of the droplets 33 in each of the sorted droplet streams 4225, 4227, 4229. 5 If a sensor 4203 fails to detect a flash of fluorescence emission 4211 when the processor 131 expects a droplet 33 containing a fluorescent particle to pass by that sensor 4203, the processor 131 can use that information to adjust the delay setting or adjust the location of the droplet break-off location 107. Likewise, the processor 131 can make an adjustment if a sensor 4203 detects a fluorescent emission 4211 when the processor 131 does not expect a droplet 33 10 containing a particle to be passing by the sensor 4203. Furthermore, the processor can compare the relative frequency of fluorescent emissions 4211 from the sorted streams 4225, 4227, 4229 to see if the frequency of detected fluorescent emissions 4211 matches the expected frequency. The processor 131 can also adjust the amplitude of the charge applied to the charging element 631 to increase or decrease the amount by which a sorted stream 4225, 4229 is deflected to 15 maximize the intensity of the detected fluorescence emissions 4211. This will maintain the alignment of the trajectory of the deflected droplet streams 4225, 4229 so the droplets pass directly through the collection volume of the epi-illumination sensor. Because the sensors 4203 are positioned to observe the streams 4225, 4227, 4225 as they move through the electrical field between the deflector plates 629, the calibration system has a shorter response time than it 20 would if it observed the streams 4225, 4227, 4229 in the freefall area downstream of the deflection plates. (ii) Empty Droplet Test Stream One sensitive indication of the quality of the calibration can be arranged by creating and 25 monitoring a calibration test stream that contains substantially only empty droplets 33. Referring to the sort calibration system 4201 shown Fig. 37, droplets 33 containing desired particles are sorted into stream 4225 and droplets 33 containing any other particles and most of the empty droplets 33 are sorted into stream 4229 (i.e., the waste stream). The test stream 4227 is created by applying a neutral charge to at least a fraction (e.g., I out of every 10) of the empty droplets 30 33. Many droplets 33 that are considered "empty" for traditional sorting purposes are actually droplets 33 for which there is a low probability that the droplet 33 contains a particle, based on the arrival time of particles at the interrogation location 115 and estimated droplet formation boundaries in the fluid stream 21. These "empty" droplets should not be sorted into the test stream 4227 because this would inevitably result in detection of some particles in the test stream 35 4227. Instead, for the test stream 4227 the processor 131 should select only droplets 33 that the processor 131 believes have substantially zero probability of containing a particle In order to create a substantially particle-free test stream 4227. The probability that any randomly selected droplet 33 contains a cell is known and is approximately the average cell analysis rate divided by 40 the droplet generation rate. This means that by monitoring the rate of mis-sorts in the test 56 stream 4227 it is possible to estimate fractional adjustment of the phase relationship of droplet charging needed to match the phase of droplet 33 formation. For example the processor 131 may select droplets that it estimates have about 15% or lower probability of containing a particle, about 10% or lower probability of containing a particle, about 5% or lower probability of 5 containing a particle, about 1% or lower probability of containing a particle, about 0.1% or lower probability of containing a particle, about 0.01% or lower probability of containing a particle, about 0.001% or lower probability of containing a particle, or about 0.0001% or lower probability of containing a particle. The probabilistic cutoff for substantially zero probability may be selected based on sort-speed, tolerance for impurity, or other sort parameters, with the cutoff including 10 higher probabilities that a droplet will include a particle for high-speed sorting or when there is more tolerance for impurity. Failure of the processor 131 to create a substantially particle-free test stream 4227 (i.e., a test stream 4227 In which the ratio of droplets 33 containing particles to the total number of droplets 33 agrees with the probabilistic cutoff used to select droplets 33 for the test stream 15 4227), as indicated by detection of more than a threshold number of droplets 33 containing particles in the test stream 4227, is a definitive indication of sub-optimal sorting and prompts the processor 131 to adjust the drop delay setting. The threshold level is determined in relation to the probabilistic cutoff used to select droplets 33 for the test stream 4227 and the total number of droplets 33 selected for the test stream 4227. Ideally, some droplets 33 can be selected for the 20 test stream 4227 even though one or more particles in the fluid stream 21 are relatively close to an estimated drop formation boundary for the respective droplet 33 to make the system 4201 more sensitive to slightly sub-optimal drop delay settings. Of course, the sort calibration system could apply a non-neutral charge to and deflect droplets selected for the test stream, without departing from the scope of this invention. The 25 relative order of the streams 4225, 4227, 4229 could also be rearranged without departing from the scope of this invention, although interposing the test stream 4227 between the waste stream 4225 and the stream of desired particles 4229 (as shown in the exemplary embodiment) reduces the risk of crossover contamination of the sorted sample by the waste stream. Further, if the particles do not emit fluorescent light, different sensors can be used to detect any scattered light 30 caused by particles in the test stream without departing from the scope of this invention. (iii) Impact of Sort Calibration System In one embodiment of the invention, the automated calibration system 4201 is operable to automatically determine and set the phase relationship between droplet formation and droplet 35 charging to within about 5% of the optimal phase (i.e., within +/- about 18 degrees. In another embodiment the system 4201 is operable to automatically determine and set the phase relationship to within about 1% of the optimal phase (i.e., within +/- about 3.6 degrees)). In another embodiment, the calibration system 4201 is operable to continuously monitor a high speed droplet sorting system and automatically maintain the phase relationship within about 10% 40 of the optimal phase (i.e., within +/- about 36 degrees). In still another embodiment, the system 57 4201 is operable to continuously monitor a high-speed droplet sorting system and automatically maintain the phase relationship without about 3% of the optimal phase (i.e., within +/- 10.8 degrees). 5 Sort System Fault Correction From time to time, a droplet 33 will stray from its normal trajectory and hit the charging element 631 or the deflector plates 629. If one or more droplets 33 hit the charging element 631, the charging element 631 may not be able to charge droplets 33 properly. Further, the normal droplet 33 trajectory through the charging element 631 can become obstructed causing even 10 more droplets 33 to accumulate on the charging element 631. Also, if stray droplets 33 strike a deflector plate 629, they can distort or otherwise disrupt electrical field lines between the deflector plates 629, thereby changing the trajectory of the sorted droplet steams 123, 125. Thus, it is desirable to have a debris removal system to remove debris from the charging element 631 and/or the deflector plates 629. In one exemplary embodiment, shown Figs. 26 and 15 27, the system 9 includes a debris removal system 5047 for the charging element 631 and a debris removal system 5049 for the deflector plates 629. Referring to Fig. 27, the charging element 631 is held in position by a support 5051 secured to board 5015 of the adjustable mounting assembly 5001. A vacuum passage 5053 (shown in phantom) extends through the support 5051 to an opening 5057 adjacent the charging 20 element 631. The vacuum passage 5053 is connected to a suitable vacuum source (not shown) by a vacuum line 5055 attached to a fitting 5058 on the support 5051. Suitable controls are provided for selectively applying a vacuum in the passage 5053 to vacuum any undesired material (e.g., stray droplets 33) off the charging element 631 and restore proper function of the charging element 631. 25 Relatedly, as shown in Fig. 27, a manifold 5061 fastened to the mounting assembly 5001 has a network of air passages 5063 therein (shown in phantom) connected via an air line 5059 and fitting 5065 to a source of compressed air or other gas (not shown). The passages 5063 have openings 5064 positioned along a side 5066 of each deflector plate 629 and the portions 5067 of the passages 5063 leading to the openings 5065 are oriented so compressed air blown 30 through the manifold 5061 will clear any stray droplets 33 or other debris off the deflector plates 629. Any material blown off the deflector plates 629 will hit a cover panel (not shown) and drain into a suitable waste collection device (not shown). In one embodiment, if the processor or other sensor determines that stray droplets 33 have hit the charging element 631 or deflector plates 629, as indicated by the sort calibration 35 system described above for example, the processor can automatically initiate a fault correction procedure or mode, which can include applying a vacuum to passage 5053 to vacuum material from the charging element 631 and/or sending compressed gas through passages 5067 to blow material off the deflector plates 629.

58 Protection of Sorted Sample Durinq Fault Mode One embodiment of the system 9 also includes a contamination prevention mechanism 4041 (Fig. 26), which can be activated by the processor 131 to limit or prevent contamination of the sorted sample any time the sorting system is in the fault correction mode. The contamination 5 prevention mechanism includes a pneumatic actuator 4043 operable to selectively move a swing arm 4045 between a shielding position (shown Fig. 26) and a non-shielding position (not shown). In the shielding position, the end 4047 of the swing arm 4045 covers the opening of the collection vessel 4033, thereby preventing collection of droplets 33 by the collection vessel 4033. In the non-shielding position, the collection vessel 4033 is uncovered. Normally, the swing arm 4045 is 10 in the non-shielding position, but the processor 131 causes the actuator 4043 to move the swing arm 4045 into the shielding position any time the processor 131 determines that there is a risk of contamination (e.g., the nozzle system 101 becomes clogged, the droplet break-off location 107 becomes unstable, or stray droplets 33 have hit the charging element 631 or deflector plates 629). The end 4047 of the swing arm 4045 is trough-shaped to drain any fluid collected by the 15 swing arm 4045 into the waste container 4035. Fluid Delivery System The system I described above is capable of effectively producing quantities of particles 20 (e.g., X-sperm cells) sorted by selected characteristics. The rate of production can be increased or decreased by varying the rates at which the fluid delivery system 15 (Fig. 2) delivers carrier fluid 17 and sheath fluid 19 to the nozzle 137. In one embodiment, the fluid delivery system includes a syringe pump 645, one example of such a pump being MICROLAB@ Model PSD/3 available from Hamilton Company. The pump 645 is operable to deliver carrier fluid 17 to the 25 nozzle 137 at a rate of about 20 pl/min. In general, the pump 645 should be operable to deliver sample fluid 17 to the nozzle 137 at a rate in the range of 10 - 50 pl/min. The pump 645 is connected by a flow line 647 to the supply 3 of carrier fluid 17, which may be a suitable vessel 649 containing a volume of material to be analyzed and sorted. Where the temperature of the particles being analyzed is a factor, as In the case of sperm cells, for example, the temperature 30 of the vessel 649 may be controlled by a suitable temperature control system, such as heating/cooling bath (not shown). The syringe pump 645 is movable through an Intake stroke to aspirate carrier fluid from the supply vessel and through a discharge stroke to dispense carrier fluid 17 through a supply line 651 to the injection needle 157 of the nozzle system 101. The pump 645 Is preferably driven by a variable speed motor (not shown) under the control of the 35 processor 131. By way of example, the pump 645 may be driven by a stepper motor which operates at selectively variable rates to pump carrier fluid 17 to the needle 159 at rates necessary to obtain the desired throughput. Other types of fluid delivery devices can be used instead of a syringe pump. To provide just one example, the vessel 649 can be pressurized by a pressurized gas source without departing from the scope of the invention. Furthermore, it is 40 desirable to keep the lines 647, 651 as short as is practically possible because the line 59 environment is not conducive to the health of sensitive cells (e.g., sperm cells) that may be in the carrier fluid 17. The supply 7 of sheath fluid 19 comprises a second vessel 661, e.g., a tank in Fig. 2, holding an appropriate volume of sheath fluid 19 connected to the radial bore 173 in the flow 5 body 133 of the nozzle system 101 by a supply line 667 having a control valve 669 therein. In the embodiment of Fig. 1, the sheath fluid vessel 661 is pressurized by a gas pressure system 671 comprising a source 675 of pressurized gas (e.g., air or other gas, such as nitrogen) communicating with the tank 661 via an air line 679 having a regulator 681 in it for controlling the pressure supplied to the tank 661. A two-way valve 683 in the air line 679 is movable between a 10 first position establishing communication between the tank 661 and the gas source 675 and a second position venting the tank 661. The gas pressure regulator 681 is a conventional regulator preferably under the control of the processor 131. By controlling the tank 661 pressure, the pressure at which sheath fluid 19 is delivered to the flow body 133 may also be controlled. This pressure may range from 16 to 100 psi, more preferably from 10 to 50 psi, even more preferably 15 15 to 40 psi, and even more preferably from about 20 to 30 psi. The pressure at which the sheath fluid 19 is supplied to the flow body 133 can be controlled in other ways without departing from the scope of the invention. In one embodiment, shown Fig. 26 the fluid delivery system 15, includes a sheath fluid tank (not shown) and a sample station 4051. The sample station includes a two-part pressure 20 container 4053 adapted to hold a sample tube 4055. The bottom section 4057 of the pressure container is moveable up and down relative to the upper section 4059 of the pressure container 4053 between an open position (shown Fig. 26), in which the sample tube 4055 may be loaded or unloaded, and a closed position (not shown) in which the two parts 4057, 4059 of the pressure container 4053 come together to form a seal to contain pressurized gas used to pump carrier 25 fluid 17 from the sample tube 4055 to the nozzle system 101. When the pressure container is open a spring-biased swing arm 4071 moves to a position beneath the line 651 that delivers carrier fluid 17 to the nozzle system 101 (See also Fig. 119 #4071'). The swing arm 4071 is trough-shaped and adapted to collect fluid backflushed through the line 651 and to drain the backflushed fluid to the waste container through port 4073. 30 As the pressure container 4053 moves from its open position to its closed position, a cam plate 4075 attached to the bottom section 4057 of the pressure container 4053 moves the swing arm 4071 against its spring bias to clear the area between the two sections 4057, 4059 and allow the pressure container 4053 to close. 35 Control Referring again to Fig. 2, the microprocessor 131 (or other digital or analog control and/or processor, or combinations thereof) controls the operation of the system 1. As noted below with regard to Fig. 39, the microprocessor may be implemented as a system control processor and four processors for handling signal processing. Alternatively, some or all 40 functions may be integrated into one or more processors. For example, the system control 60 microprocessor (see Fig. 36) may be implemented by using one of the four signal processing processors. In addition, as noted below, the signal processing may be implemented by an analog circuit (e.g., an analog cell analyzer as shown in Fig. 39) or a combination of analog and digital circuitry. 5 The microprocessor 131 provides output signals to control the fluid delivery system 15 (noted below) in response to input signals received from the epi-illumination system 415, provides output signals to control the transducers 105 in response to input signals received from the break-off sensors 389, and provides output signals to control the sorting system 119 (noted below) in response to input signals received from the epi-illumination system 415. The 10 microprocessor 131 may provide output signals to other parts of the cytometry system 9 as noted elsewhere herein. Further, the microprocessor 131 may be adapted to process information and provide output signals in real time. Broadly speaking, the term "real time" refers to operations in which the operation of the processor 131 matches the human perception of time or those in which the rate of the operation of the processor 131 matches the rate of relevant physical or 15 external processes. In one context, the term "real time" can indicate that the system reacts to events before the events become obsolete. In general, electrical signals from the epi-illumination system 415 are converted to digital information by an A/D converter 689 which supplies the corresponding digital information to the microprocessor 131. In response to the information, the microprocessor 131 controls a sorting 20 system 119 and a fluid delivery system 15, both described above. The electrical signals output from the photodetector 117 of the epi-illumination system 415 are time-varying analog voltage signals indicative of the amplitude of the emitted fluorescence 31 at any instant in time generated by each cell as it is illuminated by the laser beam 25. Thus, the analog signals (also referred to as analog output) are in the shape of time 25 varying waveform pulses 497 as illustrated schematically in Figs. 52 and 53. In general a waveform pulse 497 is defined as a waveform or a portion of a waveform containing one or more pulses or some portion of a pulse. Thus, the amplitude of each waveform pulse 497 at any instant in time represents the relative rate of photon emission 31 of each cell at that instant in time as the cell passes through the laser beam 25. X chromosome bovine sperm cells have a 30 higher DNA content than Y chromosome bovine sperm cells (e.g., about 3.8%). As a result, live X cells labeled with a fluorescent stain as noted above will produce a different waveform pulse 497 than pulses from any other labeled cells. By analyzing the pulses 497 as noted below (see Signal Processing, Slit Scanning, and Critical Slope Difference), each cell can be identified as an X cell or not identified as an X cell (-X). In general, as used herein, X cells refers to live X cells, 35 Y cells refers to live Y cells and -X cells refers to the combination of live Y cells and cells which otherwise produce a detectable fluorescence emission 31 but which cannot be identified with a reasonable probability as being live X cells. The timing of each waveform pulse 497 indicates the position of each cell in the stream 21. Since the rate at which the sheath fluid 19 is being delivered through the nozzle 137 remains 40 constant, and since the distance d (in Fig. 25) between the nozzle 137 and the droplet break-off 61 location 107 is known, the position of each droplet 33 is known and the cells, if any, within each droplet 33 are known. Thus, the microprocessor 131 can calculate the instant at which each forming droplet passes through the charging collar 631 and can control the polarity of the collar 631 and thus control whether a droplet 33 is charged for deflection by the charging elements 631 5 of the sorting system 119. Since the microprocessor 131 knows the droplet formation rate and identifies the cells within a droplet as X or -X, the microprocessor 131 knows the cell content of each droplet 33 and keeps track of (or enumerates) the number of cells in each population 123, 125. Depending on the sort strategy, see below, the microprocessor 131 determines which droplets 33 are charged for deflection and which droplets 33 are not charged so that they are not 10 deflected. Signal Processing A. Digital Samplinq Introduction As previously described, the interaction between the laser beam 25 and the particle 15 produce a "pulsed" photon emission 31 (e.g., a fluorescence emission) that is captured by the collection lens 511 of the optics system 109 and delivered to a photodetector 117. The photodetector 117 converts the photon energy at any instant in time to an analog voltage output of time-varying amplitude. This output is a series of waveform pulses 497 (Figs. 43 and 44) which contain many features that can be used to discriminate among populations of particles. 20 Among these features are the total photon emission, the rate of photon emission as a function of the particle's spatial transit through the laser beam, the maximum rate of photon emission during the transit, the average rate of photon emission during the transit, and the time required for transit. The combination of laser beam geometry 459, particle size, distribution of the emission source through the particle volume and particle velocity determine the frequency spectrum of 25 waveform pulse 497. For the system I used with bovine semen described previously it has been determined that each cell 201 produces a waveform pulse 497 of between 800 ns and 1200 ns in duration. It has also been determined that as a function of frequency, more than 97% of the power in the waveform pulse 497 is delivered at frequencies below 30 MHz. This frequency spectrum will be discussed later as it related to the Nyquist sampling theorem. Taken together 30 these waveform pulses 497 form an output signal 701 from the photodetector 117 that is a continuous, time varying, signal that represents the transit of the particle stream through the apparatus. In addition to features of individual pulses that are used to discriminate among populations, the time varying signal provides a precise record as to the relative spacing (time and position) among the individual particles that pass through the apparatus and relative velocity of 35 the particles moving through the apparatus. This precise time, position and velocity record can be synchronized with the droplet generation clock signals 703 as shown in Fig. 44 to determine which particles are members of a particular droplet 33 formed by the droplet generation apparatus 105. This information can be used as the basis for determining "coincidence" or the occurrence of a desired and undesired particle in a single droplet 33. The ability to accurately 62 determine the number and classification of each particle in a droplet 33 allows for accurate, efficient sorting. Digital signal processing 705 as illustrated in Fig. 72 may be employed to analyze detection of fluorescence pulses 31 as indicated by synchronously sampled output signals 701 5 from the photodetector 117. This processing would be implemented in pulse analysis software employing instructions and/or algorithms, as noted herein. The time-varying analog output signal 701 of the photodetector 117 is provided to an A/D (analog/digital) converter 689 which synchronously samples it. Synchronously sampling means sampling to produce digital information corresponding to the analog output. Synchronously sampling is also referred to as 10 continuously sampling or streaming acquisition. As noted below, the sampling rate depends on the frequency spectrum of the analog output. Converter 689 provides an output including digital information 707 which Is provided to the microprocessor 131 or other digital analysis device which executes the pulse analysis software to analyze the digital information 707. In general, the pulse analysis software would 15 include digital pulse detection HH3, pulse feature extraction HH4 and pulse discrimination HH7. B. Sampling Frequency & Signal Frequency Spectrum The signal output 701 from the PIT 117 is captured by a high speed analog to digital converter 689 (ADC) that samples the output 701 continuously at a frequency of 105 MHz. It is 20 well understood that when sampling a time varying signal it is necessary for the sampling frequency to be at least twice the maximum frequency contained in the signal being sampled. This is known as the Nyquist sampling theorem. For this reason the output signal 701 from the PMT 117 is first sent through a 40 MHz low-pass filter 854 (see Fig. 39) to ensure that the maximum frequency contained in the signal 701 is under the 52.5 MHz limit imposed by the 25 sampling rate. It is important to note that the optical 109, fluidic 15 and detection systems of the apparatus I have been tuned to produce a pulse waveform 497 having optimum frequency characteristics for sampling at the 105 MHz rate. The sampling rate may be varied between about 25 and 200 MHz without departing from the scope of the present Invention. 30 C. Pulse Processing Pulse processing takes place in four (4) TigerSharc DSP processors that share memory and are connected to one another by high-speed parallel ports. As illustrated in Fig. 39, the four processors are: 1) a data management processor 863 which receives data from a high-speed ADC 689 which digitizes the output signals 701 from the photodetector 117; 2) a pulse detection 35 processor 865 which detects the waveform pulses 497 represented by the digital information; 3) a feature extraction and discrimination processor 867 which extracts features from the detected pulses 497 and discriminates the pulses 497 based on the extracted features; and 4) a sort processor 873 which determines a sort classification for each pulse 497 based on the extracted features and the discrimination, which determines sort decisions for the corresponding cells and 40 droplets 33 and which is synchronized with droplet formation 105. In general a processor 863, 63 865, 867, 873 completes a task and sets a "flag" so that companion processors know there is. data available to process. Each processor 863, 865, 867, 873 runs independently of the others, maximizing the overall throughput because they do not interrupt each other. Thus, any processor 863, 865, 867, 5 873 may be capable of performing any function and one or more processors or functions may be combined into a single processor or spread out over a plurality of processors. The processor 863, 865, 867, 873 labels as used above and this application are used for convenience only and are not intended to be limiting in any way. All four processors 863, 865, 867, 873 are linked to a DSP board SDRAM 851 for 10 exchanging Information and are linked to a processor input/output (1/O) 857 for synchronization and communication with a peripheral 1/O bus 859 connected to the PC 735 and the sort pulse generator 861. The processor 1/O 857 may be implemented by two or more SharcFIN I/O processors connected by a communication link. Sort signals 853 are provided to the PC 735 via the peripheral 1/O bus 857 and are used to control the sort pulse generator 861 controlling the 15 charging of droplets 33. The processor 1/O 857 receives the output 707 from the analog/digital converter (ADC) 689, e.g., Bitware Corp. 105MHz/2-channel, 14 bit capable of 105MHz/1-channel sustained. The ADC 689 is connected to the photodetector 117 output for converting its time varying analog output signals-701 into digital information 707 and is also connected to an I/O board SDRAM 855 20 for storing the blocks of digital information from the ADC 689. In general, the analog output signals 701 from the photodetector 117 are indicative of characteristic A or characteristic B (e.g., X or -X). The A/D converter 689 converts the analog output signals 701 from the photodetector 117 of the flow cytometry system I into corresponding digital information 707. The processors 863, 865, 867, 873 analyze and classify the digital 25 information 707 and provide a sorting signal to the sorting system 119 as a function of the detected and classified digital Information. D. Data Acquisition As previously stated, the signal output 701 from the photodetector 117 is captured by a 30 high speed analog to digital converter (ADC) 689 that samples the output continuously at a frequency of 105 MHz. Data (digital information 707) are transferred Immediately into high speed memory blocks (1/O Board SDRAM) 855 which serve to buffer the incoming data. These memory blocks 855 are organized in a manner to maintain the integrity and sequence of the data stream 707. These memory blocks 855 are also accessible by the digital signal processing 35 (DSP) processors 863, 865, 867, 873 by direct memory access (DMA). In this manner the processors 863, 865, 867, 873 can access the incoming data 707 without interrupting the ADC 689. This facilitates efficient transfer of data 707 to these processors 863, 865, 867, 873 for feature extraction, analysis and sort classification. Throughout this process, the data management processor 863 keeps the pulse samples 707 in order and time indexed (relative to 40 the master clock 737, which is 128 times the droplet 33 frequency) to preserve their reference to 64 "real time" or the actual time that the cell passed through the laser beam 25. The ADC 689 ping pongs back and forth between two inputs, continuously sampling the time varying analog output signals 701 including the waveform pulses 497 and converting them into digital information 707 which is provided in blocks 855 to the I/O Board SDRAM under the control of the data 5 management processor 863. Processor 863 assembles the information 707 into a continuous stream. E. Initializing Detection Parameters In order effectively distinguish over background noise, the digital pulse detection 10 software 747 should be provided with information indicating signal background second order statistics, i.e. knowledge of the behavior of the output voltage signal 701 from the photodetector 117 when there is no fluorescence pulse 497. These statistics can be learned by software for initializing detection parameters 741 In an unsupervised manner during the initialization period immediately following startup of the system 1. In general, a pulse may be defined as 2 or 3 15 standard deviations from the background level. Due to the possibility that introduction of the carrier fluid 17 into the sheath fluid stream 191 may cause a change in background fluorescence emission, the carrier fluid 17 should be present for the initialization of the detection parameters. Simple computation of the second order statistics of a time sequence of output voltage signal values may overestimate the standard 20 deviation of the background (due to the possible presence of fluorescence pulses 497 in the sequence). An iterative procedure is therefore preferred to gradually eliminate this effect. The pulse detection software 747 accomplishes this by computing the statistics of the total signal 701 (background + pulses), using these values to apply pulse detection logic, re-computing the signal statistics without samples detected to be within pulses, and repeating this procedure until the 25 background statistic estimates converge (or a fixed maximum number of iterations occurs). By evaluating the background with cells present, a more accurate indication of the expected correct pulse 497 amplitude can be determined. Table il summarizes the detection initialization procedure for determining detection parameters for use by the pulse detection software. 30 [rest of page blank] 65 Algorithm: Initializing detection parameters Input: vector of floats PMTvolts; float statWindowSize, integer maxterations Output: float bckgmdMean; float bckgrndSTD Procedure: 1. Initialize background vector bckgrnd to last statWindowSize samples of PMTvolts vector and numIterations, lastSampleMean, and lastSampleSTD to zero: bckgrnd = PMTvolts[1 to stat WindowSize] lasSainpleMean =0 lastSainpleSTD =0 numIterations =0 2. Compute sample mean and sample standard deviation of bckgrnd and increment iteration counter: sampleMean= sum(bckgrnd) statWindowSize sampleSTD = sum(bckgrnd -sainpleMean) 2 ) statWindowSize numIlerations = nunIterations +1 3. Check for convergence or exceeding maximum number of iterations: exitFlag = ( (sampleMean -lastSampleMean) < eps A (sampleStd -lastSampleStd < eps)) v (numIterations > maxIterations) If exitFlag is true, go to step 6 (else continue with step 4). 4. Apply pulse detection algorithm, obtaining vectors of pulse samples and new estimate of background samples: [pulse, bckgrnd] = pulse_.detect(bckgrnd, sampleMean, sampleSTD) 5. Record statistics estimates from this iteration and repeat lastSampleMean =sampleMean lastSampleSTD = sampleSTD Go to step 2. 6. Set background statistics estimates to sample statistics and exit: bckgrndMean = sampleMean bckgrndSTD = sampleSTD Table If. Initialization of pulse detection algorithm parameters. In general, the A/D converter 689 converts the analog output signals 701 from the photodetector 117 into corresponding digital information 707 indicative of characteristic A or 5 characteristic B (e.g., X or -X). The digital signal processor 865 determines background characteristics of the time-varying output signals 701 from the digital information 707 corresponding thereto, detects waveform pulses 497 from the digital Information 707 as a 66 function of the determined background characteristics, and provides a sorting signal 853 to the sorting system 119 as a function of the detected pulses 497. F. Initial Discrimination Parameters 5 Similar to the detection parameters (and subsequent to their initialization as shown in Table 11), parameters for use in a discrimination algorithm may be initialized in an unsupervised fashion. Unlike the detection algorithm parameters, however, an iterative procedure is not necessary. In this case, software for Initializing the discrimination parameters 745 detects a preset number (e.g., 100,000) of fluorescence pulses 497, computes the features to be used for 10 discrimination for each detected pulse 497, and uses a clustering procedure (see Table I for a summary of candidate clustering procedures) to assign these pulses 497 to populations of interest (e.g. X, -X). Algorithm Name Algorithm Approach k-Means Iterative (local) minimization of sum of squared distance (Euclidean or Mahalanobis) between points within each population [1] Fuzzy k-Means Expectation-Maximization of (Gaussian) mixture model [21 Agglomerative Hierarchical Merging of "nearest" clusters (starting with each data point as its own cluster) until desired number of clusters is reached. Various measures for determination of "nearest" clusters include distance between closest points, distance between furthest points, distance between cluster means, and average distance between points. [1] Table 2. Summary of clustering approaches being considered for use in discrimination algorithm parameter initialization. 15 Fig. 73 contains an example of the results of application of a k-means clustering procedure to define population I and population 2 based on statistics of distribution. The second order statistics of these populations are then used to set the parameters necessary for discrimination (the coefficients of a 1 or 2"d order polynomial decision function). Table IV summarizes the discrimination initialization procedure. 20 [rest of page blank] 67 Algorithm: Intilii tion parameters in ut: Matrix of floats detectedPulseData vector of floats popPiorProbabildies Out Ut: each class pop elation I: matrix of floats W, vector of floats w, float Procedure: 1. Compute feature values from detected pulses (n values per pulse, where n is dimensionality of feature space): feature Values = feature extract(detectedPulseData) 2. Cluster feature values in feature space to obtain population memberships populations = cluster(feature Values) 3. Compute 2"d order statistics of populations: (for i 1 to m, where m is number of populations/classes) (for] = 1 to n, where n is dimensionality of feature space) popMean[ j] = sum(feature Values[populations, j]) # of samples in populations, (for k = 1 to n, where n is dimensionality of feature space) tmpVal[j, k] = (feature Values[populationsi, j] - populationMean,[j]) (feature Values[populations ,k] -populationMean; [k]) popCovariance ,k]- sum(tnpVal[j, k]) # of samples in populations. 4. Compute polynomial discriminant function coefficients: (for i = 1 to m, where m Is number of populations/classes) W = - 1/2 -popCovarinace,~' wi = popCovarinace;~' .popMean; = =-1/2. n(popCovariaice, ) 1/2 -popMeai{ .popCovariace' -popMean; + in(popPriorPzobabilitis,) Table IV. Initialization of discrimination algorithm parameters. In general, the A/D converter 689 converts the analog output signals 701 from the 5 photodetector 117 into corresponding digital information 707 indicative of characteristic A or characteristic B (e.g., X or -X). The digital signal processor 867 generates initial discrimination parameters corresponding to the digital information 707, discriminates the digital Information as a function of the initial discrimination parameters, and provides a sorting signal 853 to the sorting system 119 as a function of the discriminated digital information. 10 G. _Diqital Pulse Detection The first processing step is pulse detection performed by pulse detection processor 865 to determine whether a particular waveform is a waveform pulse 497 corresponding to a fluorescence emission 31 of a cell. The processor 865 executes a pulse detection algorithm 15 which identifies sample sets that are likely to represent either particles targeted for sorting into a 68 population or particles targeted to be avoided because they are potential contaminants to a population. In the case of bovine sperm sorting, a dye is added to quench the emission 31 of non-viable cells, causing their associated pulse intensities to be -1/3 the intensity of a live cell. Nonviable cells are not considered as sorting targets or potential contamination. They are not 5 considered detected pulses 497. Pulses 497 from live cells are detected by monitoring the intensity of samples for a successive number of samples that rise above the background levels. Once this level crosses a statistically determined threshold the processor 865 jumps to a later time that is approximately 75% of the expected pulse 497 width for a live cell. If the level is still above the threshold, the series of samples are considered to be a pulse 497. Samples from 10 detected pulses 497 are moved to a block of memory used by the feature extraction processor 867. A statistical anomaly detection approach is one embodiment which may be employed by digital pulse detection software 747 although it is contemplated that other approaches for identifying and/or isolating digitized pulses 497 may be used. Essentially, digital samples 707 of 15 the output voltage signals 701 from the photodetector 117 detecting fluorescence which are statistically anomalous from the background are considered to part of a pulse 497. For additional robustness (to minimize noise detections), additional temporal criteria may be included. Pulse detection proceeds as follows. When the voltage output signal 701 from the photodetector 117 is not a pulse, the Mahalanobis distance from the background of incoming 20 samples 707 of the signal 701 is computed and compared with a preset threshold. If the distance of a given sample exceeds the threshold, it is considered to be the potential start of a pulse 497, and the pulse detection software begins to buffer the incoming samples. If the next predetermined number of samples (e.g., 25) also exceed the threshold, a pulse 497 is considered to have started and buffering continues until the pulse end criteria are met; otherwise, 25 the buffer is reset and checking for the start of a pulse resumes. While In a pulse 497, if a sample is below the threshold, then it is considered to be the potential end of a pulse and the buffer location is recorded (but sample buffering continues). If the next predetermined number of samples (e.g., 25) are also below threshold, the pulse 497 is considered to have ended and the pulse 497 consists of the buffered samples up to the recorded location. Table V summarizes the 30 pulse detection algorithm, and Fig. 49 provides an illustration of the results of pulse detection on a digitally acquired fluorescence pulse 497. [rest of page blank] 69 Algorithm: Digital fluorescence pulse detection Input: vector of floats digSamples, float bkgrndMean, float bkgrndSigma, float pulseStartThresh, float pulseEndThresh, integer numStartSamples, integer numEndSamples Output: vector of floats pulseBuffer Procedure: 1. Initialize inPulseFlag = 0, pulseStartCount = 0, pulseEndCount = 0 2. For each sample in digSamples, compute Mahalanobis distance from background: mhDisti] - (digSampl4i] -bkgrndMean) bkgrndSigz 3. If inPulseFlag is not set, go to step 4, else go to step 6. 4. If mhDist > pulseStartThresh, place sample in pulseBuffer, increment pulseStadCount, and go to step 5; else set pulseStartCount=0, go to step 2. 5. If pulseStartCount > numStartSamples, set inPulseFlag and go to step 2. 6. If mhDist < pulseEndThresh, place sample in pulseBuffer, set lastPulseSample to current buffer position, increment pulseEndCount, and go to step 7; else set pulseEndCount to zero and go to step 2. 7. If pulseEndCount is greater than numEndSamples, return pulseBuffer(l to lastPulseSample] and exit. Table V. Summary of digital fluorescence pulse detection. In general, the A/D converter 689 converts the analog output signals 701 from the 5 photodetector 117 into corresponding digital information 707 indicative of characteristic A or characteristic B (e.g., X or -X). The digital signal processor 865 analyzes the digital information and processor 873 provides a sorting signal 853 to the sorting system 119 as a function of the detected digital information. 10 H. Feature Extraction and Discrimination The next processing step is feature extraction performed by the feature extraction and discrimination processor 867. This processor responds to flags set by the pulse detection processor 865. Samples from detected pulses are placed In memory shared with the feature extraction processor 867. Features such as area, pulse width, pulse height, Gaussian correlation 15 coefficient and/or other features are determined for each pulse 497. In some cases pulses 497 are determined to be "doublets" or invalid and features are not extracted. For the case of bovine sperm 201 features are only extracted for pulses 497 that have the general amplitude and width of a live X or Y cell. Typically, the pulse amplitude for a live sperm cell is in the range of about 700-900 mV, although this range may be as wide as 500-1000 mV. Once the features are 20 extracted they are compared to the feature spaces defined for the population(s) selected for sorting. If the features match the feature spaces identified for sorting, then processor 867 sets a flag indicating a positive sort command to the sort processor 873. In general, the classification of 70 a particular cell is made by the discrimination processor 867 and the sort decision is made by the sort processor 873. Digital information 707 representing fluorescence emissions 31 (and thus the characteristics of corresponding cells which created them) are discriminated by software 757 5 based on specific features or characteristics which exhibit distinguishably different statistical behavior in feature space (the n-dimensional orthogonal space formed by n features as the axes) for the different populations of interest. Therefore, the first step in analyzing digital information 707 for the purposes of discrimination is computation of these features, a process called feature extraction performed by pulse analysis software 749 executed by the processor 867. Table VI 10 lists the several candidate features which software 749 may use for this application. One or more of these features will be selected to form the feature space for classification. It should be noted that there are additional features providing enhanced separation so that this list is exemplary, not comprehensive. For example, the software 749 may employ a subroutine 753 to determine pulse 497 area and/or may employ a subroutine 755 to determine pulse 497 peak. 15 Feature Name Feature Description Pulse Area Approximated by sum (or average) of pulse samples Pulse Peak Maximum value of pulse samples Pulse "Inner" Area Sum (or average) of inner TBD samples of pulse (centered on pulse mean) Pulse Width Number of samples in pulse. Pulse "Gaussianity" MSE or correlation coefficient of pulse with a Gaussian shape with the same 2" order statistics. Pulse "Lagging Peak" Pulse value at TBD samples past peak (or mean) Critical Slope Difference (CSD) Slope of pulse at a point along the pulse at which the difference between the first derivative of a pulse produced by particles having characteristic A and the first derivative of a pulse produced by particles having characteristic B is at or near a maximum Table VI. Summary of candidate features currently being considered for use in digital pulse analysis relating to feature extraction. 1. Slit Scanninq 20 In general, the elliptical spot 459 provided by the illumination system 109 measures the relative DNA content differences in cells. Resolution can be improved further by analyzing the fraction of the pulse 497 of the fluorescence emission 31 detected by the photodetector 117 more likely to contain characteristics which are being evaluated. A biological phenomenon of certain cells (e.g., bovine sperm cells) is the localization of the X/Y chromosomes in a sub 25 equatorial region 225 which is immediately adjacent the longitudinal midline or equator or center of the nucleus 213 of the cell 201 and which has a length of about 1 pm. (See Fig. 6). In fact, the X/Y chromosomes are not necessarily centered in the nucleus 213. Thus, resolution can be improved by converting the time-varying analog output 701 of the photodetector 117 into digital information 707 and analyzing a portion of the digital information corresponding to the fraction of 71 the pulse 497 of the fluorescence emission 31, e.g., corresponding to the light emitted from the circumequatorial region 225 such as such as 20-60% and particularly 20-30% of the waveform pulse centered around the pulse 497 peak. As noted above, slit scanning can be employed to obtain the fluorescence measurement 5 from a portion of each cell's chromatin rather than from the chromatin as a whole. The elliptical spot 459 provided by the epi-illumination system 415 noted above measures the relative DNA content differences in cells from specific sections of the chromatin, so that the resolution of X cells and -X cells relative to one another is improved. As noted above, the slit scanning measurement technique is a fluorescence measurement approach that focuses the excitation 10 beam 25 so that a dimension of the focused spot size 459 is much less than a cell diameter as shown in Fig. 6. In this way, the cell 201 is scanned by the laser beam 25 as the cell passes through the elliptically-shaped beam spot 459. The resulting waveform pulse 497 produced by the photodetector 117 output 701 detecting the fluorescence emission 31 resulting from slit scan illumination contains information about the localization of fluorescence along the length of the cell 15 201. As shown in Figs. 45-48, as the cell 201 traverses the elliptically-shaped beam spot 459, the time-varying waveform pulses 497 (red/orange line) are the convolution of the relative beam intensity (blue line) and the relative emitted pulse intensity (which corresponds to the fluorescence emissions from stain excited by the elliptical spot as the cell traverses the beam and which varies because the fluorescence distribution along the axis of the cell varies). 20 By illuminating only a fraction of the cell's chromatin at one time, the resulting time varying analog output 701 from the photodetector 117 contains information specific to the localization of fluorescence within the chromatin along the longitudinal axis of the cell 201. Although the detected fluorescence emission 31 from slit scanning is less than the detected emission 31 from scanning by a beam 25 having a spot width comparable to the cell diameter, 25 resulting in waveform pulses 497 from slit scanning having a lower pulse amplitude, the majority of difference between the X-chromosome bearing cells and the Y-chromosome bearing cells appears in the center 20-30% to 20-60% of the waveform pulse 497. If only the rectangular area 725 in Fig. 53 is considered for discriminating X-Y sperm cells, then a larger relative difference can be measured between the localized variation in DNA content within the section of chromatin 30 that corresponds to the rectangular region 725 due to the presence of the X and Y chromosomes within that region as compared to the total DNA content of the cells. For example, bovine X-Y sperm cells have a difference in total DNA content of about 3.8%. The fluorescence emission 31 from the X and Y chromosomes will be contained in the rectangular region 725. If this rectangular region 725 accounts for 20% of the total waveform pulse 497 corresponding to a 35 fluorescence emission 31, then a 14% difference in relative DNA content within the region will exist. By measuring the relative DNA content differences from specific sections of the chromatin, the resolution of X-Y sperm cell differentiation is improved (e.g., from 3.8% to 14%). Fig. 54 illustrates the resolution attainable using slit scanning illumination and processing the areas from only the center 20% of the pulse 497 (i.e., the rectangular region 725 of Fig. 53). The histogram 40 of Fig. 54 allows a very high percentage (e.g., 98%) of the X chromosome bearing sperm and Y 72 chromosome bearing sperm to be identified with a high degree of confidence (e.g., 95%). In comparison, the histogram of Fig. 55, which illustrates the resolution obtainable when using standard illumination techniques, shows that slit scanning offers a significant improvement over the results obtained using standard illumination techniques. 5 Two approaches which can be employed to obtain the area 725 of the center portion of the waveform pulse 497 as illustrated in Fig. 53 are digital signal processing (DSP) of digitized photodetector 117 time-varying analog output 701, as discussed in this section, or analog integration using an analog threshold trigger, as noted below. As noted herein, DSP processing involves continuously sampling the time-varying analog output 701 from the photodetector 117 to 10 obtain digital information 707 corresponding to the output 701 and applying DSP algorithms to the digital information 707 to extract features, such as area size, from the digital information corresponding to the center portion 725 of the waveform pulse 497 which corresponds to the difference in DNA content due to the presence of an X or Y chromosome in different cells 201. As a simple example, the center 20% of the total area of each waveform pulse 497 would be 15 determined by analyzing the digital information 707 corresponding thereto. The analysis would be used to generate a histogram such as illustrated in Fig. 53. J. Pulsed Laser Scanning In one embodiment, it is contemplated that the system I include a pulsed laser to 20 illuminate the cells. In this embodiment, slit scanning (as described above) may or may not be employed. For example, a mode-locked solid-state laser can be used to emit a train of electromagnetic pulses having a pulse width (duration) of 1-100 picoseconds at a pulse frequency of about 50-150 MHz and at an average power output of about 100-500 milliwatts. One suitable laser is a Vanguard 350 mode-locked solid-state laser (available from Spectra 25 Physics, Mountain View, CA 94039), which is operable to emit a series of pulses about 12 picoseconds in width (duration) at a frequency of about 85 million pulses per second and at an average power of about 350 milliwatts. Because the 350 mW of power is delivered over extremely short bursts of only 12 picoseconds, the peak power output of such a laser is several hundred times (e.g., about 800 times) greater than the average power. 30 The output of such a laser can be described as quasi continuous wave (quasi-cw) because, for many applications, the pulse repetition rate is fast enough to approximate a continuous wave (cw) output. Indeed it is possible to operate the system as described above with a quasi-cw laser in much the same manner as one would operate with a cw laser. This provides certain advantages because solid-state lasers typically operate more efficiently, require 35 less extensive cooling systems, and require less maintenance than most other lasers. A quasi-cw pulsed solid-state laser can also result in significantly improved signal-to noise ratios using digital signal processing techniques. A timing circuit may be included and is operable to produce a timing signal indicative of the arrival of laser pulses at the interrogation location 115 (i.e., the area where the laser beam 25 illuminates the stream 21). For example, the 40 timing circuit may be a laser pulse sensor 3003 as shown in Fig. 40 for detecting light 73 corresponding to the laser pulse including scattered light generated by the interaction of each laser pulse with the fluid stream 21 and/or including light from the laser pulses. Alternatively, for lasers which may be triggered, a triggering signal may be provided to the microprocessor 131 and/or the A/D converter 689 to synchronize either or both to the laser pulses, as noted below 5 with regard to Fig. 50. In either embodiment, the laser pulse timing would provide a clock signal for the system. Referring to Fig. 50, a timing diagram illustrates the timing relationship between the laser pulses LP, the fluorescence emissions FE from a cell as a result of repeated excitation by the laser pulses LP as the cell passes through the beam spot 459 and the digital samples DS of the 10 photodetector output 701. As shown in FIGS. 45-49, as a cell passes through the laser beam spot 459 the fluorescence emission 31 varies depending upon the amount of illumination of the portion of the cell which generates the fluorescence emission 31. Fig. 50 illustrates twenty (20) laser pulses LP1-LP20 which impinge upon a cell as the cell passes through the interrogation zone 115 of a flow cytometer 1. Each laser pulse LP1-LP20 corresponds to a fluorescence 15 emission FE1-FE20, respectively, which exponentially decays after substantially instantaneous excitation by the laser pulse. In one embodiment, the microprocessor 131 controls the A/D converter 689 (see Fig. 40) so that the converter 689 samples the output signal 701 of the photodetector 117 at or near peak of each fluorescence emission FEI-FE20, as indicated by digital samples DSI-DS20, 20 respectively. In other words, the timing circuit synchronizes the sampling rate of the A/D converter 689 with the fluorescence emissions FEI -FE20. The resulting digital signal produced by transit of a particle through the interrogation zone 115-is the functional equivalent of the digital signal that would have been produced by the digitization of a pulse waveform 497 from a continuous wave laser. As shown in Fig. 51, for example, by considering only the fluorescence 25 intensity during the digital samples DS1-DS20 and disregarding fluorescence intensity drop-off between laser pulses LP1-LP20, the fluorescence intensity as a function of time is a pulse waveform 497. This permits feature extraction by the microprocessor 131 from the digital signal 707 generated by the pulsed laser in order to analyze the cell providing the fluorescence emissions FEI-FE20. In one embodiment, a more sensitive photodetector having relatively fast 30 response time of about 2 nanoseconds or less may be used to more accurately detect the fluorescence emissions. Thus, the pulsed laser provides advantages in a flow cytometry system I in that it Is possible to use a lower power pulsed laser to obtain substantially the same analysis that would be obtained with a cw laser operating at an average power much higher than the average power 35 of the pulsed laser. Further, the high peak power from a pulsed laser tends to saturate the fluorophores so that the fluorescence emissions are maximized thereby reducing the signal-to noise ratio of the output signals of the photodetector. In other words, by using a laser pulse that contains much more energy than is required to saturate the fluorophore, variations in the output of the laser do not result in variations in the fluorescent emissions 31.

74 Those skilled in the art will recognize that there are many ways to cause a laser to emit a series of pulses. It is understood that other pulsed lasers, including other mode-locked lasers, Q switched lasers, and cavity dumping lasers, could be used in place of the mode-locked laser discussed above without departing from the scope of this invention. Similarly, many other ways 5 to time the digital sampling and process the resulting information will be apparent from the foregoing disclosure. For example, the digital sampling could be timed so there is a different delay (or no delay) between a laser pulse and a digital sample without departing from the scope of the invention. Likewise, the number of digital samples per pulse or the number of pulses that elapse between digital sampling can also be varied without departing from the scope of this 10 invention. K. Estimation of Population Characteristics As noted above, flow cytometry can be used to discriminate X-bearing bovine sperm 15 cells from Y-bearing bovine sperm cells based on their relative 3.8% difference in DNA content. Discrimination is achieved through analysis of characteristics of the time-varying signal 701 that is produced by the photodetector 117 used to record the fluorescence emission 31 as the stained cell passes though the interrogation location 115. This interaction is illustrated in Figs. 45-48. Figs. 45-48 illustrate how a pulse waveform 497 is generated by the fluorescence emissions 31 20 resulting from the interaction between the laser beam 25 and a stained sperm cell 201. The emission pulse 497 is the convolution integral of the excitation spatial function 498 and the emission spatial function of the cell 201. Characteristics of the fluorescence pulse waveform 497 are used to classify a cell as X, Y or undetermined. In one embodiment, X-Y discrimination relies on two pulse characteristics: peak pulse height and pulse area. 25 These characteristics are illustrated on the example pulse that appears in Figs. 52 and 53. Figures 52 and 53 are examples of pulses 497 from X-bearing and Y-bearing sperm cells. The pulses 497 were generated from a computer model that assumed excitation illumination with a laser beam 25 having an elliptically-shaped beam spot 459 having a 2pm Gaussian beam waist W1 (Fig. 6) and that the DNA content difference was distributed uniformly across the center 30 20 percent of the cell 201. These assumptions are representative of slit scanning illumination of bovine sperm cells 201 having a localized DNA difference as discussed in more detail above. Integration of the pulses 497 results in a 3.8% average difference between the pulse 497 area for an X cell and the pulse 497 area for a Y cell. It is possible to generate histogram and scatter plots of the pulse 497 peak and area 35 characteristics for stained cells and nuclei. Figs. 56-59 contain histograms of the pulse area characteristic for stained nuclei and live cells, plus scatter plots of the pulse 497 area and peak characteristics for stained nuclei and live cells. Some of the items that may limit live cell discrimination, and ultimately the cell sorting rate are evident in these plots. Notably, the live cell histogram of Fig. 57, and to a lesser extent the nuclei histogram of Fig. 56, have a left shoulder 40 that is typical of fluorescence intensity histograms for mammalian sperm cells. It has been determined that the left shoulder is generated by one or more populations of slightly unaligned 75 cells (i.e., cells that generate relatively weaker fluorescence emissions due to slight deviations from the optimal alignment, but that are not so far out alignment to cause the relatively brighter fluorescence emission 31 from the narrow edge 209 of the sperm head 205 to be collected by the optics system 109). Only about half of the X cells can be easily identified in the live cell area 5 histogram. The rest overlap with the Y cell population and the non-aligned cell populations. Even when peak pulse height is added, as shown in the scatter plots in Figs. 56-59, X-bearing cell classification may be significantly limited. Figs. 60-61 illustrate the overlap of the X and Y population distributions. In Figs. 60-61, a four-component computer model has been applied to raw data 6000(Fig. 60) to estimate 10 population statistics for two populations of non-aligned cells (6001, 6003), aligned live Y cells (6005) and aligned live X cells (6007) (Fig. 61). It is desirable to discriminate the X and Y populations as a function of the coefficient of variation (CV) of the X and Y populations. For example, it is desirable to minimize the coefficient of variation (CV) of the X and Y populations in order to improve discrimination. In particular, when a population of sorted X cells is desired, it is 15 desirable for the CV of the X cell population to be less than 1.5%, more desirably about 1.3%, and even more desirably less than 1.3%. Traditionally, the CV of a distribution of fluorescence intensity of sperm cells has been considered with respect to the distribution functions for only two populations (X and Y). Quality control with respect to CV has been limited to crude subjective estimation of the CV of the X and Y populations to decide whether continued analysis or sorting 20 is worthwhile. According to one embodiment of the present invention, one function of the microprocessor 131 is to provide an automated estimation of the CV of the X population using the four-component model illustrated in Figs. 60-61. In order to estimate the CVs of the populations present in a feature (e.g. pulse area) distribution, it is necessary to estimate the 2 "d 25 order statistics of the population distributions. This may be achieved by applying a model of a known form and finding the best fit of that model to the observed data. Given the expectation of normally-distributed data, an approach consisting of Parzen Window based non-parametric density estimation (utilizing a Gaussian kernel function) followed by application of a Gaussian mixture parametric model has been chosen. Specifically, the four 30 component model illustrated in Figs. 60-61 consists of a sum (or mixture) of four uni-variate Gaussian distributions, with these four components being the feature distributions corresponding to aligned X cells, aligned Y cells, and a two-component unaligned cell population. The parameters characterizing the model then are the population means (averages) (4), population standard deviations/variances (4), and prior probabilities (expected % of the overall distribution) 35 (4). These 12 parameters can then be varied to achieve a best fit of the model to the observed data histogram. With the model component parameters thus estimated, an estimate of the CV of a population of interest (in particular, X cells) may be determined from the estimated population standard deviation and mean: 76 standard deviation 100% mean In order to reduce computational complexity, constraints have been placed on the model to reduce the dimensionality of the parameter space. In particular, the standard deviations of the 5 model components corresponding to the aligned X and aligned Y populations have been constrained to be the same. Also, the aligned X and aligned Y components have been constrained to make up the same percentage of the overall mixture - thus the non-aligned populations are assumed 50% X cells and 50% Y cells. Non-parametric density estimation is applied prior to model fitting to obtain an improved 10 estimate of the total density function (being the sum of the component densities) underlying the raw histogram data. The specific technique applied is known as "Parzen Windows" (Duda, Hart, and Stork, 2001), here utilizing a Gaussian kernel or window function due to the assumed sum of-Gaussian nature of the underlying density. The standard deviation of the Gaussian kernel is chosen to be 1% of the number of populated histogram bins; this value has been empirically 15 observed to provide adequate but not excessive smoothing of the histogram. Each data point in the histogram then contributes a kernel function centered on the histogram bin containing the data point. The density estimate is then obtained as the sum of the kernel functions. The methodology chosen for variation of the model parameters to achieve the best fit to the data is known as Expectation Maximization (See Duda R.O., Hart, P.E., and Stork, D.G., 20 2001, Pattern Classification 2" Ed., John Wiley & Sons; and Moore, A., "Very Fast EM-based Mixture Model Clustering using Multiresolution kd-trees," in M. Kearns and D. Cohn, Eds., Advances in Neural Information Processing Systems, pages 543-549, 1999, Morgan Kaufman). The specific algorithmic implementation utilized is as follows: 25 1) Initial conditions for the model parameters are set. The top two local maxima in the Parzen density estimate are used as the Initial Y and X mean locations (the initial amplitude of the maxima for both X and Y populations being estimated as the amplitude of the right peak). The initial X and Y population variance is estimated as the variance of the data to the right of the local minimum occurring between the left and right peaks 30 relative to the right peak location. Also, the initial X and Y population prior probabilities are set as the percentage of all points falling to the right of this local minimum. The initial X and Y population Gaussian density estimates are then computed using these parameters and subtracted from the total Parzen density estimate. The mean and variance of the remaining data points are then computed and used to initialize the two 35 component unaligned population model as follows. The two population means are assumed (arbitrarily) to be 5% apart (2.5% above and below the overall unaligned mean). Given an (initial) assumption of equal priors and equal variances, then, the component variances are given by: 77 1,2 tot 2 ~ where o 2 is the variance and p is the mean of the respective population. 2) Updated estimates of component population statistics (means, standard deviations, and 5 priors) are computed using the Parzen density estimate. Each histogram bin location is weighted in the statistical computations by the Parzen density estimate in that bin. Additionally, each data point contributes to all component population statistic computations weighted by the degree to which that point is believed to belong to a given population, based on the current component population parameters. This degree of 10 membership is determined as the ratio of a given component population (Gaussian) probability density value to the sum of all component population probability density values at the data point. Thus we have (for all data points x in the histogram, populations cpE[c,c,c}, and population parameter vector Op=[ppa,Pp]) population component memberships used in the computation of updated parameter estimates given 15 by: P(cIx,O,)=P expX ' a 2. memersup~ j v~i 2,,, P0c P , membership(cI,0)= P(c,\ x, 0) -PanzenDensityEstimate(x) P(cn \ XO) nep 20 Updated means and variances are then computed using the Parzen density estimate values weighted by these membership values, with updated priors given by the average membership for each component population over all data points. 3) Parameter updating procedure continues until all parameters reach steady-state (i.e., stop changing significantly from one update iteration to the next (or a maximum allowed 25 number of iterations occurs)). As previously mentioned the aligned X and Y populations are constrained in this procedure to have the same variance and prior probability. This constraint is achieved by using the average of the X and Y variance and prior values computed via the above procedure at each 30 iteration. Alternatively, a similar modeling approach can be applied to a three-component model (Figs. 62-63) in which the cells comprising the two unaligned populations 6001, 6003 in the four component model are treated as a single Gaussian distribution 6011 rather than two distinct subpopulations. The non-aligned cells can be modeled as third Gaussian distribution (shown 78 Fig. 63) having a mean and standard deviation determined by a best fit of the left shoulder and left major peak of the raw data 6010 (shown Fig 62). The three-population model also has estimated statistics for the aligned Y Population 6015 and aligned X Population 6017. One advantage of the three-component model is that it requires only 9-dimensional parameter space 5 (compared to 12-dimensional parameter space required for the four-component model). However, it has been found that the four-component model typically results in an estimated density function that more closely matches the raw data. Those skilled in the art will recognize that a wide variety of statistical techniques can be used to estimate the characteristics of the aligned X and aligned Y populations. Thus, the four 10 component model, the three-component model, or other models may be implemented by any parametric or non-parametric computer algorithms to estimate the characteristics of the aligned X cell and/or aligned Y cell populations without departing from the scope of this invention. L. CV-Based Selection of Staining Conditions 15 Several factors affect the efficiency of sorting stained cells within a population into enriched subpopulations of cells. Among these factors is the amount of differential fluorescence between the various subpopulations of cells within a stained population. Differential fluorescence is affected by dye uptake, which varies based upon staining factors, such as for example, the concentration of the stain, the length of the staining period, the temperature at which staining 20 occurs, and the number and concentration of any additives that may be included with the stain or added to the staining mixture. Accordingly, adjustments to any or all of these factors may be made to increase the sorting efficiency (the rate at which cells may be sorted into at least one enriched subpopulation of cells with certain degree of purity and/or a minimal loss of desired cells) of the population of stained cells. Further, one can increase efficiency of a multi-sample 25 sorting system by adjusting one or more of these factors for each sample, thereby countering any sample-to-sample variations. In the context of bovine sperm sorting, for example, sorting efficiency can be improved by adjusting one or more of the foregoing staining factors from one semen sample to the next to counter bull-to-bull variations or sample-to-sample variations within the same bull. 30 A determination of the coefficient of variation ("CV") for a given fluorescence emission characteristic of a population of cells to be sorted is one manner in which to determine if adjustments to the staining conditions could be made to achieve a desired sorting efficiency. For example, one may adjust the staining conditions as a function of the CV of any feature extracted from the pulse waveform generated by movement of a cell through the interrogation location, 35 such as any feature indicative of total fluorescence intensity or peak fluorescence intensity (including total fluorescence intensity and peak fluorescence intensity). As previously discussed in greater detail, CV is an indicator of the homogeneity or consistency of a distribution of a measurable property or characteristic of a population, such as for example a fluorescence emission characteristic of a particular subpopulation of a given population. CV may be 40 determined by dividing the standard deviation of the measured characteristic of a sample by the 79 sample mean. CV can also be determined automatically by the flow cytometry system 9, such as by implementation of the iterative CV estimation algorithm discussed in detail above. The lower the CV, the greater the homogeneity or consistency of the distribution of the measured characteristic. 5 As applied to the staining and separation of sperm cells, the CV of a particular fluorescence emission characteristic for a sample of X and Y chromosome bearing sperm cells may be affected by the staining conditions. The concentration of the stain, the length of the staining period, the temperature of the staining mixture, and/or the number and concentration of additives affect the CV of a given fluorescence emission characteristic. Increasing the 10 concentration of the stain, the length of the staining period, and the temperature of the staining mixture and/or decreasing the number and concentration of additives will generally lower the CV. Such conditions may be altered individually or in combination. In addition, if any one of these factors is such that it would tend to increase the CV of a fluorescence emission characteristic, such as for example, by shortening the staining time, then any one or more of the other 15 conditions may be adjusted such that it counteracts the effect of the first, such as for example, by increasing the dye concentration, with the overall result being a decrease in the CV of the fluorescence emission characteristic to a level sufficient to achieve a desired sorting efficiency. Accordingly, by manipulating any one or any combination of these factors in this manner, the CV of a fluorescence emission characteristic of the X and Y chromosome bearing populations may 20 be decreased to a value that enables sorting of the sperm sample into a subpopulation of gender enriched semen comprising a desired percent purity of X chromosome bearing cells. Unfortunately, changes that tend to lower the CV of the X bearing sperm may have negative consequences such as increased cost or decreased sperm motility or fertility. For example, other things being equal it is desirable to use lower stain concentrations and shorter 25 staining periods to minimize any harmful impact of the staining process on the sperm. With this in mind, one may predetermine a CV at which an acceptable sorting efficiency will be achieved. Thereafter, a fraction of the cell sample to be sorted is stained and subjected to flow cytometric analysis. A fluorescence emission characteristic of the fraction is determined, and the fraction is classified into subpopulations based upon the characteristic. The CV of the fluorescence 30 characteristic is determined with respect to the cells of one of the subpopulations (an enriched subpopulation). If the CV of the fluorescence emission characteristic of the cells of the enriched subpopulation is equal to or less than the predetermined CV at which sorting is to occur, then the remainder of the cell sample is stained according to the conditions under which the fraction was stained. The sample is thereafter sorted, for example, according to the methods disclosed 35 herein. If the CV of the particular fluorescence emission characteristic of the cells of the enriched subpopulation is greater than the predetermined CV at which sorting is to occur, then another fraction of the same sample is analyzed in a similar manner, but under staining conditions believed to achieve a yet lower CV. In such a situation, the CV may be lowered by, for example, increasing the length of the staining period, increasing the concentration of the dye, increasing 40 the temperature at which the fraction is stained, or any combination thereof. This series of steps 80 (i.e., removal of a fraction from the sample to be'sorted, adjustment of the staining conditions, and a determination of the CV) is repeated until the CV of the particular fluorescence emission characteristic of the cells of the enriched subpopulation is determined to be equal to or lesser than the predetermined CV. Thereafter, the remainder of the sample is stained accordingly and 5 may be sorted, for example, according to the methods disclosed herein. In a particular embodiment of the invention, the cell sample comprises a semen sample, and the cells of the enriched subpopulation comprise X chromosome bearing sperm cells. Accordingly, one embodiment of the invention is a process for evaluating a set of conditions for staining a population of cells for sorting, the population comprising a first type and 10 a second type of cell. The process comprises (a) staining a fraction of the population of cells with a fluorescent dye under a set of staining conditions; (b) exposing the stained cells to electromagnetic radiation as the stained cells are passed through an interrogation location of a flow cytometer at a rate, R; (c) determining a fluorescence emission characteristic of the exposed cells; (d) using the determined fluorescence characteristic to classify the cells into two or more 15 sub-populations, one of the subpopulations being an enriched subpopulation of the first cell type; (e) determining a coefficient of variation for the fluorescence emission characteristic of the cells of the enriched subpopulation; and (f) determining whether to modify any staining condition under which the cells are to be stained or the rate, R, at which the stained cells are passed through the interrogation location of the flow cytometer. In another embodiment, another fraction of the 20 population of cells is stained under a different set of staining conditions and steps (b) through (e) are repeated with that fraction. This process may be performed on two, three, four or any number of additional fractions. In another embodiment, multiple fractions of cells are drawn from the sample at the same time. Each fraction may be stained simultaneously, or each may be stained subsequent to the previous fraction being passed through the flow cytometer. In the 25 former case, each fraction may be stained with its own unique set of staining conditions and step (f) may comprise using the respective CVs to determine a set of staining conditions to be used to stain additional cells. In the later instance, the staining conditions of the subsequently stained fractions may be altered according to the determination of step (f) with respect to a previously analyzed fraction. In one embodiment the process is repeated until the CV is determined to be 30 about equal to or less than a specified CV (e.g., 1.3%). Alternatively, once one has predetermined a CV at which an acceptable sorting efficiency will be achieved, the entire cell sample may be stained. A fraction of the cell sample is removed and subjected to flow cytometry analysis. A fluorescence emission characteristic of the fraction is determined and used to classify the cells into two or more sub-populations. The CV of 35 the fluorescence characteristic is determined with respect to the cells of an enriched subpopulation. If the CV of the fluorescence emission characteristic of the cells of the enriched subpopulation is equal to or less than the predetermined CV at which sorting is to occur, then the remainder of the cell sample is thereafter sorted. If the CV of the particular fluorescence emission characteristic of the cells of the enriched subpopulation is greater than the 40 predetermined CV at which sorting is to occur, then a second fraction from the same sample is 81 analyzed in a similar manner and the CV of the same fluorescence characteristic is determined. The CV of the second fraction may be lowered by, for example, increasing the length of the staining period, increasing the concentration of the dye, or any combination thereof. This series of steps (i.e., removal of a fraction from the sample to be sorted and a determination of the CV) is 5 repeated until the CV of the particular fluorescence emission characteristic of the cells of the enriched subpopulation is determined to be equal to or lesseF than the predetermined CV. Thereafter, the remained of the sample may be sorted, for example, according to the methods disclosed herein. In a particular embodiment of the invention, the cell sample comprises a semen sample, and the cells of the enriched subpopulation comprise X chromosome bearing 10 cells. Accordingly, another embodiment of the invention is a process for evaluating a set of conditions for staining a population of cells for sorting, the population comprising a first type and a second type of cell. The process comprises (a) staining a fraction of the population of cells with a. fluorescent dye under a set of staining conditions; (b) exposing the stained cells to 15 electromagnetic radiation as the stained cells are passed through an interrogation location of a flow cytometer at a rate, R; (c) determining a fluorescence emission characteristic of the exposed cells; (d) using the determined fluorescence emission characteristic to classify the cells into two or more subpopulations, one of the subpopulations being an enriched subpopulation of the first cell type; (e) determining a coefficient of variation for the fluorescence emission characteristic of 20 the cells of the enriched subpopulation; (f determining whether to modify any staining condition under which the fraction of cells are to be stained or the rate, R, at which the stained cells are passed through the interrogation location of the flow cytometer; and (g) applying the modified staining condition to the remainder of the population of cells. In another embodiment, steps (a) through (f) are repeated at least once with at least one other fraction of the population of cells. 25 Steps (a) through (f) may be repeated once, twice, three times, four times or a greater number of times. In another embodiment, multiple fractions of cells are drawn from the sample at the same time. Each sample may be stained simultaneously, or each may be stained subsequent to the previous fraction being passed through the flow cytometer. In the later instance, the subsequent staining of the fractions may be altered according to the determination of step (f) with respect to a 30 previously analyzed. In still another embodiment, the process further comprises prior to step (g), selecting the modified staining condition that results in the lowest coefficient of variation for the fluorescence emission characteristic. In yet another embodiment, the process comprises the repetition steps (a) through (e) until the coefficient of variation for the fluorescence emission characteristic of at least one of the fractions is about 1.3% or less. In another embodiment of the 35 invention, the process further comprises prior to step (g), selecting the modified staining condition that results in a coefficient of variation of about 1.3 or less. In addition to performing such an analysis before sorting the entire sample as detailed above, a similar analysis may be performed while the staining and sorting of the sample is occurring in an effort to ensure that sorting efficiency is maintained. Accordingly, in another 40 embodiment, the CV of a fluorescence emission characteristic of the cells of an enriched 82 subpopulation of a fraction of a sample that has been previously stained, a portion of said sample which is in the process of being sorted, is determined as described above. Adjustments to the staining conditions under which these sample was stained are made according to the methods discussed above with respect to the presort adjustments. 5 The selection of a predetermined CV at which an acceptable sorting efficiency will be achieved is based upon several factors, including for example, the type of cell being sorted, the rate of sorting, and the degree of purity desired with respect to sorting of the population into enriched subpopulations. Generally, a CV is selected that will allow for sorting to the desired percent purity of the enriched subpopulation while minimizing the amount of time necessary to 10 achieve the same, such as for example, by achieving an 85% degree purity of the enriched subpopulation while minimizing the length of the staining period. With these factors in mind, the CV of the fluorescence emission characteristic of the cells of an enriched subpopulation is generally between about 2.0% and about 1.0%, preferably between about 1.5% and about 1.0%, more preferably about 1.4%, and still more preferably about 1.3%. 15 M. Critical Slope Difference Feature Extraction The microprocessor 131' with digital signal processing (DSP) illustrated in Fig. 40 employed as part of a cell sorter makes it possible to extract features of the time resolved fluorescence emission pulse, particularly features that cannot be easily or inexpensively obtained 20 using analog technology. In particular, a pulse feature which exhibits non-linear properties and which significantly improves the separation and thus the resolution of particles A and B (e.g., improves the discrimination of live, aligned X sperm cells) is a feature referred to as critical slope difference (CSD). CSD is a quantification of the slope of the fluorescence emission pulse at a signal amplitude where the difference between the first derivative of a pulse produced by particle 25 A (e.g., a X-bearing cell) and the first derivative of a pulse produced by particle B (e.g., a Y bearing cell) approaches a maximum. Functions that describe fluorescence emission pulses may be expressed in terms of signal amplitude as a function of time: y = x(t). Within the context of detecting CSD features, a function may be defined that describes the fluorescence emission pulses in terms of pulse 30 duration time as a function of signal amplitude. This function may be referred to as an M function. The M function is obtained by transposing the fluorescence emission pulse function as shown below. Fluorescence Emission Pulse function: y=x(t) 35 M Function: t = M(y) t= pulse duration y= signal amplitude Comparison of the M functions for typical X and Y bovine sperm cells illustrates the 40 discriminating power of the CSD feature. The top panel of Fig. 64 shows average M plots for X- 83 bearing and Y-bearing sperm cells. The middle panel in Fig. 64 shows a graph of the first derivatives of these average M plots (i.e. M') for signal amplitude values less than the peak height of the average Y-bearing fluorescence emission pulse. It can be seen in this plot that as signal amplitude approaches the average peak height of the Y-bearing pulse, the difference 5 between the first derivatives (M'y and M'x) increases significantly. Plotted in the bottom panel of Fig. 64 is the difference between the first derivatives (M'x - M'y) as a function of signal amplitude. The CSD feature quantifies the slope of M (M') for an individual pulse near the region where the maximum difference in first derivatives occurs (or the slope at a corresponding point on the fluorescence emission pulse function). For the purpose of discriminating X and Y bearing sperm 10 cells, CSD is determined for each pulse at the point where the leading edge of the pulse intersects the CSD threshold, as shown in Figs. 62-63. In some embodiments, CSD may depend upon the characteristics of the illuminating beam such as beam width whether the beam is continuous or pulsed. An algorithm for determining CSD is discussed below with regard to Fig. 65. 15 Figure 64 illustrates that in some cases the CSD feature has a non-linear nature, such as in the case of sorting X-Y sperm cell populations. The difference between the derivatives (M'x M'y) Increases as the CSD threshold approaches the peak of the Y pulse. The nonlinear characteristic of this difference places the mean value of the nonaligned cells and the aligned Y cells 45% lower than the mean value of the aligned X cells in the CSD feature space. The 20 standard deviation in the CSD feature space of the aligned X cells is largely unaffected (i.e. similar to that seen in the peak or area feature spaces). It is this nonlinear, high gain nature of the CSD feature that increases the number of aligned X cells that can be accurately discriminated. One computationally efficient method for determining the CSD value for a given pulse is 25 illustrated in Fig. 65. A CSD threshold may be determined as a function of a peak height of the fluorescence emission pulses. In particular, it may be determined based on the average peak height of the fluorescence emission pulses. The CSD threshold is maintained at a point where about 25% of the pulse peaks from live, aligned cells fall at or below the threshold. Therefore, the CSD threshold is adjusted dynamically during the sort based on a running peak height 30 distribution (i.e., relative to an average peak height). For example, the threshold may be based on a weighted running average of peak height (with more recent measurements being given more weight than older measurements). The CSD value is the slope of a line that passes through two points on the pulse. These points are the CSD pulse threshold and the pulse peak. Thus, in this embodiment the CSD value is only an approximation of the slope of the pulse 35 waveform 497 at the intersection of the leading edge of the pulse and the CSD threshold. However, other methods of computing the CSD value for a given pulse are readily apparent, some of which can provide more precise CSD values If desired. In another embodiment, the CSD threshold is dynamically adjusted as a function of the CV of the CSD feature extraction for a subpopulation of particles. In the case of sorting sperm 40 cells for example, by increasing the CSD threshold from a relatively low level (e.g., the pulse 84 detection threshold) the CSD threshold will reach a level that results in a substantial increase in the CV of the CSD of the Y cells but is still low enough that the increase in the CV of the CSD for the X cells is significantly lower in comparison to the CV increase in the Y cells. This effect can be observed in the CSD distribution as a fanning out of one subpopulation in the overall CSD 5 distribution. Good discrimination from the CSD feature can be achieved by maintaining the CSD threshold at this level. It should be noted that the discriminating power of the CSD feature is enhanced by use of slit scanning approach to flow cytometry. The shape of the beam spot 459 can influence the shape of the pulse waveform 497. For example, by using a beam spot 459 having a relatively 10 small width W1, a localized fluorescence difference in a sample particle (e.g., the localized fluorescent intensity difference resulting from localization of the X or Y chromosome in the central region 225 of a sperm nucleus 213) has a greater influence on the first order derivative of the pulse waveform. Accordingly, one embodiment of the present Invention includes using the slit scanning techniques in combination with CSD feature extraction. Conversely, using a laser 15 having a beam waist that is too large (e.g., equal to or greater than the diameter of the particles) may prevent effective use of the CSD feature to discriminate particles. The acceptable range for the width of the beam waist of the focused illumination beam will depend on a number of factors including the size and shape of the particles, the distribution of dye within the particles being analyzed, and the amount of difference between the typical waveform pulses for the particles to 20 be discriminated. In the case of sperm cells, CSD feature extraction from waveform pulses 497 generated by excitation of bovine sperm cells 201 with a laser having a beam waist of less than 3 pm has worked well as indicated below. Of course, CSD feature extraction with any form of slit scanning discussed in the slit scanning section is considered to be within the scope of this aspect of invention. 25 Use of the CSD feature substantially increases the yield of the system, particularly in the case of sorting X-Y sperm cell populations because it allows collection of many more aligned X cells. Due to the overlap in the populations defined in peak vs. area or rise-time vs. area feature spaces, no more than about 70% of the aligned X cells can be discriminated with a certainty about or greater than 85%. When the CSD feature is used, 95% or more of aligned X cells can 30 be discriminated, which significantly increases the percentage of live X cells that can be collected without reducing the purity of the population of collected X cells below a desired level of purity. This is seen graphically in the live cell data shown In Figs. 66-69. The non-linear nature of the CSD feature allows X cells to be isolated for sorting. The gross selection on CSD applied in the scatter plot shown Fig. 68 results In a 70% pure X area population. When bi-variate sort 35 discrimination is applied in the area and CSD feature spaces (Fig. 68), > 95% of the aligned X cells can be discriminated for sorting. The data in Figs. 66-69 were collected at a total cell throughput of about 22,000 live cells per second on one channel of a four-channel cytometry system (see multi-channel system discussion below). Even with coincidence detection enabled (high purity), over 6,000 X cells per second were collected at a purity level of at least 85% purity.

Figures 66-69 illustrate one advantage of the CSD feature when used to discriminate

X

bearing and Y-bearing sperm cells. Figures 66 and 67 are histograms of the area feature of the fluorescence emission pulses for the feature space defined in the scatter plots shown Figs. 68 and 69. In Fig. 68, the CSD feature has moved most of the non-aligned and aligned Y cells 5 completely out of the display of the scatter plot. This leaves a 70% pure X population in the frame of the scatter plot, which is what is shown in the pulse area histogram in Fig. 66. Non CSD discrimination is shown in the pulse area/ rise time scatter plot shown in Fig. 69. Aligned X cells make up about 30% of the corresponding area histogram (Fig. 67). More than 95% of the aligned X cells can be collected at > 85% purity using the CSD feature for discrimination. By 10 comparison, no more than 70% of the aligned X cells can be discriminated using the traditional feature space on the right. Several live cell sorts have been completed using the CSD vs. pulse area, bi-variate discrimination technique. Figure 70 is an example of how a sort region set in this two dimensional feature space can be used to exclude non-aligned cells and Y cells. Figure 70 illustrates a bi 15 variate sort region set on a scatter plot of CSD vs. pulse area scatter. Notice how the sort region drops lower on the area feature for high values of CSD (CSD Increase from left to right and area increases from bottom to top) and moves higher on the area feature as CSD drops to lower values. The bi-variate sort region set on the above CSD vs. pulse area scatter plot was used to sort X cells at a sort decision rate > 6000 X cells per second with a input live cell rate of 26,000 20 cells per second. Purity based on flow cytometry re-analysis was 87%. The CSD feature makes possible a high yield, no-coincidence abort (i.e., coincident accept or high recovery) sorting strategy. In some embodiments, a pulse feature could provide nearly baseline separation and thus 100% accurate classification of live X and Y sperm cells. This condition would make it possible to sort cells at reasonably high rates without aborting 25 droplets that contain both a cell classified as X and non-X (either unknown or Y). This sorting strategy is referred to as the high recovery or coincidence accept strategy. An experiment was performed to test this using the CSD feature. Coincidence accept sorts were performed with an input rate of 12,000 live X cells per second on one channel of a four-channel flow cytometer. 77% of the X cells were properly aligned, making 4,600 X cells per second potentially available 30 for sorting. Under these conditions, 4,300 cells per second were sorted into the population of X cells. Subsequent purity analysis indicated a purity from this sort of > 87% without correction for dead cells and 89% with correction for dead cells. A high purity, coincidence reject detection sort was performed immediately after this sort under the same conditions. A collection rate of 3200 3500 cells per second was observed. Purity analysis indicated a purity of 92% without correction 35 for dead cells and a purity of 94% with dead cell correction. The results of the above experiment indicate that at 12,000 live cells per second input, > 92% of aligned X cells can be collected at a purity > 85%. This is an indication that the CSD feature provides 95% accurate classification of all aligned X cells. Under these circumstances, yield from the cell sorter Is limited primarily by correct cell alignment.

86 Figure 71 illustrates one embodiment of flow cytometry re-analyses for a test in which the left panel corresponds to the high recovery/coincident accept sort strategy (no coincidence abort strategy) and the right panel corresponds to the high purity/coincident reject sort strategy (coincident abort strategy). The left panel (87% pure) was for an output of 4,400 X cells per 5 second without coincidence aborts. The right panel was from a sort completed under the same conditions except droplets containing contaminating cells were aborted. Purity for this sort was about 92%. These sorts demonstrate that high recovery, no coincidence abort sorts are possible when the CSD feature is used for discrimination. Use of the CSD feature is not limited to sorting of sperm cells or any particular species of 10 sperm cells. As those skilled in the art will appreciate from the foregoing disclosure, the CSD feature can be adapted to improve discrimination between any groups of particles that generate signal pulses having different first order derivative characteristics regardless of the cause of the difference. 15 N. Discrimination Once the features of the pulses have been extracted by pulse analysis software 749, discrimination (e.g., classification) of pulses is accomplished by pulse discrimination software 757 executed by processor 867 employing a logic application such as Bayes Minimum Risk decision rule. This rule is a modification of a Bayes Minimum Error decision rule that allows 20 assignment (and adjustment for) differing costs associated with making different erroneous classification (e.g., discrimination) decisions. Bayes Minimum Error computes the decision boundary 763 or decision surface as the surface of equal a posteriori probability between populations in feature space. For the case of (assumed) Gaussian probability distributions this surface is in general quadratic, although in 25 certain conditions may be linear (or be able to be closely approximated by a hyper-plane). The classification (e.g., discrimination) decision is made by first computing the a posteriori probabilities for a given point in feature space (generally from class-conditional probability densities and known/assumed a priori population probabilities using Bayes Rule) then choosing the class label as that of the population having the highest a posteriori probability. 30 Bayes Minimum Risk includes a factor to allow adjustment of the decision boundary 763 in the case when it is desired to assign different costs for making different classification errors (e.g. it may be costlier to classify "Y' cells as " cells than vice versa). In this application, this allows a trade-off between sorted sample purity and recovery. In this decision rule, the "risk" of assigning each possible class label to a point in feature space is computed as the sum of the a 35 postenon probabilities of membership in each population times the cost associated with classifying as the current population given true membership in each other population. Table 6 summarizes the procedure for Bayes Minimum Error classification. Note that for multi-variate Gaussian densities, evaluation of Bayes rule to obtain the a posteriori probabilities may be reduced to evaluation of the quadratic function seen in Table VII, given that the coefficients W, w, 40 and w 0 are as computed in the discrimination algorithm parameter initialization procedure given 87 in Table 3. Fig. 74 shows a graphical example of classification by this procedure. The illustration on the left is a schematic illustration of the two populations I and 2 and the decision boundary 763 separating the populations. The histogram on the right shows two concentric sets of ellipses defining the X and Y regionn, with the decision boundary 763 being a line defined by the 5 intersection of the ellipses. Algorithm: Bayes Minimum Error fluorescence pulse classification (discrimination) Input: vector of floats pulseFeatures, for each class population i: matrix of floats W, vector of floats w, float wo Output: integer classLabe/ Procedure: 1. For each class/population i, compute value of discriminant function gi: 2. pulseFeatures' -W -pulseFeatures + w| -pulseFeatures + w -. For each class/population i, compute value of risk function risk,: Initialize risk=0, then for each class/population j: risk = risk + cost * g1 3. Findjs.t. risk= min(risk,) V I. Return c/assLabe/=j and exit. Table V11. Summary of digital fluorescence pulse classification (discrimination) by Bayes Minimum Error decision rule. 10 For additional robustness, an additional step is taken in the classification of digital fluorescence pulses. The Mahalanobis distance of a pulse in feature space from the population assigned via Bayes Minimum Error is computed, and if greater than a threshold, the pulse is labeled as "not classified" or some other appropriate indication that it is not likely a member of any known population. Fig. 75 illustrates the effect of this additional step, again using features 15 computed from digitally acquired fluorescence pulse data. In general, the AID converter 689 converts the analog output signals 701 from the photodetector 117 into corresponding digital information 707 indicative of characteristic A or characteristic B (e.g., X or -X). The digital signal processor 865 extracts features from the digital information and processor 873 provides a sorting signal 853 to the sorting system as a function 20 of the extracted features. 0. Sort Classification and Droplet Synchronization The fourth, sort processor 873 manages droplet classification, implements sorting strategy and delivers a sort trigger pulse 853 that is synchronized with the droplet selected for 25 sorting. This processor 873 receives cell classification Information from the discrimination processor 867 and relates that information to the droplet generation clock 703 (i.e. aligns the position of particles classified for sorting into a population with the formation of droplets). It determines if there is coincidence within a droplet and manages that coincidence based on pre determined sort strategies. It maintains a FIFO of all cell classifications and droplet sort decisions 30 that sets the correct delay between when the particle was observed in real time and when the 88 particle arrives at the last attached droplet. It will produce a properly timed output pulse 853 of appropriate polarity and amplitude for each droplet selected for sorting. In general, the A/D converter 689 converts the analog output signals 701 from the photodetector 117 into corresponding digital information 707 indicative of characteristic A or 5 characteristic B (e.g., X or -X). The digital signal processor 867 discriminates the digital information 707 as indicative of characteristic A or as indicative of characteristic B (e.g., X or -X) and provides a sorting signal 853 to the sorting system 119 as a function of the discriminated digital information. In general, the digital signal processors 863, 865, 867, 873 include instructions for 10 detecting waveform pulses represented by the digital information, instructions for extracting features in the detected pulses and instructions for discriminating the detected pulses as a function of their extracted features. In addition, the processors include instructions for defining a decision boundary 763 discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. Further, the processors 863, 865, 15 867, 873 may optionally adjust the relative location of the decision boundary 763 with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of the at least one population with respect to either characteristic A particles or characteristic B particles, and (2) the quantity of characteristic A particles or characteristic B particles in the at least one 20 population relative to the total quantity of characteristic A particles or characteristic B particles in the stream. For example, the processor may move the decision boundary 763 to include less of population I and more of population 2, or visa versa, based on the output of a particular sample or based on the desired output (e.g., as noted above with respect to the Bayes Minimum Risk decision rule to adjust the decision boundary for differing costs). 25 P. Drift Compensation Given that over time the waveform pulses corresponding to the fluorescence emissions may vary or exhibit drift over time (due to staining variations, temperature change, sample age and/or other factors, for example), the system may optionally employ drift analysis software 761 30 (Fig. 72) defining dynamic thresholds which vary to compensate for any effects of drift. In particular, the pulse detection thresholds employed by software 747 may be adjusted for any slow variations in the signal background characteristics, and the discrimination algorithm of software 757 may adjust the decision boundary 763 (Fig. 74) to account for any drift in the populations in feature space. 35 In the case of the algorithm(s) employed by pulse detection software 747, the drift compensation software 761 accomplishes drift compensation by updating the background mean and standard deviation estimates based on sample statistics estimates computed within a moving window of a given length of samples (e.g., 10-100 samples) ending with the current sample. Given the (assumed) slow drift rate relative to the data acquisition frequency, the 40 background statistics need not be updated every sample; rather, background statistic updates 89 may occur periodically (e.g., every 6 seconds; see reference character 795 and Fig. 82). Additionally, the window may contain less than unity weighting to allow a "forgetting" rate to de weight older samples relative to newer samples in the statistics computations. Fig. 76 illustrates the concept of statistic (mean) computation within a moving window without and with a 5 "forgetting" rate. Similar to the detection algorithm drift compensation, the discrimination algorithm(s) employed by pulse discrimination software 757 achieve drift compensation by periodic updates of the 2 n order statistics of the populations in feature space. In this case, however, only those feature values from pulses assigned to a given population are used to update the statistics of that 10 population. Again, non-unity weighting may be used to include a "forgetting" rate. Fig. 77 shows a conceptual illustration of the effects of applying this technique to populations in feature space. Fig. 77 illustrates an example of drift compensation for population statistics in feature space. Yellow denotes population 1 (X), green population 2 (Y), diamonds the class mean estimates (with an exaggerated illustration of drift), and block arrows changes in the population covariance 15 estimates reflected in deformation of the constant-sigma ellipses. In general, the digital signal processor 863 employs a detection threshold for analyzing the digital information, which threshold is a function of a background mean estimate and a standard deviation of the sampled time-varying output signals computed within a moving window of samples ending with the current sample. 20 Q. Advantage of All Digital Techniques Over Analo Techniues One of the main advantages for using an all digital system for sorting is that there is no 25 "dead time" associated with the detection and analysis of a pulse. With analog systems there is always a finite "switching time" required for electronics to reset after the occurrence and detection of a pulse. This time is usually on the order of at least one microsecond. Since the digital system captures a continuous stream it really has no dead time. Another advantage of a digital system is the ability to look forward and backward in time 30 around a pulse classified for sorting. In general, the digital signal processing requires about five (5) droplet periods for analysis. Preferably, the time delay between droplet illumination 115 and droplet formation 107 is about seven (7) droplet periods. This allows the system to classify a particular particle based on the probability that it will contaminate the usable population as Indicated by the features of the particular particle and based on the proximity of the particular 35 particle to another classified particle. As an example, the sort processor 873 may reject a particle viewed as having a 50% probability of being a live X cell whereas the sort processor 873 may accept a particle viewed as having a 50% probability of being a live X cell when the particle is coincident with a second particle viewed as having a 95% probability of being a live X cell.

90 R. Analoq Cell Analysis It is also contemplated that the time-varying output signals from the photodetector may be processed by analog circuitry 819, such as a field programmable gate array, which may be less expensive than a digital cell analyzer. Fig. 42 is a block diagram of one embodiment of an 5 analog cell analyzer which may be employed as part of the system according to the invention. Fig. 53 graphically illustrates the analog analysis. A threshold is set to produce a trigger based on pulse height. The threshold opens an integration window which gates an analog integrator to accumulate charge. The window remains open either for a fixed period or until the pulse amplitude fall below the trigger threshold. In this way, only the area of the portion of the pulse 10 within the integration window is used for relative fluorescence measurements. Referring to Fig. 42, the output 701 of the photodetector 117 is supplied to an integrator 825 which integrates the output signal 701 in synchronization with the droplet clock 703. The integrated signal is provided to a width/area comparator 827 for comparing the level of the integrated signal to a threshold level defining a pulse (e.g., a pulse may be defined as an 15 integrated signal with 40% of certain a certain threshold.). A dynamic threshold calculator 829 functions similarly to the drift compensation noted above in that monitors the integrated signal level and it varies the threshold level which the width/ area comparator uses as a function of variations in the average integrated signal level. The pulse discriminated signal is provided to a window comparator 837 to confirm that 20 the pulse area is within an acceptable range. The pulse discriminated signal is also provided to a pulse width and trigger logic circuit 839 to confirm that the pulse width is within an acceptable range. If the area and width are acceptable, the logic provides a trigger signal to an 1/O controller 843 which indicates the sort decision 841. Thus, the window comparator 837 and the pulse width and trigger logic 839 make the decision as to whether a cell should be classified as an X 25 cell or a -X cell. The 1/O controller 843 provides the sort decision 841 to the sort controller board 847 in the form of a X or -X signal. The 1/O controller 843 also includes a Universal Serial Bus (USB) interface 849 for connecting to the PC 735 and may have I/O port for connecting to slave controllers 845 of the other channels. The analog cell analyzer also includes a Joint Test Access 30 Group (JTAG) port 833 for programming the width/area, comparator, the window comparator and the pulse width and trigger logic. It is also contemplated that the analog cell analyzer may be employed simultaneously with the digital cell analyzer 705. For example, the analog analyzer may be used to adjust voltage thresholds used by the digital analyzer. On the other hand, the digital analyzer may be 35 used to identify various features of the pulse and this feature information may be used to configure the analog cell analyzer, particularly if it is implemented with a gate array. Control Strategies In general, the microprocessor 131 is programmed to implement control and sorting 40 strategies which are intended to optimize the efficiency of the system 1 in terms of throughput 91 and/or loss of desirable particles to meet any cost requirements of the sorted product. This may involve, for example, balancing the need for high purity of at least one collected population and the need to recover at least a minimum percentage of desirable particles from the sample being sorted. Achieving such a balance is important, particularly in the context of commercial 5 applications where cost and profitability are important considerations. To this end, the microprocessor 131 implements a control strategy which is a series of instructions and/or algorithms that control system variables such as fluid delivery rate and/or sort parameters. The microprocessor also implements a sorting strategy which defines the decision process for determining how each particle or group of particles is sorted. Each particular control 10 strategy may employ one or more sort strategies. Various sorting strategies may be used depending on such factors as the selected control strategy, the particle detection system and/or information relating to the particle distribution in the fluid stream. Regarding particle distribution, Fig. 78 illustrates a fluid stream containing an exemplary. distribution of particles. In this particular example, the stream Is formed by a nozzle similar to the 15 nozzle described above and contains a mixture of particles having different characteristics A and B, e.g., X and Y sperm cells. As shown, the cells follow generally one after another in a series which can be viewed as comprising sequential sets of particles. These sets include first particle sets each comprising one or more particles having a characteristic A (e.g., indicating a live X sperm cell), second particle sets each comprising one or more particles having a characteristic B 20 (e.g., Indicating a Y sperm cell or, more generally, a sperm cell which is not a live X cell (-X), such as a Y cell, or a dead X or Y cell), and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B (e.g., one more X sperm cells and one or more -X sperm cells). Third particle sets are also hereinafter referred to as "coincident" particle sets. 25 Whether a particular particle is considered as constituting a set by itself or part of another set will depend primarily on its spatial position and/or separation relative to adjacent particles. For example, in a droplet sorting system, the various particle sets will be defined by the particles in the droplets. In a photo-damage sorting system where a laser is used to ablate (kill or otherwise damage) selected particle sets to provide a collected population having a 30 desired content, as discussed below in the "Photo-Damage Sorting" section, the various particle sets will be defined by the spatial proximity of the particles, i.e., whether the spatial separation between particles is sufficient to enable accurate classification of the particles and/or the ablation of one or more undesired particles by the laser without also ablating one or more desired particles. Similarly, in a fluid-switching sorting system where portions of the stream containing 35 selected particles are diverted to provide a collected population having a desired content, as is discussed below in the "Fluid Switching Sorting" system, the various particle sets will be defined by the spatial proximity of the particles, i.e., whether the spatial separation between particles is sufficient to enable accurate classification of the particles and/or diversion of selected particles. It will be observed from the foregoing that sort decision applied to the different particle 40 sets may be varied, depending on the desired result or throughput of the system. For example, 92 in a droplet sorting system, the sorting strategy used may depend on the treatment of "coincident" droplets, i.e., droplets containing third particle sets. In the handling of bovine sperm cells in a flow cytometry droplet sorting system and method as described herein, for example, to enhance the number of X sperm cells in at least one collected population, it may be desirable to 5 use a strategy where each coincident droplet containing an X sperm cell is accepted and sorted as if it contained only X sperm cells, even though the droplet may also contain an -X sperm cell (coincident accept strategy). On the other hand, to enhance the purity of X sperm cells collected in the stated population, it may be desirable to reject each coincident droplet containing a -X sperm cell even though the same droplet may also contain an X sperm cell (coincident 10 reject strategy). In general, as will be pointed out below, there are many control strategies which may be employed to maximize particle throughput and there are many sorting strategies that may by employed with each particular control strategy. The strategies can be applied to various sorting techniques using flow cytometry, such as droplet sorting, photo-damage sorting, and fluid-switching sorting. Further, the above strategies can be used to sort any type of particle 15 according to any desired characteristic or characteristics of the particle. According to one embodiment, the microprocessor controls the rate at which the fluid delivery system delivers the fluid containing the particles as a function of other variables of the system. For example, the microprocessor can the control the fluid delivery rate as a function of a desired output result. Since the microprocessor determines the identity of each particle and 20 determines whether such is directed to at least one collected population, the microprocessor can determine and control the output result by varying the control strategy and/or by varying the sorting strategy. A desired output result may generally be defined as at least one of the following: (1) the purity of at least one collected population with respect to characteristic A particles or characteristic B particles ("high recovery"), and (2) the quantity of characteristic A 25 particles in the stated population relative to the total quantity of characteristic A particles in the stream, or the quantity of characteristic B particles in the stated population relative to the total quantity of characteristic B particles in the stream ("high purity"). As another example, the system may employ a substantially constant fluid delivery rate and the microprocessor can the control the sort parameters as a function of a desired output result. In this latter example, the 30 desired output result may generally be defined as a combination of (1) the purity of the particles in at least one collected population and (2) the quantity of desired particles available in the stream but not included in the stated population ("constant flow rate"). In general, it my be assumed that when sorting two populations an identified cell could have a 50/50 probability of being part of one population or the other. However, it is also 35 contemplated that an unidentified cell may in fact have some other probability other than a 50/50 probability of being part of one population or the other. This other probability may be determined by empirical analysis or from other characteristics regarding the sample being sorted. Several different control strategies are discussed in more detail below.

93 A. High Recovery Control Strategy One type of control strategy may be referred to as a "high recovery" control strategy. The objective of this strategy is to maximize the number of desired particles sorted into the population of desired particles as long as the purity of that population is at or above an 5 acceptable purity. Pursuant to this strategy, the first particle sets described above are sorted into the population of desired particles because each of these sets contains one or more particles having a desired characteristic A. The third particle sets are also sorted into the population of desired particles (coincident accept) because each of these sets also contains one or more particles 10 having a desired characteristic A, albeit accompanied by one more particles having characteristic B. On the other hand, the second particle sets are rejected (i.e., not sorted into the population of desired particles) because they do not contain a particle having the desired characteristic. To optimize throughput using this strategy, the microprocessor increases the fluid delivery rate as long as the purity of the collected population is at or above an acceptable level. Stated in the 15 converse, the fluid delivery rate is increased as long as the probable level of contamination of the population of desired particles is at or below an acceptable level. As an example, consider the use of a high recovery control strategy for sorting X and Y sperm cells in the fluid stream of Fig. 78. The desired result may be to sort all of the X cells Into a population of X cells so long as the population remains at or above an acceptable purity, e.g., 20 so long as X/(X+Y) is greater than 85% or some other acceptable level. To obtain this result, the first particles sets are sorted into a population of X cells because they contain only one or more X cells. The third particle sets are also sorted into the population of X cells because they also contain one or more X cells, even though they may also contain a Y (or -X) cell. The second particle sets are sorted into some other population because they do not contain one or more X 25 cells. In this example, the rate at which the fluid delivery system delivers the fluid containing the cells to the nozzle would continue to be increased as long as the purity of the population of X cells is greater than 85%. Conversely, if the purity of the population of X cells falls below 85%, the fluid delivery rate is decreased. In the context of a droplet sorting system, it is known from Poisson's equation that for 30 any given droplet generation rate, the number of multiple-cell droplets will increase as the cell delivery rate increases. In other words, increasing the delivery rate of fluid containing the cells will Increase the number of multiple-cell droplets. Therefore, if the coincident accept sorting strategy is used and coincident droplets containing third particle sets are sorted into the population of desired particles, increasing the fluid delivery rate will result in a decrease in the 35 purity of the collected population because at higher fluid delivery rates more coincident droplets are being generated and collected. Figure 79 illustrates this result for a two (2) particle fluid so that 100% of the desired particles are captured. As shown, at very low fluid delivery rates (FDR along x axis), the purity (y axis) of the resulting collected population is very high because very few coincident droplets containing third particle sets are being generated and collected. As the 40 fluid delivery rate increases (FDR increases to the right along the x axis), the percentage of 94 coincident droplets generated increases resulting in more coincident droplets being collected and reducing purity of the usable population (along the y axis). In the specific example illustrated, the fluid delivery rate is 30K particles/second at about 80% purity. The results of using a high recovery strategy can be dramatic, as illustrated by a simple 5 example where X and Y sperm cells are sorted using a droplet sorting process. Assume, for example that droplets are generated at a rate of 60K/sec, and that sperm cells are delivered to the interrogation location at a rate of 30K/sec. According to Poisson's equation, if all droplets containing X cells are sorted into the population of X cells, including coincident droplets containing X and Y cells, about 15,000 X cells will be collected every second. The collected 10 population will include about 2,600 Y cells, reducing the purity of the population with respect to X cells to about 85.2%. However, the number of collected X cells (15,000) represents a substantial increase relative to a strategy where coincident droplets are not collected, as in the high purity strategy or mode discussed below. In the high purity mode, operating at a droplet frequency of 40K/sec and cell delivery rate of 40K/sec (10K cells/sec more than in the high recovery mode 15 example above), only about 11,800 X cells are collected every second, or about 3,800 X cells less than in the high recovery strategy. Further, when the high purity strategy is used, about 9,200 X cells are lost or wasted because coincident droplets are not sorted into the population of X cells. Therefore, if less than 100% purity is acceptable, it may be desirable to use the high recovery mode to increase the number of X cells collected or, stated conversely, to decrease the 20 number of X cells lost. In summary, in the high recovery control strategy using the coincident accept sorting strategy, the particle delivery rate is inversely related to the purity of the collected population of desired particles (sometimes referred to as the "usable" population). B. High Purity Control Strategy 25 A second type of control strategy may be referred to as a "high purity" control strategy. The objective of this strategy is to maintain the purity of the collected population with respect to particles having a desired characteristic at high level, so long as the quantity of desired particles in the collected population relative to the total number of desired particles available in the stream is at or above an acceptable quantity (i.e., so long as the quantity of desired particles in the 30 stream which are not collected remains below an acceptable quantity). Pursuant to this strategy, the first particle sets described above are sorted into the population of desired particles because each of these sets contains one or more particles having a desired characteristic A, and because these sets contain no contaminating particles. On the other hand, the second and third particle sets are sorted into one or more "unusuable" populations (coincident reject) because they 35 contain contaminating particles (i.e., characteristic B particles). To optimize throughput using this "high purity" strategy, the microprocessor increases the fluid delivery rate as long as the quantity of desired particles that are sorted into the usable population relative to the total number of desired particles available in the stream remains at or above an acceptable quantity. As an example, consider the use of a high purity control strategy for sorting X and Y 40 sperm cells in the fluid stream of Fig. 78. The desired result may be to sort all of the X cells in a 95 into a population of X cells so long as the quantity of X cells collected from the stream remains at or above an acceptable quantity, e.g., at least 60%. To obtain this result, the first particles sets are sorted into the usable population because they contain only one or more X cells. On the other hand, the second and third particle sets are sorted into one or more unusable populations 5 because they contain one or more contaminating (-X) cells. In this example, the rate at which the fluid delivery system delivers the fluid containing the cells to the nozzle would continue to be increased as long as the quantity of X cells collected in the usable population as a percentage of the total available quantity of X cells that have been sorted remains at or above 60%. Conversely, if the quantity of X cells not collected in the usable population rises above 40% of 10 the total number of available X cells that have been sorted, the fluid delivery rate is decreased. As noted above in the context of a droplet sorting system, it is known that increasing the fluid delivery rate will increase the number of multiple-cell droplets, and thus the number of coincident droplets containing third particle sets. Since coincident droplets are not sorted into the population of collected X cells when using a coincident reject sorting strategy, this means that 15 increasing the fluid delivery rate will result in a increase in the quantity of live X cells lost to the unusable population. Figure 80 illustrates this result for a two (2) particle fluid so that the usable population has 100% purity of desired particles. As shown, at very low fluid delivery rates (FDR along x axis), the percentage of desired particles in the usable population is very high because very few 20 coincident droplets are being generated and rejected. As the fluid delivery rate increases (FDR increases to the right along the x axis), the percentage of coincident droplets containing third particle sets increases and more such sets are rejected. This reduces the quantity of desired particles that are sorted into the usable population relative to the total quantity of desired particles available in the stream (i.e., the percentage of desired particles from the stream which 25 are collected in the usable population). In the specific example illustrated, the fluid delivery rate is about 40K particles/second and about 75% of the desired particles are sorted into the usable population. In summary, in the high purity control strategy implementing the coincident reject sorting strategy, the particle delivery rate is inversely related to the percentage of desired particles in the 30 collected population (i.e., high purity of desired particles in the usable population). C. Constant Flow Rate Control Stratey A third type of control strategy may be referred to as a constant flow rate control strategy. In this strategy, the microprocessor maintains the fluid delivery rate constant (or within 35 a constant range) and varies the percentage of collected (or rejected) coincident droplets as long as the purity of at least one collected population is at or above an acceptable level and as long as the quantity of desired particles in that population is at or above an acceptable quantity relative to a total quantity of desired particles that have been processed. Stated in the converse, the fluid delivery rate is constant and the percentage of accepted (or rejected) coincident droplets 40 varies as long as the probable level of contamination of the usable population is at or below an 96 acceptable level of purity and as long as the probable quantity of desired particles that is lost to a population other than the stated (usable) population is at or below an acceptable quantity. As an example, consider the use of a constant flow rate control strategy for sorting the fluid stream shown in Fig. 78. The desired result may be to sort X sperm cells into a usable 5 population having a purity of at least 85% and to collect at least 60% of the X cells in the stream so that no more than 40% of the X cells are sorted into the unusable population. In this example, the rate at which the fluid delivery system delivers the particles would be maintained constant and the percent of collected or rejected third particle sets (coincident sets) would be varied as long as the purity of the usable population with respect to X cells is equal to or greater than 85%, 10 and as long as the percentage of X cells sorted into the unusable population is less than 40% so that the percentage of desired particles sorted into the usable population is equal to or greater than 60% (variable coincident accept sorting strategy). As the percentage of accepted third particle sets increases, the purity of the usable population decreases, but the quantity of desired particles (e.g., X cells) sorted into the unusable population decreases. Conversely, as the 15 percentage of accepted third particle sets decreases, the purity of the usable population increases, but the quantity of desired particles (e.g., X cells) that are sorted in the unusable population Increases. As noted above, it is known from Poisson's equation that the number of multiple-cell droplets (and thus the number of coincident droplets containing third particle sets) Is constant for 20 a constant fluid (cell) delivery rate. Since the number of coincident droplets is constant in this control strategy, the percentage of coincident droplets sorted into the usable population will impact both the purity of the usable population and the quantity of X cells that are wasted by being sorted into an unusable population. This is because the percent of unwanted Y (or -X) cells in coincident droplets which are accepted and sorted Into the collected unusable population 25 is inversely related to the percent of X cells in coincident droplets which are rejected and thus not sorted into the collected usable population. Figure 81 illustrates the constant fluid delivery rate control strategy in a flow cytometry droplet sorting system and method as described herein implementing a variable coincident reject sorting strategy for a two (2) particle fluid. As shown, line OL illustrates the inverse relationship 30 between the percentage of rejected coincident droplets (x axis) compared to the percentage of accepted coincident droplets (y axis). When there is a very low percentage of accepted coincident droplets, there is a very high percentage of rejected coincident droplets. Conversely, when there is a very high percentage of accepted coincident droplets, there Is a very low percentage of rejected coincident droplets. Line OL illustrates this inverse relationship and 35 represents the operating line of the variable coincident accept sorting strategy at a given constant particle flow rate. At point P in Fig. 81 along operating line OL, the purity of the usable population is a given percentage depending on particle flow rate, e.g., 85% purity. As the percentage of accepted coincident droplets increases (to the left and upward) along operating line OL, the number of undesired particles that are sorted into the usable population increases 40 and the purity drops below 85%, which may be unacceptable. As the percentage of accepted 97 coincident droplets decreases (to the right and downward) along operating line OL, the purity goes above 85% and is acceptable. At point LL along operating line OL, 75% of the coincident droplets are rejected (i.e., sorted into the unusable population) so that the percentage of desired particles that are wasted 5 by being sorted into the unusable population is a given percentage based on the particle delivery rate, e.g., 40%. As the percentage of rejected coincident droplets increases (to the right and downward) alpng operating line OL, the percentage of desired particles that are sorted into in the usable population decreases (e.g., to <60%), which may be unacceptable. As the percentage of rejected coincident droplets (to the left and upward) along operating line OL, the percentage of 10 desired particles sorted into the usable population increases (e.g., to >60%) and is acceptable. Thus, according to this aspect of the invention for a constant flow rate control strategy implementing a variable coincident accept sorting strategy, the microprocessor may operate the system so the percentage of accepted and rejected coincident droplets varies in an operating range between point P1 and LL as indicated by arrow OR. Note that operating range OR may 15 encompass more or less of the operating line, depending on the level of tolerance for impurity and loss of desired particles to the unusable population. In summary, in the constant flow rate control strategy using the variable coincident accept sorting strategy, the percentage of third particle sets which are accepted is inversely related to the purity of the usable population and inversely related to the quantity of desired 20 particles wasted by being sorted to a unusable population. D. Summary of Control Strateqies The following Table summarizes the control strategies noted above. [rest of page blank] 98 NTROL HIGH RECOVERY HIGH PURITY CONSTANT FLOW RATE SRATEGY Controlled parameter Fluid delivery rate Fluid delivery rate Sort parameters Controlling Purity of population Quantity of desired Purity of population AND parameter: particles in population Quantity of desired particles in o ulation Sorting strate Co incident acce t Coincident re ct Variable coincident accep XN Sorting strategy ColIect X droplets and Collect X droplets; Collect X droplets; vary X+-X droplets; reject -X reject X+-X droplets percentage of collected X+-X dro lets and -X dro lets droplets; reject -X droplets Definition The fluid delivery rate is The fluid delivery rate The percentage of coincident increased as long as the is increased as long droplets in the population is purity of the population as the quantity of increased as long as the purity with respect to X particles desired particles in of the population with respect is at or above an the usable population to X particles is at or above an acceptable level relative to the total acceptable level; to continue quantity of X particles oeration, the quantity of in the stream is at or desired particles in the usable above an acceptable population relative to the total quantity quantity of X particles in the stream must be at or above an Converse De7finition nc~f eaui fuid deliery rate The fluid delivery rat efdd eate is pnrb dabilyo g 9s te is increased as long increased as long as the contamintio ofth as the probability of probability of contamination of conbleinpopulath oss of the quantity of the usable population is at or usable population is at or desired particles in below an acceptable level of below an acceptable level an unusable purity AND as long as the of purity population is at or probability of loss of the below an acceptable quantity of desired particles in quantity the unusable population is at or beow. an acceptable quantity Desired result > minimum acceptable >minimum > minimum acceptable purity purity; e.g., >85% purity acceptable quantity; and >minimum acceptable e.g., >60% of desired quantity; e.g., >85% purity and particles captured >60% of desired particles (<40% of desired captured (<40% of desired articles lost articles lost) Relatedly, a sorted sample obtained using one of the above control strategies can be combined with a second sample to obtain a final (e.g., commercial) sample having the desired characteristics. For example, a sample sorted according to the high purity strategy to produce a 5 100% pure population can be combined with a population of the same volume sorted to 80% purity to produce a final sample having a purity of 90%. Or in the case of animal sperm sorted to a high purity, an aliquot amount of the sorted sperm can be combined with an aliquot amount of unsorted sperm to produce a final sample of desired purity at lower cost than sorting the entire amount of sperm using any of the above sorting methods. 10 The above description of the control strategies assumes accurate identification and sorting of each droplet including each coincident droplet. In practice, 100% accuracy is not possible for any number of reasons. In order to minimize contamination, therefore, it may be desirable to reject particles which cannot be classified with certainty as belonging to the desired population. On the other hand, if certain particles can be identified and classified as being in the 15 desired population within a certain selected probability (e.g., greater than 50% in the case of 99 sperm cells), it may be desirable to classify the particles as belonging to the desired population so that they are not lost to the unusable population. Thus, as discussed earlier, particles such as sperm cells may be accepted or rejected for sorting into a population of desired cells based on the probability that such particles belong in the usable population. 5 The terms "usable" and "unusable" as used in the above table and this application are used for convenience only and are not intended to be limiting in any way. Thus, a "usable" population includes any "first" population, regardless of how or whether it is used, and an unusable" population includes any "second" population different from the usable population, regardless of how or whether it is used. Similarly, a "desired" population means any population 10 which is sorted according to selected particle characteristics. The microprocessor and its signal processing software constitutes a system for processing the electrical signals from the photodetector to classify particles (e.g., particles in general and sperm particles in particular) according to characteristics of the particles and to obtain information relating to the distribution of the particles as described above with respect to 15 Fig. 78. Furthermore, the microprocessor constitutes a control system responsive to the signal processing software for varying the rate at which the fluid delivery system delivers particles to the nozzle system as a function of the obtained information relating to the distribution of the particles. Furthermore, the microprocessor constitutes a control system responsive to the signal processing software for varying the sorting strategy as a function of the obtained information 20 relating to the distribution of the particles. In general, the microprocessor constitutes a control system responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system. In other words, the microprocessor is capable of operating in a first mode to vary the sorting strategy, is capable of operating in a second mode 25 for controlling the fluid delivery system, is capable of operating in a third mode to vary the sorting strategy and for controlling the fluid delivery system, and may be capable of operating in other modes. When operating in the first or third mode, the microprocessor is capable of varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of the at least one population with respect to either characteristic A particles or characteristic B particles, 30 and (2) the quantity of characteristic A particles or characteristic B particles in the at least one population relative to the total quantity of characteristic A particles or characteristic B particles in the stream.

100 Collection System A collection system is needed to collect the droplets after they pass between the deflector plates. The collection system for a conventional cytometer may be no more than collection vessels disposed to catch the droplets in the various droplet streams after they pass 5 between the deflection plates. Similar conventional collection systems can be used in some embodiments of the present invention. However, it may be difficult to use a conventional collection system in embodiments of the present invention in which the nozzle is oriented to direct the fluid stream at an upward angle, thereby giving the droplets a horizontal velocity component. One issue is that the droplets would 10 travel some horizontal distance along their arched trajectories before they begin downward movement that would be suitable for landing in a collection vessel. For example, if the nozzle is pointed upward at a range of 450 to 60 and the droplets exit at a velocity between 15 m/s and 20 m/s, the droplets will be a horizontal distance of several meters away from the nozzle before they reach the apex of their trajectories and begin downward movement. Thus, a good deal of lab 15 space would be occupied by the droplet streams. Furthermore at a range of several meters it could also be difficult to make sure the droplets land in the proper collection vessels. The trajectories of the droplet streams can change whenever one or more operating conditions for the cytometer change (e.g., adjustment to the fluid delivery rate resulting in a change in the fluid velocity at the nozzle orifice). Changes in the trajectories of the droplet streams will be magnified 20 by the distance that the droplets travel. Thus, changes in the trajectories that do not result in an appreciable change in droplet location at a point relatively near the nozzle could result in a significant change in location of the droplets at a location that Is farther away from the nozzle. As discussed above, some embodiments of the present invention employ feedback to the droplet formation and/or sample fluid delivery systems that could result in droplet streams that constantly 25 alter their trajectories. One may also want to vary the pressure at which the sheath fluid is delivered to the nozzle. Air currents, temperature variations, and humidity variations could also alter the trajectories of the droplet streams. Any factor that could change the trajectory of the droplet streams could also require the collection vessels to be repositioned so the droplets land In the appropriate collection vessels. In contrast, the trajectories of droplets streams In a 30 conventional cytometer having a downward pointing nozzle are less susceptible to variation. For example, the fact that the droplet streams have a substantially downward initial velocity means that variation in fluid velocity at the orifice does not result in any significant variation in the trajectories. Furthermore, the collection vessels are relatively close to the nozzle which makes the collection system more tolerant to trajectory variations in the droplet streams. 35 Figs. 83-85 show one embodiment of a collection system, generally designated 2201, that may be used to collect sorted droplets in a system of the present invention. The collection system is particularly suited for collection of droplets 33 when the cytometer nozzle system 101 is oriented to direct the fluid stream 21 at an upward angle or any other angle having a horizontal component. As the droplets pass between the deflector plates 629, they are sorted into multiple 40 droplet streams 123,125 (e.g., two) having different arched trajectories. As shown in Figs. 84 101 and 85, the trajectory of each droplet stream leads to one of two droplet intercepting devices 2203. If the droplets are being sorted into more than two droplets streams, a separate intercepting device would need to be provided for each additional droplet stream. Thus, the number of intercepting devices in a collection system of the present invention will depend on the 5 number of streams into which the droplets are being sorted. Each intercepting device 2203 in the exemplary collection system has an impact surface 2205 positioned to span the trajectory of one of the droplet streams to divert droplets moving along that trajectory to a collection vessel 2207 Positioned beneath each intercepting device. The impact surfaces are preferably made of a pliable material. Without being bound by a particular 10 theory, it is believed that pliable materials cushion the impact of droplets striking the surface of the intercepting device, thereby reducing damage to the particles (e.g., sperm cells) in the droplets. For example, the intercepting devices may be constructed of polypropylene, polyethylene, or other similar polymers. Referring to Figs. 86 and 87, the intercepting devices 2203 have been constructed by cutting a droplet entryway 2211 (e.g., rectangular window) in one 15 side of the bulb 2213 of a pipette 2215. Thus, a portion of the inside wall 2217 of the bulb opposite the droplet entryway forms a curved impact surface 2205 which spans the trajectory of the respective droplet stream. Convenient, the tube of the pipette serves as a guide 2225 for directing fluid from the impact surface to the collection vessel. Referring to Fig. 84, the intercepting devices are fastened to a collection system frame 20 2227, which holds them in place. In order to account for variability in the trajectories of the droplet streams, it is desirable to allow adjustment of the positions of the intercepting devices. For example, the vertical height of each intercepting device may be adjusted by sliding the guide tube up and down In a circular bore through a holder 2229. When the intercepting device is at the desired height, a set screw 2231 may be tightened to hold it at that height. The holder may 25 be attached to a mounting plate 2233 which is attached to the collection system frame, for example by set screws 2235 (e.g., two set screws). The set screws 2235 pass through a horizontal slot 2241 in the mounting plate to allow lateral adjustment of the intercepting device. After adjustment, the set screws may be tightened to hold the circular holder in the desired location. Those skilled In the art will recognize that a variety of other fastening devices could be 30 used to adjust the position of the intercepting device without departing from the scope of the present invention. The collection vessels 2207 are held beneath the intercepting devices in slots 2241 in a tray 2243 for holding the collection vessels. Thus, each collection vessel may be moved within a respective slot as necessary for it to remain in position under the respective intercepting device. Also, a water bath (not shown) may be provided around the collection vessel 35 if desired to control the temperature of the contents of the collection vessel. Referring to Fig. 85, in one embodiment of the present invention an exit window 2245 (e.g., a rectangular window) has been cut in the back of one of the intercepting devices 2247 to allow one or more droplet streams to pass through the intercepting device. A second intercepting device 2249 is positioned behind the exit window to intercept the droplets that pass 40 through this window. An exemplary entry window for the second intercepting device may be 102 approximately the same size as the exemplary exit window for the first intercepting device. For reasons that will be apparent, it is desirable for the exit window to be significantly smaller than the entry window for the first intercepting device. For instance, an exemplary entry window for the first intercepting device is about 5/8 of an inch high and about 3/8 of an inch wide. In 5 contrast, an exemplary exit window may be 1/8 of an inch high and 5/16 of an inch wide. During operation of the cytometer, the collection system operates to intercept the droplets in the sorted streams. The intercepted droplets then drain down through the guide tubes 2225 of the intercepting devices 2203 and into the collection vessels 2207. In a case in which a cytometer has an upward pointing cytometer nozzle that directs droplet streams along arched 10 trajectories, for example, the intercepting devices allow the droplets to be intercepted at a point on their trajectory that is significantly closer to the nozzle in comparison to the point at which the droplets would be collected by a conventional collection system (i.e., a collection system without intercepting devices). Intercepting the droplet streams relatively early along their arched trajectories (e.g., while 15 they are still moving upward) reduces the amount of variation in the location of the droplets at the time the droplets first encounter the collection system. Accordingly, the collection system can tolerate more variation in the trajectories of the droplet streams than a convention collection system could tolerate. Similarly, the droplets are less likely to be buffeted by air currents because of their shorter paths to the collection system. 20 A balance must be struck between moving the intercepting devices 2203 closer to the nozzle 101 to increase tolerance for trajectory variations and moving the intercepting devices farther away from the nozzle orifice to reduce or minimize the force of impact when droplets impact the intercepting devices, as by positioning the intercepting devices so they intercept the droplet streams substantially at the apex of their trajectories. Accordingly, the best location for 25 the intercepting devices will depend on the durability of the particles (e.g. sperm cells) being sorted, the droplet velocities, and the expected magnitude of variation in the droplet stream trajectories. In the case of droplets containing bovine sperm cells having a velocity at the nozzle orifice of about 16 to 20 m/s, for example, the intercepting devices may be positioned in the range of 4 - 6 inches from the nozzle orifice. In the embodiment in which a first intercepting 30 device has a exit window and a second intercepting device is positioned behind the first intercepting device, for example, the first intercepting device may be in the range of about 4 and 5 inches from the nozzle. More desirably, the first intercepting device is about 4.5 inches from the nozzle. The second intercepting device may be in the range of about 5 to 6 inches from the nozzle. More desirably, the second intercepting device is about 5.5 inches from the nozzle. 35 The configuration in which one intercepting device 2203 is positioned to intercept the droplets that pass through an exit window of another intercepting device is particularly advantageous when one is not concerned about the purity of one of the sorted populations (e.g., Y chromosome-bearing sperm in the case of sperm sorted for use in breeding dairy cattle). Those skilled in the art will know that a number of stray droplets 2265 (e.g., a mist of stray 40 droplets) having unknown contents may be produced by the cytometer in addition to the droplets 103 in the sorted streams as shown in Fig. 85. The first intercepting device should be positioned so that the stream of droplets that are being sorted into the population for which there is the greatest tolerance for impurities hit the impact surface 2205 of the first intercepting device and the stream for which purity is most critical passes through the exit window 2245 to hit the impact surface of 5 the second intercepting device. This way the majority of the stray droplets are collected into the collection vessel 2207 containing the population for which there is ress concern about purity, as shown in Fig. 85, and will not contaminate the population for which purity is critical. Also by intercepting and collecting the stray droplets, one avoids the need to clean as often as if the stray droplets escape the collection system. In contrast to the first intercepting device, the second 10 intercepting device only diverts droplets that pass through the smaller exit window. This facilitates maintenance of the purity of the population collected by the second intercepting device. Those skilled in the art will recognize that the exemplary collection system could readily be modified in a number of ways without departing from the scope of the present invention. For example, it would be possible to construct a droplet intercepting device having an integrally 15 formed (or otherwise attached) collection vessel beneath it, without departing from the scope of this invention. Similarly, although the intercepting devices in the embodiment shown in Figs. 83 87 are modified pipettes, it is understood that the intercepting devices 2203 can be any of a variety of shapes without departing from the scope of this invention. For example, each intercepting device may comprise a flat or curved sheet, a spoon, a bowl, or other similar shape. 20 The only requirement is that the intercepting device is operable to intercept droplets moving along a respective trajectory of a droplet stream and to divert the intercepted droplets into a collection vessel. However, one advantage to constructing the intercepting devices out of a readily available and relatively inexpensive product, such as a pipette, is that it may be more economical to replace and dispose of the used intercepting devices after each sample run rather 25 than clean the intercepting devices between sample runs. This could help reduce costs of operating the collection system. Collection Fluid The sorted sperm are collected in a vessel that contains a collection fluid 2301 (Figs. 56 30 and 57). Generally, the purpose of the collection fluid includes cushioning the impact of the sperm cells with the collection vessel or providing a fluid support for the cells. Consistent with these considerations, the collection fluid may comprise a buffer or buffered solution and a protein source. If included, examples of buffers or buffered solutions that may be used in the collection 35 fluld are disclosed above with respect to sample collection and dilution. Typically, these buffers or buffer solutions will be in a concentration of about 0.001 M to about 1.OM and have a pH of about 4.5 to about 8.5, preferably of about 7.0. In one embodiment, the collection fluid contains buffer comprising 0.96% Dulbecco's PBS (w/v) at a pH of about 7.0 In another embodiment, the collection fluid contains a metabolic inhibitor comprising 0.

2 04g NaHCO 3 , 0.

4 33g KHCO 3 , and 104 0.473g CrH 8 07-H 2 0 per 25mL of purified water (0.097 moles/L of NaHCO 3 . 0.173 moles/L of

KHCO

3 , 0.090 moles/L C 6

H

8 0 7

H

2 0 in water). If included, the protein source may be any protein source that does not interfere with the viability of the sperm cells and is compatible with the particular buffer or buffered solution being 5 used. Examples of common protein sources include milk (including heat homogenized and skim), milk extract, egg yolk, egg yolk extract, soy protein and soy protein extract. Such proteins may be used in a concentration from about 1% (v/v) to about 30% (v/v), preferably from about 10% (v/v) to about 20% (v/v), and more preferably about 10% (v/v). While milk may be used in combination with a buffer or buffered solution, generally milk is used in the absence of the same, 10 as milk is a solution itself that may serve the same purpose of a buffer or buffered solution. In such instances, the collection fluid may contain about 80% (vlv) to about 90% (v/v) milk. In addition to or in lieu of the protein source, the collection fluid may also comprise seminal plasma. Seminal plasma serves the dual benefits of improving sperm viability and motility and of stabilizing the sperm membrane (thereby preventing capacitation during the 15 collection and storage of the sperm). Maxwell et al., Reprod. Ferf. Dev. (1998) 10: 433-440. The seminal plasma may be from the same mammal from which the semen sample was obtained, from a different mammal of the same species, or from a mammal of a different species. If included in the collection fluid, typically the percentage of seminal plasma will be in the range of about 0.5% (v/v) to about 10% (v/v). If used in combination with a protein source, such as for 20 example egg yolk or milk, the total percentage of seminal plasma and protein source will range from about 1% (v/v) to about 30% (v/v). In such instances, the percentage of seminal plasma will be inversely proportional to the percentage of the protein source. Accordingly, in one embodiment, the collection fluid comprises seminal plasma. In another embodiment, the collection fluid contains seminal plasma in an amount of about 0.5% (v/v) to about 10% (v/v), 25 preferably in an amount of about 4% (v/v) to about 6% (v/v), and more preferably in an amount of about 5% (v/v). In another embodiment, the collection fluid contains a protein source and seminal plasma. In yet another embodiment, the collection fluid comprises seminal plasma and egg yolk, the percentage of both totaling between about 1% (v/v) and about 30% (v/v). Optionally, the collection fluid may also contain a range of additives that are beneficial to 30 sperm viability or motility. Examples of such additives include an energy source, an antibiotic, and a composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly, each of which is discussed above with respect to sample collection and dilution. Such additives may be added to the collection fluid in accordance therewith. Accordingly, in a certain embodiment, the collection fluid comprises 0.96% Dulbecco's 35 PBS (w/v), 1% (w/v) fructose, 10% (v/v) egg yolk in water, at a pH of about 7.0. In yet another embodiment, the collection fluid further comprises 10mM pyruvate, 1000M vitamin K, or 1mM of lipoic acid. Alternatively, and in lieu of the use of a collection fluid, the sorted cells may be collected into a vessel containing or coated with a cryoextender used in the subsequent cryopreservation 40 steps and further described below. Accordingly, in one particular embodiment, the sorted cells 105 are collected into a cryoextender. In another embodiment, the collected cells are sorted into a cryoextender comprising water, Triladyl* (Minitube, Verona, WI, comprising glycerol, tris, citric acid, fructose, 5mg/1 00ml tylosin, 2 5mg/100ml gentamycin, 30mg/100ml Spectinomycin, and 15mg/100ml Lincomycin), egg yolk, and pyruvic acid. In yet another embodiment, the collection 5 fluid is the cryoextender comprising 25g Triladyl@, 25g egg yolk, and 10mM pyruvic acid in 75mL of water. It is to be understood that the percent concentrations of protein in the collection fluid disclosed herein are those prior to the addition of the flow sorted cells. The addition of the flow sorted cells will dilute the final concentration of the collection fluid to about 1/20 that of what it 10 was prior to the addition of the flow sorted cells. Therefore, for example, the collection fluid may initially contain about 10% (v/v) egg yolk. After the flow sorted cells are collected in the collection vessel containing the collection fluid, the final concentration of egg yolk will be reduced to about 0.5% (v/v). 15 Pre-Treatment of ntercepting Devices and/or Collection Vessels In order to minimize possible damage to particles (e.g., sperm cells) that may be sorted according to the present invention, the intercepting devices 2203 and/or collection vessels 2207 (Figs. 56-60) may be treated prior to use. Such pre-treatment may comprise, for example, contacting or soaking the intercepting devices and collection vessels in a bath containing a 20 composition that will serve to minimize the impact between the particle and the intercepting device. Upon removal of the intercepting devices and collection vessels from the bath, a certain amount of the composition will remain on the intercepting devices and collection vessels and serve as a cushioning agent for the particles in the droplets. The composition, therefore, should have characteristics suitable for providing the desired cushioning effect. In addition, the 25 composition should also be compatible with the particle or cell being sorted, the sheath fluid, and the collection fluid. Consistent with these considerations, the composition used to treat the intercepting devices and collection vessels may comprise a buffer or buffered solution, a sheath fluid, a collection fluid, a cryoextender, any components contained in the buffered solution, sheath fluid, collection fluid, or cryoextender, or any combination thereof. Buffers, buffered 30 solutions, sheath fluids, and collection fluids used for the staining and separation of sperm cells according to the methods of the present invention are described above. Accordingly, in one embodiment, the intercepting devices and collection vessels are contacted with (e.g., soaked in or brushed with) sheath fluid. In another embodiment, the intercepting devices and collection vessels are contacted with collection fluid. In yet another embodiment, the intercepting devices 35 and collection vessels are contacted with a cryoextender described below. The contacting or soaking of the intercepting devices and collection vessels with the composition preferably occurs for a period of time sufficient to allow the composition to adhere to the surfaces of the intercepting devices and collection vessels. Such a period of time is generally less than about 90 minutes, preferably less than about 60 minutes, more preferably about 30 to 40 about 60 minutes, and most preferably about 60 minutes. In still another embodiment, the 106 intercepting devices and collection vessels are merely contacted with the composition prior to use. In lieu of or in combination with the contacting of the intercepting devices and collection vessels with the above-described composition, the intercepting devices and collection vessels 5 may also be contacted with specific components contained in the sheath fluid, the collection fluid, and/or the cryoextender, such as for example, BSA, SSS, egg yolk, egg yolk extract, milk (including heat homogenized and skim), milk extract, soy protein, and soy protein extract. Accordingly, in one embodiment, the intercepting devices and collection vessels are contacted with sheath fluid and subsequently contacted with 0.1% (v/v) bovine serum albumin. In another 10 embodiment, the intercepting devices and collection vessels are contacted with sheath fluid and subsequently contacted with 10% (v/v) egg yolk. In another embodiment, the intercepting devices and collection vessels are soaked in collection fluid and subsequently contacted with 0.1% (v/v) bovine serum albumin. In another embodiment, the intercepting devices and collection vessels are soaked in collection fluid and subsequently contacted with 10% (v/v) egg 15 yolk. Although the intercepting devices and collection vessels receive the same pre-treatment in each embodiment described above, it is possible to use different pre-treatment protocols for the intercepting devices and the collection vessels without departing from the scope of this invention. Likewise, some of the intercepting devices or collection vessels could receive one pre 20 treatment and others of the intercepting devices or collection vessels could receive a different pre-treatment without departing from the scope of this invention. Certain advantages of the pre treatment can also be obtained by pre-treating only the intercepting devices or only the collection vessels, again without departing from the scope of this invention. 25 Concentration As noted above, the sorted sperm collected by the flow cytometer have been diluted by the addition of various buffers and extenders, the staining fluid, the sheath fluid, and the collection fluid. Typically, the concentration of sperm cells after sorting by flow cytometry as described above is in the range of about 0.7 - 1.4 x 106 sperm cells/ml. Therefore, it is important 30 to concentrate the sorted sperm cells to minimize the dilution shock to the sperm and to attain the proper concentration of sperm for cryopreservation and artificial insemination. Standard practice in the animal breeding industry, for example, is to perform artificial insemination with sperm at a concentration of either about 20 x 106 or about 40 x 106 sperm cells/mi. One way to concentrate the sperm cells is through centrifugation of the fluid collected by the cytometer. 35 Another way to concentrate the sperm is to pass the fluid collected by the cytometer through a filtration system. These methods are discussed in more detail below. A. Centrifuqation Any conventional centrifuge can be used to concentrate sperm. However in a 40 commercial operation it is preferable to use a centrifuge having the capacity to centrifuge a large 107 batch of sperm cells at once. During centrifugation a majority of the sperm cells will collect in a pellet at the bottom of the centrifuge tube due to the centrifugal force acting on the sperm cells. The magnitude of the centrifugal force is conventionally stated as the number of times the centrifugal force exceeds the gravitational force. Because the centrifugal force is the critical 5 parameter and because the magnitude of the centrifugal force at any given speed (angular velocity) will vary depending of the length of the radius of curvature, the speed of centrifugation is typically specified by stating the magnitude of the centrifugal force. For example, a 600g force means the angular velocity of the centrifuge is selected so the resulting centrifugal force will be 600 times the force of gravity. The majority of the fluids and any sperm cells that escape being 10 centrifuge into the pellet will be in the supernatant. Generally, the supernatant is removed and the sperm cells in the pellet are resuspended for further processing as described below. It is important to maximize the percentage of sperm that are concentrated in the pellet, while at the same time minimizing damage to the sperm cells. According to one method of the present invention, a centrifuge tube containing about 10 15 x 106 sorted sperm cells is placed in a centrifuge. To facilitate concentration, centrifuge tubes may be used as the collection vessels in the collection system of the cytometer. This avoids the need to transfer the sorted sperm cells to a centrifuge tube before centrifugation. The tube is centrifuged at a speed and for a duration that is sufficient to cause a pellet of concentrated sperm cells to form in the bottom of the tube. The speed and duration of the centrifugation is desirable 20 selected in consideration of several factors, including: the fact that sperm cells are fragile and can be damaged by centrifugation at an excessive speed; the size of the centrifuge tube will affect the time required for sperm cells to move to the bottom of the tube; and the sperm cells are more likely to be damaged by centrifugation at a given speed the longer the centrifugation continues. Thus, in one embodiment of the present invention the centrifuge tube is centrifuged at 25 55 0- 8 00g for a period of about 6 - 10 minutes. According to another embodiment of the present invention, the centrifuge tube is centrifuged at 65 0- 7 50g for a period of about 6 - 10 minutes. In still another embodiment, the centrifuge tube is centrifuged at 700g for a period of about 6 - 10 minutes. In yet another embodiment, the centrifuge tube Is centrifuged at 7OOg for a period of about 7 minutes. 30 As demonstrated in the following experiments, the speed of the centrifuge and the duration of centrifugation may affect the percentage of sperm cells recovered and the motility of the recovered sperm cells. The experiments were conducted without actually sorting the sperm cells. Instead, various fluids including buffers, extenders, sheath fluids and a staining fluid were added to semen samples to simulate the sorting process. The samples were then centrifuge in 35 an attempt to concentrate the sperm cells. Centrifuge Example I In centrifuge example I bovine semen was collected and evaluated as described above. The semen sample was diluted with a quantity of Tris-citric acid ("TCA") having a pH of 7.3 to 40 attain a concentration of 150 x 106 sperm cells/mi. Spermatozoa were stained with Hoechst 108 33342 (100 pM) at 41* C for twenty minutes. Two 15 ml tubes were prepared with buffers for the simulation. Tube I was partially filled with 750 pl of phosphate buffered saline ("PBS") with 10% egg yolk and 14.25 ml PBS with 0.1 % bovine serum albumin ("BSA"). Tube 2 was partially filled with 750 ul TCA with 10% egg yolk and 14.25 ml PBS with 0.1% BSA. Each of the two tubes 5 received 100 ul of the solution containing the stained spermatozoa, which were then incubated at room temperature for 20 minutes. The two tubes were then divided into two aliquots of 7 ml each. One aliquot from each tube was centrifuged at 2250 rpm (about 540g) for 7 minutes in a fixed bucket centrifuge. The other aliquot from each of the two tubes was centrifuged at 2500 rpm (about 660 g) for 7 minutes. Immediately after centrifugation, 10 ml pipettes were used to 10 remove and save the supernatant from each aliquot. -The pellets were resuspended in 200 ul of TCA with. 10% egg yolk (pH 7.0). Pre- and post- centrifuge sperm motility was observed under a phase contrast microscope. Fifty ul of a fixative (0.1% glutarldehyde in 3.4% Na citrate) was added to each pellet and supernatant to immobilize the sperm for concentration determination with a hemacytometer. Total numbers of spermatozoa were calculated on the basis of volume 15 used/recovered multiplied by the corresponding sperm concentration as determined by the hemacytometer. The recovery rate was calculated as the total number of sperm in the pellet divided by the sum of the total number of sperm in the pellet and the total number of sperm in the supernatant. The results, as shown in Figs. 88 and 89 show there is little difference in sperm cell 20 motility caused by varying the centrifuge speed. The results also show that motility was slightly better using TCA compared to PBS. Centrifuge Example II In centrifuge example il semen samples from three bulls were collected and evaluated 25 as described above. One of the samples was disqualified for failure to meet initial quality control standards. The other two semen samples were diluted with a quantity of TCA having a pH of 7.3 in order to obtain a sperm concentration of 150 x 106 sperm/ml. The spermatozoa were stained with a 10 pM Hoechst 33342 solution at 410C for twenty minutes. A simulated buffer containing 1500 pi PBS with 10% egg yolk and 28.3 ml PBS with 0.1% BSA was added to each of two 30 tubes. Two hundred p1 of the stained spermatozoa (30 x 104 sperm cells) were added to each tube and incubated at room temperature for twenty minutes. Three 9 ml aliquots of semen mixture were taken from each of the two tubes for centrifugation. One aliquot from each of the two samples was centrifuged for seven minutes in a 15 ml centrifuge tube at each of the following speeds: 550g; 650g; and 750g. The temperature during centrifugation was 22*C. 35 Immediately after centrifugation, supernatant was removed with a 10 ml pipette, leaving about 200-300 pl supernatant in the pellet. The pellets were resuspended with 200 pl of TCA having 10% (v/v) egg yolk having a pH of 7.0. Pre- and post- sort sperm motility was observed under a phase contrast microscope. Severe sperm agglutination was noted in the post-centrifuge samples from one of the two bulls. Fifty pl of a fixative (0.1% glutardehyde in 3.4% Na citrate) 40 was added to each supernatant and pellet to immobilize the sperm for concentration 109 determination. Recovery rate was determined according to the formula set forth in centrifuge experiment I. The results are shown in Fig. 90. The results show improved recovery rate of sperm cells at 650g compared to 5 50g. However, there was little difference in recovery rate between 5 650g and 75 0g. There was no significant difference in sperm cell motility caused by varying the speed of the centrifuge. Centrifuge Example I// For centrifuge example l1l, the procedure of centrifuge example 1I was substantially 10 repeated with the same three bulls on a different day. The results are shown in Fig. 91. The results confirm that there is little difference in the recovery rate at 650g compared to 750g. Centrifuge Example IV Semen was collected from two different bulls on two different days. Semen was 15 transported and evaluated in the manner described above. Based on sperm concentration of raw semen, spermatozoa were diluted with Tris-citric acid (TCA, pH 7.3) plus 10mM pyruvate, to a concentration of 150x10 6 sperm/mI The spermatozoa were stained with 10 iM Hoechst 33342 at 41'C for 20 min. After staining, 267 pL of the solution containing the stained spermatozoa were diluted to a concentration of vv06sperm/mI by addition of the following simulated buffers: 20 2 ml PBS with 10% (vfv) egg yolk; and 37.733 ml PBS with 0.1% (w/v) bovine serum albumin (BSA). The stained spermatozoa and simulated buffers were incubated at room temperature for at least 20 minutes. Four 9 ml aliquots were taken from the stained spermatozoa and simulated buffer mixture obtained from each bull. The four aliquots from the first bull were centrifuged at varying combinations of centrifuge speed and duration in the following sequence: 25 (1) 700g for 7 minutes for the first aliquot; (2) 700g for 10 minutes for the second aliquot; (3) 6 50g for 10 minutes for the third aliquot; and (4) 650g for 7 minutes for the fourth aliquot. 30 The four aliquots from the second bull were centrifuged at varying combinations of centrifuge speed and duration in the following sequence: (1) 700g for 10 minutes for the first aliquot; 35 (2) 700g for 7 minutes for the second aliquot; (3) 650g for 10 minutes for the third aliquot; and (4) 650g for 7 minutes for the fourth aliquot. All centrifugation was performed in 15 ml centrifuge tubes in a swing head centrifuge (Allegra 6R, 40 Beckman Coulter Inc. Fullerton, CA) at 220C. The time interval between semen collection at 110 farm and centrifugation in lab was 4-5 hours. Immediately after centrifugation, supernatant was removed with 10 ml pipettes, leaving -250 pl supernatant with each pellet. The pellets were resuspended in 250 pl of Delbecco's PBS (pH 7.0). Sperm motility and progressive motility were observed using a Hamilton-Thorn Motility Analyzer (two slides per sample; two chambers per 5 slide) after staining but before centrifugation and again after centrifugation. Sperm concentration was determined by hemacytometer measurement of a 100 pi aliquot of the pre-centrifuge stained spermatozoa and simulated buffer mixture that had been placed in the freezer and a 10 RI aliquot of the resuspended pellet mixed with 90 pl fixative (0.1% glutaraldehyde in 3.4% Na citrate). Recovery rate was determined as in Centrifuge Example 1. The results are shown in Figs. 92 10 and 93. The data indicate that > 85% of the spermatozoa can be recovered after centrifugation at 650g or 700g, for 7 or 10 minutes (Fig. 92). However, recovery rate was slightly better (95%) at 700g. The decline in motility after centrifugation (compared to before centrifugation) in all treatments could be due to the presence of dead/abnormal/fragile spermatozoa which could not 15 withstand the stress of centrifugal force. Sperm motility declined by 10-14% (Fig. 93) in all treatments. The higher decline in sperm motility (14%) at 650g for 7 min might be due to the longer exposure of sperm to simulated buffer as centrifugation at 650g was conducted after 700g. Centrifugation did not show any adverse effect on progressive motility of spermatozoa, rather there was improvement by 2-3%. 20 Centrifuge Example V Semen was collected from one bull on two different days. Semen was evaluated, diluted and stained with Hoechst 33342, and further diluted in simulated buffers as described in Centrifuge Example IV. Four 9 ml aliquots of the stained spermatozoa and simulated buffer 25 mixture were obtained for each of the two semen samples. The aliquots from the first sample were centrifuged at one of the following combinations of centrifuge speed and duration in the following sequence: (1) 750g for 10 minutes for the first aliquot; 30 (2) 750g for 7 minutes for the second aliquot; (3) 700g for 10 minutes for the third aliquot; and (4) 700g for 7 minutes for the fourth aliquot. For the aliquots obtained from the second sample, the combinations of centrifuge speed and 35 duration were the same, but the sequence was modified as follows: (1) 750g for 7 minutes for the first aliquot; (2) 750g for 10 minutes for the second aliquot; (3) 700g for 7 minutes for the third aliquot; and 40 (4) 700g for 10 minutes for the fourth aliquot.

111 Centrifugation was conducted in a 15 ml centrifuge tube in a swing head centrifuge (Allegra 6R, Beckman Coulter Inc. Fullerton, CA) at 22 0 C. The interval between semen collection at farm and centrifugation in laboratory was about 6.5 hours for the first sample, and about 4 hours for the 5 second sample. Post centrifugation processing, i.e. removal of supernatant, resuspension of pellet, determination of sperm concentration, and motility estimation via Hamilton-Thorn Motility Analyzer, were conducted following the same procedure as described in Example IV. The results are shown in Figs. 94 and 95. The results show that > 85% of the sperm population in highly diluted suspension can be 10 recovered with 700g or 750g in 7 minutes or 10 minutes (Fig. 94). An increase in g force to 750g did not improve the recovery rate significantly. As was the case in Centrifuge Example IV, the decline in motility after centrifugation (as compared to before centrifugation) was observed in all treatments. In the present experiment, sperm motility declined by 13-20% (Fig. 95) which is little higher than in Centrifuge Example IV. The variation could be due to variation in semen sample 15 and longer time interval from semen collection to centrifugation (6 hours) in one replicate. As explained in Example IV, the decline in sperm motility (about 20%) at low speed centrifugation (700xg, for 7 or 10 min) might be due to the longer exposure of sperm to simulated buffer as they were centrifuged after 750g centrifugation. The decline in progressive motility was negligible (1 5%). 20 B. Secondary Centrifuqation In order to recover sperm that might otherwise be lost in the supernatant, it is possible to centrifuge the supernatant after it has been separated from the pellet. Without being bound by a particular theory, applicants believe the pellet/supernatant interphase impedes movement of 25 spermatozoa into the pellet. Removal of the interphase by separating the pellet from the supernatant will allow further centrifugation of the supernatant to cause sperm cells that would have remained in the supernatant to form a second pellet. The second pellet can be resuspended and added to resuspended sperm from the first pellet. 30 C. Filtration An alternative concentration method that may be used to avoid loss of sperm cells in the supernatant is filtration. As shown in Fig. 96, according to one exemplary embodiment a filter 2415 is incorporated in a collection vessel 2403. The size of the pores In the filter are desirably in the range of about 0.2 - 1 microns. It Is also desirable that the filter is not a depth filter (e.g., a 35 filter having tortuous passages In which sperm tails can be caught). Rather it is desirable that the filter be as thin as possible. For example, it is desirable that the filter thickness be in the range of 50pm to 500pm; more desirable that the filter thickness be in the range of 75pm to 250pm; and most desirable that the filter thickness be in the range of 100pm to 150pm. A low level vacuum 2417 is applied to remove the fluids through the filter as the droplets 33 are 40 collected. It is important to use a low level vacuum (less than 20 inches of mercury, e.g., 15 112 inches of mercury) to avoid inflicting damage to the sperm cells. In one embodiment the vacuum is low enough that the fluid removal rate is about 1.0 ml/1 5 seconds. According to another embodiment of the present invention, the vacuum is applied intermittently to allow the sperm cells a chance to recover. In still another embodiment, the filter 2415 is constructed of a material 5 that is compatible with sperm cells, yet has no binding affinity for them. At the completion of the sort, about 80-90% of the fluids will have been removed through the filter. However, enough fluid remains (about 10-20%) that the sperm cells are in a concentrated slurry 2405, thereby preventing the sperm cells from forming a filter cake. The concentrated suspension may be transferred to another container 2419, as shown in Fig. 97 for example. A syringe mechanism 10 2409 with a cannula-tip filter 2411 can be used to remove some of the remaining liquid from this container 2419. However, enough fluids are left in the container to prevent the sperm cells from caking on the filter 2411. The same considerations apply to the cannula tip filter 2411 as the filter 2415 in the collection vessel. Thus, the cannula filter 2411 pore size is desirably in the range of about 0.2 - 1.0 microns and the cannula filter is relatively thin to avoid having sperm 15 tails getting caught in tortuous passages in the filter. For example, a DynaGard@ hollow polypropylene fiber syringe tip filter, which is commercially available from Spectrum Laboratories, Inc. of Rancho Dominguez, CA may be used for the cannula tip filter. As shown in Fig. 98, a resuspension fluid 2413 is flushed through the cannula-tip filter to-wash cells that may be sticking to the filter surface back into the slurry. The resuspension fluid may include a quantity of the 20 filtered fluid and/or a suitable extender. After a quantity of resuspension fluid sufficient to remove sperm cells from the filter has been back flushed through the filter, additional resuspension fluid may be added if desired. The total quantity of resuspension fluid is selected to bring the concentration to a desired concentration (e.g., about 20 x 106 sperm cells/ml). Thus, the filtration process of this embodiment is a three-step process involving the use of a filter in the collection 25 vessel, filtration using a cannula filter, and resuspension to obtain the desired concentration. In an alternative two-step filtration process, the first and second steps of the three-step process described above are combined so that removal of all fluid is through a cannula filter. In this process the sorted sperm cells are directed to a collection vessel that does not have a filter. The fluids are removed by low vacuum and/or intermittent vacuum as described above that is 30 applied through the cannula-tip filter 2411. When the sperm cells are in a concentrated slurry, a resuspension fluid, such as for example, an extender, is flushed back through the cannula filter to obtain the desired concentration of sperm cells. Filtration Example / 35 Filtration example I shows the recovery rate and motility of sperm cells after concentration by a three-step filtration process of the present invention. Semen samples were collected from three bulls and evaluated as provided in the sample preparation section above. One of the three semen samples was disqualified for failing to meet minimum initial quality criteria. Two remaining samples were diluted with a quantity of TCA (pH 7.3) necessary to attain 40 a concentration of 150 x 106 sperm cells/ml. Five hundred ul PBS with 10% egg yolk and 9.5 ml 113 PBS with 0.1% BSA was added to each of two 15 ml test tubes. Sixty-seven ul of semen sample (about 10 x 10 sperm cells) was added to each test tube and incubated for twenty minutes at room temperature. Referring to Fig. 99, a vacuum pump 2427 was used to apply negative pressure to draw a four ml aliquot of the diluted semen 2423 through a filter 2425. The filtrate 5 2429 was collected in a syringe 2421. After filtration sperm cells on the filter were flushed back with 1 ml TCA buffer in a 15 ml tube. Sperm motility was assessed visually. Pre- and post filtration samples were mixed with a fixative (0.1 % glutardehyde in 3.4 Na citrate) to immobilize the sperm cells. Sperm concentration was determined using a hemacytometer. Total number of sperm cells was calculated on the basis of volume multiplied by the concentration of sperm cells. 10 The recovery rate was calculated as the total number of sperm cells in the flushed back portion divided by the total number of sperm cells in the aliquot prior to filtration. The process was repeated with a different filter. The experiment tested both of the following filters: (1) a 1.0 pm PTFE (not FTPE) membrane disc (syringe) filter (which is available from Pall Corporation, Life Science Group, Ann Arbor, MI, Cat # PN4226T or VWR, Batavia, IL, Cat. # 28143-928); and (2) 15 0.8 SFCA (surfactant free cellulose acetate) membrane disc (syringe) filter (Corning, Inc., Corning, NY, Cat. # 431221; VWR Batavia, IL, Cat. # 28200-028). The results are shown in Fig. 101. More spermatozoa were recovered with cellulose acetate filters as compared to PTFE filter, i.e. 67 vs 33% due to low protein binding affinity of cellulose acetate. Visual motility of spermatozoa recovered ranged from 63% (PTFE) to 68% (Cellulose acetate). 20 Filtration Example |I Filtration example il shows the recovery rate and motility of sperm cells after concentration by at two-step filtration process of the present invention. Semen samples were collected from three bulls and evaluated as provided in the sample preparation section above. 25 The three samples were diluted with a quantity of TCA (pH 7.3) necessary to attain a concentration of 150 x 106 sperm cells/ml. One and one half ml of PBS with 10% egg yolk and 28.3 ml PBS with 0.1% BSA was added to each of 50 test tubes. Two hundred pl of semen sample (about 30 x 10r sperm cells) was added to each test tube and incubated for twenty minutes at room temperature. Referring to Fig. 100, a syringe 2431 was used to apply negative 30 pressure to draw a 6 ml aliquot of the diluted semen 2433 from each test tube through a filter 2435. The filter was placed in a filter holder 2437 (a Swinnex filter holder from Millipore Corporation, Billerica, MA Cat # SX0002500,). After filtration, the filtration holder 2437 was disconnected from the syringe and the tubing, keeping the filter holder intact. Spermatozoa on the filter were collected by turning the filter assembly upside down and back flushing 1 with ml of 35 TCA buffer using a 3 ml syringe having a small piece of tubing at the tip in a 15 ml test tube. Sperm motility was assessed visually. Pre- and post- filtration samples were mixed with a fixative (0.1 % glutardehyde in 3.4 Na citrate) to immobilize the sperm cells. Sperm concentration was determined using a hemacytometer. Total number of sperm cells and the recovery rate were calculated as specified in Filtration example 1. The process was repeated 40 twice to test different filters. The experiment tested both of the following filters: (1) a 0.2 pm 114 Teflon membrane filter (which is available from X-Partek, P.J Cobert Associates Inc. St. Louis Cat. # 944106; and (2) a 0.8 cellulose acetate membrane filter (Millipore Corporation, Billerica, MA Cat. #AAWP 02500). The results are shown in Fig. 102. In both filters, the recovery rate of spermatozoa was low(-25%). It was low in Teflon filter as in example 1. However, low recovery 5 rate and visual motility of flushed back spermatozoa in cellulose acetate filter might be due to the material used by different vendor and/or ability of spermatozoa to attach with filter holder/assembly. D. Dense Medium Concentration 10 Another alternative method of concentrating the collected sperm relies on flotation of sperm cells in a high-density medium. According to this method, a high-density medium is added to the collected sperm cells to raise the specific gravity of the suspension above about 1.3. For example, a colloidal silica suspension such as is available under the Percoll@ and Isolate@ tradenames may be used to increase the specific gravity of the suspension. The sperm cells will 15 float to the top of the suspension, where they can be skimmed or otherwise collected, because of the increased specific gravity of the suspension. A resuspension fluid is added to the cells that have been collected from the surface to bring the final concentration to about 20 x 106 sperm cells/ml. Some of the suspension fluid may be removed by one of the filtration methods described above prior to addition of the high density medium to reduce the quantity of high 20 density medium required to attain the desired specific gravity. Cryoextension A. Cryoprotection Once the sperm have been sorted and collected in the collection vessels, they may be 25 used for inseminating female mammals. This can occur almost Immediately, requiring little additional treatment of the sperm. Likewise, the sperm may also be cooled or frozen for use at a later date. In such instances, the sperm may benefit from additional treatment to minimize the impact upon viability or post-thaw motility as a result of cooling and freezing. Generally, a cryoextender comprises a buffer or buffered solution, a protein source, and 30 a cryoprotectant. Examples of buffers and buffered solutions that may be used in the cryoextender are disclosed above with respect to sample collection and extension. Typically, these buffers will be in a concentration of about 0.001M to about 1.0M and have a pH of about 4.5 to about 8.5, preferably of about 7.0. If included, a protein source may be added to provide support to the cells and to cushion 35 the contact of the cells with the collection vessel. The protein source may be any protein source that does not interfere with the viability of the sperm cells and is compatible with the particular buffer or buffered solution being used. Examples of common protein sources include milk (including heat homogenized and skim), milk extract, egg yolk, egg yolk extract, soy protein and soy protein extract. Such proteins may be found in a concentration from about 10% (v/v) to 40 about 30% (v/v), preferably from about 10% (vlv) to about 20% (v/v), and more preferably about 115 20% (v/v). While milk may be used in combination with a buffer or buffered solution, generally milk is used in the absence of the same, as milk is a solution itself that may serve the same purpose of a buffer or buffered solution. In such instances, the cryoextender would contain about 80% (v/v) to about 90% (v/v) milk. 5 A cryoprotectant is preferably included in the cryoextender to lessen or prevent cold shock or to maintain fertility of the sperm. Numerous cryoprotectants are known in the art. Selection of a cryoprotectant suitable for use with a given extender may vary, and depends upon the species from which the sperm to be frozen were obtained. Examples of suitable cryoprotectants include, for example, glycerol, dimethyl sulfoxide, ethylene glycol, propylene 10 glycol, trehalose, Triladyl" and combinations thereof. If included, generally, these cryoprotectants are present in the cryoextender in an amount of about 1% (v/v) to about 15% (v/v), preferably In an amount of about 5% (v/v) to about 10% (v/v), more preferably in an amount of about 7% (v/v), and most preferably in an amount of about 6% (v/v). In one particular embodiment, the cryoextender comprises water, Triladyl, egg yolk, and 15 pyruvic acid. In yet another embodiment, the cryoextender comprises 25g Triladyl*, 25g egg yolk, and 10mM pyruvic acid in 75mL of water. Optionally, the cryoextender may also contain a range of additives that are beneficial to sperm viability or motility and that prevent or lessen the detrimental side effects of cryopreservation. Such additives may include, for example, an energy source, an antibiotic, or a 20 composition which regulates oxidation/reduction reactions intracellularly and/or extracellularly, each of which is discussed above with respect to sample collection and dilution. Such additives may be added to the cryoextender in accordance therewith. B. Cryopreservation of Sorted Sperm Cells 25 In most cases, it will not be possible to use the sperm cells that have been sorted as described above for immediate artificial insemination. Particularly in the case of a commercial sperm sorting operation, the sorted sperm cells must be stored and/or transported before they can be used for artificial insemination. This will usually require cryopreservation of the sperm cells. The sorted sperm may be loaded into elongate cylinders (known as "straws" in the 30 breeding industry) and cryopreserved to preserve the sperm during transportation and storage. Cryopreserved sperm cells can be stored for long periods of time in liquid nitrogen. To use the cryopreserved sperm, the straw may be Immersed in a heated water bath to thaw the sperm. Then the straw is loaded into an artificial insemination gun which is used to inseminate a female animal. Several precautions must be taken to protect the sperm cells during cryopreservation. 35 Otherwise the sperm cells will be so damaged (as indicated by a low post-thaw motility rate of 5 10%) that they are not suitable for use in artificial insemination. Conventional cryopreservation methods involve sequentially adding a protein source (e.g., egg yolk), cooling the sperm to a temperature of about 4 - 50C, adding a cryoprotectant (e.g., glycerol), maintaining the sperm and cryoprotectant at a steady temperature in the range of 40 about 4 - 5'C for a period of time sufficient to allow the sperm cells to equilibrate with the 116 cryoprotectant, and then supercooling the sperm, as by immersing the sperm cells in liquid nitrogen at -196 *C for storage. Those skilled in the art will recognize that the purpose of the protein source is to protect sperm from damage as they cool from about 14*C to about 8 0 C, which is the temperature at which sperm cells are most susceptible to cold shock. In contrast, 5 the cryoprotectant protects the sperm cells from damage at temperatures below 0*C. Even though the temperatures involved in cryopreservation are well below freezing and the term "freezing" is sometimes used to describe cryopreservation, those skilled in the art will also know that cryopreserved sperm are not actually frozen. To be precise, the cryopreserved sperm are in a supercooled state. The conventional period during which sperm cells and cryoprotectant are 10 maintained at a steady temperature can last anywhere from 60 minutes to many hours. The overall time to complete cryopreservation using conventional methods generally exceeds four hours. Furthermore, it is believed that up to 50% of the sperm cells are killed in conventional cryopreservation processes. Though sperm are cryopreserved using conventional methods according to some embodiments of the present invention, other embodiments of the present 15 Invention employ Improved cryopreservation methods to reduce the time required for cryopreservation and/or to improve the health of the cryopreserved sperm. Fig. 103 shows a work flow diagram outlining the steps of one exemplary embodiment of an improved method of cryopreserving sperm according to the present invention. At step 2501, the concentration of a solution containing sorted sperm cells is adjusted to be in the range of 20 about 1 million - 40 million sperm/ml, depending on the standard used by the targeted consumer (e.g., breeding association). For example, the sperm concentration may be adjusted to be in the range of about 20 million to 24 million sperm/ml. Adjustment of the sperm concentration may include addition of resuspension fluid, buffers and/or extenders to concentrated sperm as described above. At step 2503, a cryoprotectant (e.g., glycerol) is added before the sperm are 25 cooled. The sperm cells begin equilibrating with the cryoprotectant as soon as they come into contact with the cryoprotectant. At step 2505, a protein source (e.g., egg yolk) is also added to the solution containing the sperm cells as described above. The sperm cell solution, protein source, and cryoprotectant are loaded into conventional 0.5 or 0.25 ml artificial insemination straws using a conventional loading machine at step 2507. 30 Those skilled in the art will be familiar with a number of conventional apparatus and techniques that may be used to load semen into straws. For example, United States Patent No. 5,249,610, issued October 5, 1993 to Cassou, et al. and incorporated herein by reference, provides instruction about the filling of straws with bovine semen using a disposable injector nozzle. Moreover, equipment for filling straws is commercially available from Minitube of America, 35 located in Verona WI. Any of these or similar conventional loading methods and apparatus can be used to load the sorted sperm cells Into straws. After loading, the sperm cells are cooled to a holding temperature at step 2509. In general, the holding temperature should be selected with the following considerations in mind: holding sperm cells at a temperature that is too high (e.g., 10'C) may cause unnecessary 40 damage from cold shock; equilibration of sperm cells with a cryoprotectant (e.g., glycerol) is 117 believed to be most active at temperatures in the range of 4-5 0 C; and holding sperm cells at temperatures that are too low (e.g., < 0*) is believed to be damaging to the sperm cells. Thus, according to one embodiment, the holding temperature is in the range of 0-8 0 C. More desirable, the holding temperature is in the range of 2-6 0 C. Even more desirably, the holding temperature 5 is in the range of 4-5'C. In another embodiment, the cooling rate used for this step 2509 is selected to minimize damage to the sperm cells. For example, the cooling rate may be controlled (e.g., substantially constant) to provide homogenous cooling and to prevent the sperm from suffering temperature shock. The cooling rate should also cool the sperm quickly enough to reduce their metabolism before they incur membrane damage, but slowly enough that they do 10 not suffer from temperature shock. One can control the cooling rate by placing the straws containing the sperm cells in a programmable freezer (e.g., an IceCube 1810CD freezer which is available commercially from Minitube of America, located in Verona, WI) to cool them. According to one embodiment, the programmable freezer cools the sperm from about room temperature (typically in the range of about 22 and 24*C) at a constant cooling rate of 0.1 and 0.3 *C/ minute. 15 More desirably, the cooling rate is in a range of about 0.15 and 0.25 *C/min. Even more desirably, the cooling rate is about 0.2 *C/min. In another embodiment, the cooling rate is selected so the sperm are cooled from their initial temperature to the holding temperature in about 90 minutes. In still another embodiment, the cooling rate is selected to cool the sperm from their initial temperature to the holding temperature at a constant cooling rate in about 90 20 minutes. The cooling rates referred to above actually refer to the rate of the cooling of the chamber of the programmable freezer, but because of the thin walls and long, thin shape of the straw (e.g., about 5.25 inches long, less than 3 mm in diameter, and about 0.15 mm in wall thickness) and the conductive properties of the straw, the temperature difference between the sperm cells and the cooling chamber Is not significant. 25 After the sperm cells have been cooled to the holding temperature, at step 2511 they are kept at or near that temperature for a period to allow substantial completion of their equilibration with the cryoprotectant. For example, the programmable freezer described above can be programmed to hold the sperm cells at a steady temperature during the period. According to another embodiment of the present Invention, the sperm cells are held at the holding temperature 30 for a period that is shortened compared to conventional methods because the sperm have already been equilibrating with the cryoprotectant during the cooling process. For example, the period may be in the range of about 10 and 60 minutes. More desirably, the period Is in the range of about 20 and 40 minutes. Even more desirably, the period is about 30 minutes. In another embodiment the period is less than 60 minutes. In yet another embodiment, the period 35 is less than 40 minutes. The relatively short holding period offers a number of advantages in a commercial sperm sorting process. First, It reduces the time required to process sorted sperm which can translate to cost savings. Also, the sperm cells still perform metabolic processes at temperatures in the range of 0-8*C so reducing the time for which sperm need to held at this temperature can improve the health of the sperm cells, which will increase the value of the sperm 40 cells to animal breeders who are concerned about artificial insemination success rates.

118 After the sperm cells have been held at the holding temperature for a period described above, the sperm cells are cooled at step 2513 to a temperature that approaches the critical temperature zone for sperm cryopreservation. Those skilled in the art will know that the critical temperature zone is the zone at which ice crystal formation and changes in osmotic pressure 5 damage the sperm cells. This temperature may vary depending on the solution in which the sperm cells are cryopreserved, but the critical temperature zone is generally in the range of -18 and -35*C. Sometimes this critical temperature zone is reported to be in the range of about -18 and -30*C. Thus, according to yet another embodiment of the present invention, the cooling rate used to cool the sperm cells from the holding temperature to a temperature that approaches 10 18 0 C (e.g., -15*C) is selected to protect the health of the sperm. Relevant factors to consider include that fact that the sperm cells are still equilibrating with the cryoprotectant during this period, the fact that sperm are still performing some metabolic functions, and the fact that the sperm are still somewhat sensitive to rapid temperature change. Again, it is desirable that the cooling rate be a controlled rate, such as a rate that may be programmed into the programmable 15 freezer described above. More desirably, the cooling rate used to cool the sperm from the holding temperature to a temperature that approaches about -1 8 0 C is a constant cooling rate. Thus, according to another embodiment of the present invention, the sperm cells are cooled from the holding temperature to about -1 5C at a cooling rate in the range of about 1.0 - 5.0 *C/ min. More desirably, the cooling rate is in the range of about 2.0 - 4.0 *C/min. Even more desirably, 20 the cooling rate is about 3.0 *C/min. Step 2515 involves rapidly cooling the sperm cells through the critical temperature zone to limit the time sperm cells dwell therein. Thus, according to one embodiment of the present invention, the cooling rate through the critical temperature zone about (e.g., -18OC to about 30*C) is selected to be much faster than the cooling rate used to cool sperm cells to the holding 25 temperature and the cooling rate used to cool sperm cells to the temperature approaching the critical temperature zone. Thus, the steeper cooling rate is desirably in the range of from about 8 - 40*C per minute. More desirably, the steeper cooling rate is in the range of from about 8 - 12'C per minute. Most desirably, the steeper cooling rate is about 10*C per minute. The temperature range over which the steeper cooling rate is used may extend beyond the critical temperature 30 zone. Thus, in yet another embodiment of the present invention, the sperm cells are cooled at one of the steeper cooling rates described above from about -1 5*C to about -40 0 C. In still another embodiment, the sperm cells are cooled at one of the steeper cooling rates described above from about -1 5'C to about -80 0 C. The step of cooling the sperm through the critical temperature zone at a steeper rate may be accomplished in the programmable freezer described 35 above. After the sperm cells have been cooled below the critical temperature zone (e.g., to 80 0 C), the straws containing the sorted sperm are immersed in liquid nitrogen (-196*C) at step 2517 to provide maximum useful life of the sorted sperm cells. The use of liquid nitrogen to store cryopreserved sperm is widespread in the animal breeding industry in the context of unsorted 40 sperm. Thus, those skilled in the art will be familiar with technologies involving the transportation 119 and storage of sperm in liquid nitrogen, which need not be discussed in great detail herein. It is sufficient to note that conventional containers are available to provide for long term storage of bulk quantities of artificial insemination straws in liquid nitrogen and that smaller and more portable containers are also available for providing storage of artificial insemination straws in 5 liquid nitrogen for transport to customers and/or for transport to a farm having one or more female animals to be inseminated with cryopreserved sperm. One advantage of the cryopreservation methods described herein is that the cryopreservation can be completed in less time than is required according to conventional methods. Perhaps relatedly, the decline in motility due to cryopreservation according to the 10 present invention is only about 5-11%, as indicated by the example discussed below. Thus, cryopreservation according to the present invention preserves the health of the sperm cells as indicated by tests showing that sperm cells cryopreserved according to the present invention have greater than 50% (e.g., about 60%) motility after they are thawed in a 37*C water bath for about 50 seconds. As discussed above, sperm motility may be analyzed by an automatic 15 machine (e.g., the IVOS sperm analyzer from Hamilton Thorn Research) or by visual examination. It should be noted that the cryopreservation methods described above are contemplated as being used in a commercial scale sperm sorting process. Thus, according to one embodiment of the present invention, the steps of the inventive methods described herein are 20 performed simultaneously on a batch of sorted sperm cells to quickly cryopreserve the entire batch of sperm cells in a manner that preserves their health. For example, by using the multi channel flow cytometry apparatus described below, it is possible to obtain about 840 x 106 sorted X chromosome-bearing sperm cells in the collection system of the apparatus in about 20 minutes. This is enough sperm cells to fill several dozen straws. Moreover, a batch can include 25 the combined sperm cells by two or more different sorting cytometers. After being concentrated as described above, the sperm cells can be loaded into any number of straws and cryopreserved as a batch. For example, according to one embodiment of the invention, it takes about 5 minutes to add an extender (including both a protein source and a cryoprotectant) to a batch of sperm cells, and about 15 minutes to load the sperm cells into artificial insemination straws using an 30 automatic loading machine. All the straws in the batch are cooled simultaneously in a programmable freezer. Furthermore, the capacity of some programmable freezers allows simultaneous cryopreservation of thousands of artificial insemination straws. For example, the IceCube 1810CD freezer referred to above has the capacity to cryopreserve simultaneously over 2,500 0.5 ml straws or over 3,800 0.25 ml straws. Thus, one could wait to start the cooling step 35 until multiple batches have been obtained. Alternatively, multiple batches could be obtained substantially at the same time by running multiple multi-channel flow cytometry machines (see below) in parallel and simultaneously cooling multiple batches obtained therefrom together in a programmable freezer. In one embodiment of the present invention, it takes a period of less than 220 minutes to cool the sperm cells from room temperature to a supercooled state and immerse 120 them in liquid nitrogen (-1 96*C). In another embodiment, the supercooling period is less than 190 minutes. In still another embodiment, the supercooling period is less than 150 minutes. Those skilled in the art will recognize that substantial modifications may be made to the foregoing exemplary methods without departing from the scope of the present invention. For 5 example, the sperm cells may be cryopreserved in a container other than an artificial insemination straw. Likewise, the steps in the method that involve changing or maintaining temperature may be performed by any suitable means, including water baths, liquid nitrogen vapors, and conventional programmable or non-programmable freezers, for example. Furthermore, a wide variety of substances or combinations of substances could be used as the 10 protein source and/or the cryoprotectant without departing from the scope of the present invention. These substances include substances and concentrations of substances listed above in connection with the discussions regarding buffers, extenders, cryoprotectants, sheath fluids, and collection fluids. Moreover, the order of some steps in the method may be varied without departing from the scope of this invention. Although Fig. 95 indicates that the cryoprotectant is 15 added after the concentration of the sorted sperm is adjusted, it is also contemplated that a cryoprotectant can be added before the concentration is adjusted without departing from the scope of the present invention. For example, the cryoprotectant may be provided in the collection fluid or in the sheath fluid used in connection with a flow cytometer. Some of the benefits of the present invention may also be obtained by partially cooling the sperm cells and 20 then adding the cryoprotectant. Likewise, the order in which the protein source is added may be varied as long as the protein source is effective to protect the sperm cells from cold shock as they pass through the temperature range of about 14 to 80C. Cryopreservation Example I 25 Bovine semen was collected, transported, and evaluated as described above. Two test tubes containing 5 ml each of TCA buffer (pH 7.3) were placed in one of two water baths for at least five minutes. One water bath was at a temperature of 350C and the other water bath was at 41 C. Spermatozoa at 24"C were added to each tube so that the final concentration in each tube was 150 x 10" sperm/ml. The two tubes were each divided into two aliquots which were 30 kept in respective water baths. After the sperm had equilibrated with the TCA buffer for five minutes, 80 pM Hoechst 33342 was added to one of 350C aliquots and one of the 41*C aliquots. After addition of the Hoechst 33342, all four aliquots were incubated for 20 minutes in their respective water bath. After incubation, the test tubes were removed from the water baths and left at room temperature (about 25*C) for five minutes. Then the contents of each test tube were 35 diluted with a TCA extender containing 20% egg yolk and 6% glycerol (v/v) (pH 7.0) to a final concentration of 20 x 106 sperm/mi. The contents of each test tube were then used to fill a 0.5 mi artificial insemination straw. Each of the four straws was placed in a programmable freezer (an IceCube 1810CD freezer from Minitube of America, WI). The following cooling sequence was programmed Into the programmable freezer: (1) 220C to 4*C @ -0.2 *C/min; (2) hold at 40C 40 for 30 min; (3) 4*C to -150C @ -3.0 *C/min; and (4) -15 *C to -80 "C @ -10.0 *C/min. After 121 reaching -80 *C, the straws were immersed in liquid nitrogen (-1 96 0 C) for 45 minutes. Then the straws were immersed in a 37'C water bath for 50 seconds to thaw. Sperm motility was checked under a phase contrast microscope both before and after cryopreservation. The results are shown in Fig. 104. The post-thaw motility was generally on the order of 60%. This represents a 5 decline in motility of only about 5-11% compared to before cryopreservation. Analysis of variance revealed no significant effect of either Hoechst 33342 or incubation at 41 C on post thaw sperm motility. Operation of the System 10 The overall operation 813 of the flow cytometry system 9 will now be described with reference to Fig. 82 and in the specific context of sperm cells (e.g., bovine sperm cells), but it will be understood that the description is exemplary only, and that the system can be used to process other types of particles. The first series of steps leading up to the six second repeat loop involve calibration of the 15 system. After initializing 769, a system check 771 is performed to confirm, among other things, that the processor 131 or processors are operational. If an error is detected after three failed system checks 775, user interaction 773 is requested. If the system check is positive, the microprocessor directs the system to flush 777 the nozzle system with a suitable fluid, and then a quality control material 779, such as beads or bovine nuclei, are run through the system to 20 initialize the detection parameters (see 739 in Fig. 72) and confirm that the system is operating within an acceptable quality control. This involves an evaluation of the control material to test the sensitivity and precision of the system to confirm that the system can adequately discriminate a sample. If the quality control is not confirmed after three attempts 775, user intervention 773 is requested. 25 If the quality control material indicates an acceptable level of quality control, a sample 781 is aspirated and a portion or aliquot of the sample to be sorted is checked for quality 783. Sample quality may be determined by a calculation of a quality factor (Q-factor) of the sample. For example, the type of cells may be detected in a first aliquot of the sample. During this detection, the initialized detection parameters (741) are rechecked and the initial discrimination 30 parameters (745) are generated. If the type of cells detected in the aliquot indicates that the sample meets or exceeds a preset standard (e.g., that the sample can be discriminated to yield a certain purity or motility and, in particular, that there are sufficient live X cells available for processing), then the system continues operation. If sample quality fails three times 775, user interaction is requested. 35 Continued operation involves sorting 785 of the remainder of the sample employing a six second repeated loop. At the beginning of the loop, the microprocessor confirms that sorting of the sample is not complete 789. If the sorting of the sample is complete 789, the microprocessor proceeds to aspirate the next sample 781 if it is available or to turn off the sorting operation 793 if additional sample is not available. If the sample is not complete 789, the microprocessor initially 40 checks the X/Y discrimination 795 of the sample to confirm that it is within an optimum range. In 122 other words, drift analysis as noted above (761 in Fig. 72) is conducted. If any changes should be made, such changes are implemented and the discrimination 795 is again checked. If the discrimination is still unacceptable at this point, the sort is turned off 793 and user interaction is requested. 5 Otherwise, the system proceeds to determine whether the fluid delivery system Is delivering fluid and cells at a rate which is within an optimum range 801. This determination depends on the type of control strategy used. For the high recovery control strategy, the optimum rate would be determined by evaluating purity or looking at X/x+-X of the collected population. If the determined purity is higher than a required purity level, the feed input rate of 10 the cells is increased by increasing a rate control signal provided to the syringe pump 803. This would tend to increase coincident cells and decrease purity because more coincident cells including -X cells would be collected with the X cells. If the determined purity is lower than the required purity, the feed input rate of the cells is decreased by decreasing a rate control signal provided to the syringe pump to reduce the frequency of coincident cells 803. Thus, the cell 15 input rate is a function of the determined purity of the collected population as compared to a desired purity level, e.g., a function of the identified -X sperm cells collected. For the high purity control strategy, the optimum rate would be determined by calculating lost X cells, e.g., discarded X/ discarded X + collected X. If the quantity or percentage of lost X cells are less than an acceptable level, the input rate of the cells is increased by increasing a rate 20 control signal provided to the syringe pump 803. This would tend to increase coincident cells and increase the number of discarded X cells because more cells including X cells would be discarded with the Y cells. If the quantity or percentage of lost X cells is higher than the acceptable level, the input rate of the cells is decreased by decreasing a rate control signal provided to the syringe pump 803 to decrease coincident cells. Thus, the cell input rate is a 25 function of the determined lost X cells of the discarded population as compared to number of X cells in the collected population, e.g., a function of the number of X sperm cells not collected. If this modified rate is acceptable 805, the system proceeds to another system check 807. If the system check is acceptable 807, the sort continues in the six second loop. If not, the system is reset 809. If after reset the system is not acceptable or if the revised feed rate is not 30 acceptable 811, the sort is tumed off 793 and user intervention is requested 773. The sorted droplet streams are collected by the collection system 2201. Droplets that are sorted into the population of X cells pass through the exit window 2245 in the first intercepting device 2247 to be intercepted by the second intercepting device 2249. From there, the droplets containing the X cells flow into a collection vessel 2207. Other droplets are 35 Intercepted by the first intercepting device 2247 and directed to the waste trough 2805. Of course droplets intercepted by the first intercepting device could also be saved, as noted above. When a suitable amount of X-bearing sperm cells have been collected in the collection vessel, sorting may be interrupted to allow concentration of sperm cells in the collection vessel 2207. A new collection vessel may be placed under the first intercepting device 2247 or the collected fluid 40 may be poured into a different container and the collection vessel replaced. Then sorting may 123 resume. The sperm cells in the collected fluid are concentrated, loaded in straws, and frozen as described above. Temperature Control During Operation 5 Temperature control throughout the process may be used to improve the results of the process. As has already been discussed above, the temperature of the sperm may be controlled during various steps in the process (e.g., staining and cryopreservation). In several embodiments of this invention, the temperatures of the sperm cells throughout the various steps of the method are controlled to achieve improved results. 10 For example, Fig. 105 is a work flow diagram of one embodiment of a method of temperature control according to the present invention. The temperature of semen samples at the time they are collected will be determined by the body temperature of the animal from which they are collected. For example, at step 2601 bovine semen samples are collected at about 37 0 C. An insulated container is used for transportation of the semen samples to the lab from the 15 collection site at step 2603. The insulated container retards cooling of the sperm. During sample evaluation at step 2605, the temperature is maintained below the collection temperature, but in excess of a temperature corresponding to a glass transition temperature below which the sperm cells suffer membrane damage. For example the temperature may be maintained in the range of about 18 - 37 C. In another embodiment, the 20 temperature may be maintained in the range of about 24 - 37*C during sample evaluation. In a particular embodiment, the sperm cells are placed In an environment having a temperature in the range of about 22 - 25*C during sample evaluation. Depending on the temperature of the sperm upon arrival at the lab, the effect of placing them in an environment having a temperature in the range of about 22 - 25 0 C may be to continue slow cooling of the sperm, to maintain the 25 temperature of the sperm, or to slightly raise the temperature of the sperm. In one embodiment, the temperature may be elevated (e.g., to 400C or higher) for staining at step 2607 as discussed in the staining section. In another embodiment, the temperature of the sperm cells during the staining step may be in the range of about 20-40*C, as is also discussed above. At step 2609, the stained semen mixture is held in a water bath until such time that the 30 mixture is introduced into a flow cytometer. The temperature of the water bath may be similar to the temperature used for the staining step. In one embodiment the temperature of the water bath is in the range of about 40 - 47*C. In another embodiment, the temperature of the water bath is in the range of about 20 - 37*C. In still another embodiment, the temperature of the water bath is in the range of about 20 - 250C. After being held in the water bath for any time between one 35 minute and two hours, the stained sperms cells are sorted by flow cytometry as discussed above at step 2611. At step 2613, the collected sperm cells are concentrated. Concentration may be performed in an environment that has a temperature that will not significantly change the temperature of the sperm cells. For example, in one embodiment, concentration may be performed in an environment having a temperature in the range of about 20 and 25*C. An 40 extender, protein source, and cryoprotectant are added to the concentrated sperm at step 2615.

124 Then, at step 2617 the sperm cells are loaded into artificial insemination straws. In one embodiment, the loading step is performed in an environment having a temperature that will not significantly change the temperature of the sperm cells. Finally, at step 2619 the temperature of the sperm is controlled during cryopreservation as discussed above. 5 In another embodiment, sperm cells may be stained at still lower temperatures without departing from the scope of the present invention. For example, it may be desired to sort the sperm cells in a flow cytometer at a relatively low temperature (e.g., about 0 0 C to about 8 0 C). This may require modification of the overall temperature control. First, when cooling the sperm cells prior to introduction into a flow cytometer, egg yolk and other common protein sources that 10 protect the sperm cells from cold shock at temperatures below the glass transition temperature generally may not be used as such protein-containing substances tend to foul and/or clog the fluidics of the flow cytometer. Thus, it is desirable to cool the sperm cells before performing the staining step in order to take advantage of natural cold shock protectants found in neat semen, such as for example, the seminal fluid. Any attempt to stain the sperm cells prior to cooling 15 would require addition of buffers to protect the sperm which would dilute the neat semen and reduce the natural protection against cold shock. Accordingly, one embodiment of the present invention for sorting the sperm cells at a temperature in the range of about 00C to about 80C includes placing the sperm cells in an environment having a temperature less than about 80C to cool the sperm cells to a temperature 20 in the range of about 0*C to about 8"C prior to staining. Any method may be used to cool the sperm cells, but it is desirable to use a method that protects against rapid temperature fluctuations of the sperm cells during the cooling process. For example, in one embodiment, a container holding the sperm cells is placed in a room temperature water bath, which in turn is placed In an environment having a temperature less than about 8 0 C. In another embodiment, the 25 temperature of the sperm cells is monitored and ice is added to the water bath to further cool the sperm cells. The staining step may be performed as described above except that the staining mixture is subjected to a temperature in the range of about 0*C to about 8*C. Due to the lower temperature, the incubation period required to stain the cells is considerably longer. Once the sperm cells have been cooled to 8*C or below, it is desirable to avoid warming them. Thus, 30 another embodiment of the present invention is to operate the flow cytometer in an environment having a temperature in the range of about 00C to about 8*C. Similarly, another embodiment of the present invention is to collect the sorted sperm cells in a collection vessel that is surrounded by an environment having a temperature in the range of about 00C to about 80C. Still another embodiment of the present invention is to add any extenders, cryoprotectants, buffers, protein 35 sources, antibiotics, antioxidants, or other additives at a temperature in the range of about 0*C to about 80C. With respect to addition of the cryoprotectant, it may be desirable to add slightly more of the cryoprotectant than would be added absent sorting the sperm cells at a temperature in the range of about O'C to about 8 0 C. Thus, in one particular embodiment, a cryoprotectant containing 7% glycerol (v/v) is added to sperm cells after the sperm cells have been sorted at a 40 temperature in the range of about 00C to about 8*C.

125 Supercooling of the sperm cells from the temperature in the range of about 0*C to about 8'C proceeds generally as described in the cryopreservation section above. However the sperm cells will need to be held at a temperature in the range of about O'C to about 8'C for a period of time after addition of the cryoprotectant before supercooling to allow time for the sperm cells to 5 equilibrate with the cryoprotectant. Thus, according to one embodiment, the sperm cells are allowed to equilibrate with the cryoprotectant for a period in the range of about 30 minutes to about 3 hours. In another embodiment, the sperm cells are allowed to equilibrate with the cryoprotectant for a period in the range of 1 -2 hours. In another particular embodiment, the sperm cells are allowed to equilibrate with the cryoprotectant for a period of about 90 minutes. col C onventional temperature control apparatus and methods (e.g., water baths, incubators, coolers, and freezers) may be used to heat or cool the sample to attain or maintain the specified temperatures in the foregoing embodiments of the invention. It is understood that placing a sample In an environment having a different temperature than the sample, will cause the temperature of the sample to change over time. There may even be temperature variations 15 within the sample. As has been mentioned, it is desirable to change the temperature of the sample gradually to help maintain the health of the sperm. Gradual temperature change also serves to reduce the temperature variation within the sample. As is well known by those skilled in the art, the rate of temperature change of the sample will be Influenced by many factors, including the volume of the sample, the size and shape of the sample container, and the 20 magnitude of the temperature difference between the sample and the environment. However, those skilled in the art will readily be able to select an appropriate method and apparatus to achieve the desired temperature control after considering all the relevant factors. Those skilled in the art will recognize that there is room for substantial variation in the exemplary temperature control without departing from the scope of the invention. In general, 25 once the sperm cells have been chilled, it is desirable to avoid warming them. Furthermore, temperature variations discussed above in connection with sample collection, staining, sorting, droplet collection, concentration and cryopreservation can be incorporated into the overall temperature control without departing from the scope of the present invention. Moreover, the time at which sperm cells remain at any temperature can also impact the health of the sperm. 30 Thus, processing according to the embodiment in which temperature Is controlled throughout the process is desirably completed within a timeline as discussed below. Tiel!e for.Oeration Generally, it is desirable to complete the sperm sorting process in the least amount of 35 time possible to reduce the damage to the sperm. As discussed above, the present invention may include staining at an elevated temperature to reduce the time needed to stain the sperm cells. For example, certain embodiments of the improved staining method described reduce the time require for staining to about 10 minutes. Likewise, the novel cytometer described above may be used to sort sperm cells in less time than would be required by a conventional cytometer. 40 For example, a flow cytometer using the technology discussed above can collect between 2,000 126 and 10,000 sperm cells having a desired DNA characteristic per second. Furthermore, the cryopreservation process may be used to reduce the time needed to complete cryopreservation of the processed sperm cells compared to conventional cryopreservation methods. Accordingly, one embodiment of the present invention involves processing sperm pursuant to an overall 5 method to take advantage of one or more of the timesaving innovations to reduce the time required to complete the entire process. For example, according to one embodiment of the present invention, a batch of sperm cells (e.g., an ejaculate) is collected from a male mammal (e.g., bull), evaluated for quality control, stained, sorted according to a specified DNA characteristic, loaded into one or more containers (e.g., straws), and cryopreserved within a 10 period of about 12 hours from the time of collection. In another embodiment, the period is less than about 8 hours. In another embodiment, the period is less than about 6 hours. In still another embodiment, the period is less than about 3 hours. In yet another embodiment, the period of time is less than about 2 hours. In another embodiment, the period of time Is less than about I hour. 15 MULTI-CHANNEL SORTING APPARATUS AND METHOD In order to sort more sperm in less time, it is possible to use more than one cytometry unit in parallel to sort that same sperm sample. One way to do this is to simply divide the stained sperm cells into multiple aliquots and run each aliquot through a different cytometer. However, 20 as will be discussed below, certain advantages may be obtained by designing an apparatus that comprises multiple cytometry units in a single integrated multi-channel cytometry unit. Multi-Channel Sstem Sharing Integrated Platform Figs. 106-116 show one embodiment of the invention comprising a multi-channel 25 cytometry system, generally designated 1001, where multiple single-channel flow cytometry units, designated 1003, are ganged together as an integrated system to produce sorted product. Four such units are illustrated in this particular embodiment, but this number can vary. The units may be integrated in various ways, as by sharing an integrated platform comprising one or more of the following elements (1) a common supply of particles 1005; (2) a common source of 30 electromagnetic radiation 1007; (3) a common housing 1009; (4) a common input for controlling operation of the units 1011; (5) a common output 1019 allowing evaluation of the operation of one unit relative to another unit; (6) a common fluid delivery system 1021; (7) a common temperature control system 1023; (7) a common power source 1025; (8) a common waste recovery system 1027; (9) a common deflector plate system 1029; and (9) a common cleaning 35 system 1031. In one embodiment, the system includes all of these elements, but it will be understood that a multi-channel system of this invention can include any combination of elements. The use of common elements is beneficial because it allows the system to be run more efficiently and profitably, achieves more consistent results among channels by reducing the number of variables, facilitates any trouble-shooting that may be needed, and is economical.

127 The multi-channel approach also makes the sorting system more amenable to scale up or scale down. Each of the cytometry units 1003 has components similar to certain components of the flow cytometry apparatus 9 of the previous embodiment and, for convenience, corresponding 5 parts are designated by the same reference numbers with the addition of a prime ('). In general, each unit comprises a nozzle system 101', a mount for mounting the nozzle system 331', a transducer 105', and an epi-illumination optics instrument 417' for focusing a beam of light 25' on the fluid stream 21' exiting the nozzle orifice 103', all as previously described. Each unit further comprises a photodetector 117' operable as in the first embodiment to detect fluorescence 10 emissions 31'from the particles in the stream 21' and to convert the emissions 31' to electrical signals 701' which are processed to classify the particles by a specified DNA characteristic. Each unit 1003 is also equipped for sorting the droplets 33' into different groups or populations 123', 125' according to the classification of particles contained in the droplets 35'. The populations of droplets sorted by the units are collected by the collection system 2201. 15 A. Common Housinq and Modularity The flow cytometry units are mounted in a modular arrangement in a common housing 1009. In the embodiment shown in Figs. 106 and 109-113, the housing has a base 1069 and two side walls 1071 extending up from the base. The side walls have a lower pair of shoulders 20 1073 for supporting a lower cover panel 1075 at the front of the housing 1077, and an upper pair of shoulders 1081. A lower cover panel 1075 at the front of the housing 1077 is mounted between the lower shoulders 1073. The upper shoulders 1081 support an upper cover panel 1083 at the rear of the housing 1085. The front and rear of the housing 1077, 1085 are substantially open to provide access to the equipment inside. It will be understood that the 25 housing 1009 may have other configurations without departing from the scope of the invention. Further, it will be understood that the various units could be installed in separate housings. The flow cytometry units 1003 are mounted side-by-side as modules on an appropriate framework 1087 in the housing 1009. Specifically, the nozzle mounts 331' for positioning the nozzles 101' are releasably attached to a cross bar 1089 (Fig. 106) affixed to the side walls 1071 30 of the housing, and the bases 429' of the epi-illumination instruments 417' are releasably fastened to an angled mounting plate 1093 extending between the side walls 1071 of the housing toward the rear of the housing 1085 (Fig. 109), the arrangement being such that a particular unit can be installed or removed as a module. This modularity facilitates installation, removal for maintenance and/or replacement, and enables any number of flow cytometry units 1003 to be 35 readily added as needed or desired to increase the throughput capacity of the system. B. Common Fluid Supply and Delivery Systems The fluid delivery system 1021 of this embodiment is equipped to provide appropriate fluids to each of the cytometry units 1003. As illustrated schematically in Fig. 108, the system 40 generally comprises a pump 1105 for conveying carrier fluid 17'from a common supply of carrier 128 fluid 1107 under pressure, a gas pressure system 1115 for conveying fluid from a common supply 1117 of sheath fluid 19' under pressure, and a manifold system 1121 for receiving the fluids from respective supplies and delivering the fluids under pressure to the various cytometry units 1003, as needed. In the specific embodiment of Fig. 116, the supply of carrier fluid 5 comprises a vessel 1123 containing a suitable volume of such fluid (e.g., 5 ml.). The vessel is held by a holder 1125, which may be a block 1133 having a cavity 1135 sized to receive the vessel 1123. The block also has a second cavity 1137 for holding a vessel 1139 containing a suitable buffer material for conditioning the system during use, as will be described later. The pump 1105 for delivering carrier fluid from the vessel is desirably (but not 10 necessarily) a syringe pump 1141 as previously described. The plunger of the pump is movable through an intake stroke to aspirate a selected volume of carrier fluid 17' from the vessel 1139 and through a discharge stroke to dispense carrier fluid through a supply line 1147 to the manifold 1177 and from there to the various nozzles 101' of the system. The syringe pump Is also operable to aspirate fluid from the vessel 1139 containing buffer and to pump the buffer 15 through the system in a manner to be described. A three-way valve 1149 controls the flow of carrier and buffer fluids to and from the pump 1141. The pump is driven by a variable speed motor under the control of the processor 131'. By way of example, the pump may be driven by a stepper motor which operates at selectively variable speeds to pump carrier fluid to the manifold system 1121 at rates necessary to obtain the desired throughput from the units 1003. Multiple 20 syringe pumps or other types of fluid delivery devices can be used instead of a single syringe pump. In one embodiment the supply 1117 of sheath fluid comprises a vessel 1155, e.g., a tank connected to the manifold 1177 by means of a supply line 1157. The gas pressure system 1115 is operable to pressurize the tank and comprises a source of pressurized gas 1161 (e.g., air or 25 nitrogen) communicating with the tank via a gas line 1163 having a regulator 1165 in it for controlling the pressure supplied to the tank, and a two-way valve 1167 which, in a first position, establishes communication between the tank and the gas source, and in a second position, is operable to vent the tank. The gas pressure regulator 1165 is a conventional regulator adjustable to control the pressure supplied from the air source. The gas pressure system 1115 30 also includes a gas line 1169 for pressurizing a supply 1173 of cleaning solution (e.g., de-ionized water in a tank) which can be used to flush the fluid circuitry in a manner to be described hereinafter. Flow through the gas line is controlled by a two-way valve 1167 operable In the same manner as valve 1167. In one embodiment, the manifold 1177 comprises a laminated block 1179 (Fig. 112) of 35 material having passages 1181 formed in it to define a fluid flow circuit 1185 such as that shown diagrammatically in Fig. 116. (The passages may be formed by machining grooves in faces of the laminations prior to assembly of the laminations to form the block.) The fluid circuit includes inlets 1189, 1191 connected to the syringe pump 1141 and to the supply 1117 of sheath fluid and sets of outlets 1193, for providing such fluids to the flow cytometry units 1003, each such set 40 including a carrier fluid outlet and a sheath fluid outlet. Flow through the various flow passages 129 1181 is controlled by valves V1-V6 which, in one embodiment, are solenoid-operated valves in housings attached to the manifold block 1179. The block is desirably of substantially transparent material (e.g., acrylic plastic) to facilitate monitoring of the system 1121 and trouble-shooting. In the embodiment shown, the manifold 1177 is attached to a frame member 1203 extending 5 between the side walls 1071 of the housing 1009 adjacent the bottom of the housing below the nozzle systems 101'. The inlets and outlets 1193, of the manifold 1177 may comprise fittings 1205 threaded into the block, such as flangeless nut and ferrule fittings available from Upchurch Scientific, a division of Scivex. It will be understood that the design and construction of the fluid circuit 1185 in general and the manifold 1177 in particular may vary without departing from the 10 scope of the present invention. Referring to Fig. 116, the manifold fluid circuit 1185 for the carrier fluid 17' includes a sample reservoir 1207 for holding a limited supply of carrier fluid (e.g., 1.0 ml). If the carrier fluid contains sperm cells, for example, providing such a reservoir close to the nozzles 101' is beneficial to the viability and motility of the sperm cells, since the storage of such cells, even for 15 short periods of time, in small spaces may be detrimental to motility. Flow of carrier fluid from the sample reservoir 1207 to the nozzles 101' is controlled by a series of two-way valves VIA-VID, one for each nozzle. Each valve VIA-V1D has a first position establishing fluid communication between the needle 1217 of the sample reservoir and the needle 157' of a respective nozzle for delivery of carrier fluid 17' to the needle under pressure generated by the syringe pump 1141, 20 and a second position establishing fluid communication between the needle 1217 and a waste system, generally designated 1221, which is common to all of the flow cytometry units 1003. In the embodiment shown, the waste system 1221 comprises a waste tank 1223 for holding waste material, a mechanism 1225 such as a vacuum pump for generating a vacuum in the waste tank, and waste lines 1227 connecting the valves V1A-V1 D and the waste tank. A valve V3 is 25 provided in the waste line upstream from the waste tank for opening and closing the waste line, as needed. A suitable hydrophobic filter 1233 is provided in the line connecting the waste tank 1223 and the vacuum pump 1225. The manifold fluid circuit 1185 for the sheath fluid 19' includes a plurality of valves V2A V2D. Each valve has a first position establishing fluid communication with the supply 1117 of 30 sheath fluid in the tank for delivery of sheath fluid 19' to a respective flow body 133' via a sheath supply line 1241, and a second position establishing fluid communication between the flow body and the waste tank via a waste line 1247. The pressure at which the sheath fluid is delivered to the flow bodies 133' will depend on the sheath tank pressure (as controlled by the regulator 1165) which may range from I to 100 psi, more desirably from 10 to 50 psi, even more desirable 35 15 to 40 psi, and even more desirably from about 20 to 30 psi. While the use of a common supply for all of the units has various advantages, it is contemplated that at least some of the flow cytometry units could be supplied with sample material from separate sources. 40 130 C. Common Power SUpPly and Input and Output Controls The flow cytometry units 1003 also share a common power supply 1025, common power delivery systems, a common input (GUI) 715' for controlling operation of the channels by the microprocessor 131', and a common output provided to the microprocessor allowing evaluation 5 of the operation of one channel relative to another channel. For example, the common output includes providing the digitized signals from each epi-illumination system to the microprocessor for an indication of the fluorescence intensity measured by each channel, for an indication of the rate at which each channel is separating particles, for an indication of the staining variations (which may be indicated by the intensity difference of fluorescence pulses from X and Y cells) 10 and for an indication of the decision boundaries 763 used by each channel for discriminating between particles. As another example, the common output includes providing the output signals from the break-off sensors 389' to the microprocessor for an indication of the droplet break-off location 107' of each channel. 15 D. Common Temperature Control Optionally, a temperature control system, generally designated 1257, is provided to regulate the temperature of the contents of the vessels 1123 in the holding block 1133 and the temperature of the manifold 1177. Such temperature control reduces the variability of the system, thus providing more consistent measurements between channels and, for certain types 20 of cells (e.g., sperm cells), helping to maintain the viability of the cells. In one embodiment, the temperature control system 1257 comprises a fluid flow circuit 1259 comprising fluid passages 1263 in the holding block 1133 and fluid passages 1269 in the manifold block 1179, and a control unit 1265 for circulating a thermal fluid (e.g., water) through the circuit at a selected temperature. The temperature is desirably such as to maintain the fluid, 25 especially the carrier fluid, at an optimal temperature to maximize cell viability and, if sperm cells are involved, sperm motility. A valve shut-off V6 is positioned in the circuit for controlling flow through the circuit. The temperature control unit may be used to maintain the sperm cells at the desired temperature prior to sorting as discussed above. All of the valves in the fluid delivery system 1021 are operated by conventional means, 30 such as solenoids, under control of an operator or suitable programming. The various fluid flow lines connecting the components of the system outside the manifold block 1179 are desirably of substantially transparent plastic tubing for observing any blockages. For example, the tubing may be 0.0625 in. OD tubing of FEP polymer. The flow lines of the temperature control system 1257 are desirably somewhat larger (e.g., 0.125 in. OD) to provide greater flow capacity. 35 E. Common Liht Beam and Beam Slittin System As previously noted, the multi-channel system shares a common source of electromagnetic radiation or beam light 1007. By way of example (and not limitation), the source may be a laser beam from a UV multiline laser primarily having wavelengths of 351.1 nm and 40 363.8 nm. Alternatively, it may be desirable to use a pulsed laser (e.g., a mode-locked laser), 131 particularly to synchronize digital sampling with a Pulsed laser (as discussed in the Pulsed laser section) in order to increase the effective Power delivered to each cytometry unit, thereby increasing the number of cytometry units that can be operated with a single laser. The power required to generate the laser beam will vary depending on the requirements 5 of each flow cytometry unit and the number of units. For example, if there are N units and each unit requires a light beam having an effective power of W watts, then it will be necessary to generate a laser beam having a power of (W x N) + L, where L equals the system power loss among the optical elements of the system. Using a single laser to supply all of the flow cytometry units is economical compared to a system using multiple lasers. It is also efficient and 10 provides for more consistent measurements from one channel to the next, because there is no variability on account of different beam characteristics (e.g., beam intensity, light polarity, beam divergence) or electrical noise resulting from the use of multiple lasers. According to one embodiment of the present invention, a beam splitting and guidance system is used to split a single laser beam into three or more separate beams. As shown in Fig. 15 117, for example, a 50/50 beamsplitter 1270 (i.e., a beamsplitter that is operable to divide a single beam into two separate beams having approximately equal intensity) can be used to split a single beam 25'into two beams 1270A, 1270B. By using a second 50/50 beamsplitter 1271 to split one of the two beams 12708 into two additional beams 1271A, 1271B, one can generate a total of three beams 1270A,.1271A 1271B from a single beam 25'. Each beam can be directed 20 into the optics system of a flow cytometer, for example an epi-illumination optics system 415' as shown in Fig. 117. One could also use additional 50/50 beamsplitters to split the single laser beam into any number of additional separate beams. As shown schematically in Fig. 118, for example, a third beamsplitter 1272 can be added to the 3-way beamsplitting system (Fig. 11 7 )so that the three 50/50 beamsplitters 1270, 1271, 1272 can be used to split a single 25 beam into 25 four separate beams 1271A, 1271 B, 1272A, 12728. From this one can readily appre ciate that the single beam can be split into any number of separate beams. Other beam splitting arrangements may be used to split the incoming source beam into multiple light beams for the various units. One desirable embodiment of a beamsplitting system is shown in Figs. 106 and 109. A 30 beam guidance system 1273 is provided for guiding the common beam 1007 to the optics instruments 417' of the various flow cytometry units 1003. In the embodiment illustrated in Figs. 106 and 111, the guidance system 1273 Includes a lower mirror assembly 1279 mounted on one side wall 1071 of the housing 1o0, an upper mirror assembly 1281 mounted on the side wall 1071 above the lower mirror assembly, and a series of reflecting filters 1283, one associated with 35 each optics instrument 417'. The lower mirror assembly is operable to reflect a beam 1007 from a suitable source upwardly to the upper mirror assembly, and the upper mirror assembly is operable to reflect the beam through an opening in the side wall 1071 to the reflecting filters 431' of the various instruments 417'. In one embodiment, the lower mirror assembly includes a base 1285 fastened to the side 40 wall 1071 of the housing 1009, a stage 1289 movable vertically on the base by a suitable 132 mechanism 1291, such as a micrometer, a tiltable platform 1293 on the stage (e.g., a kinematic optical mount Model P100-P available from Newport), and a mirror 1295 on the platform, the position of the mirror being adjustable by moving the stage and the mirror platform to the appropriate locations. The upper mirror assembly is similar to the lower assembly, comprising a 5 base 1297, a vertically movable stage 1299, a tiltable platform on the stage 1301, and a mirror 1303 on the platform. A pair of target plates 1309 are affixed to the side wall of the housing 1009 between the upper and lower mirror assemblies. The target plates 1309 have vertically aligned holes 1311 therein to facilitate adjustment of the upper and lower mirrors so that an incoming beam 1007 is precisely reflected toward the reflecting filters 431' of the instruments 417', all of 10 which filters are aligned with the incoming beam. Each of the first three reflecting filters 1315, 1317, 1319 functions as a beam splitter, i.e., it functions to reflect a specified percentage of the beam and to pass the remaining percentage of the beam. For example, in the case of four epi-illumination instruments, the reflecting filters 431' of the first three instruments each reflect a percentage of the laser light 1007, so that each of the 15 first three units of the series receives 25% of the electromagnetic radiation of the original beam 1007. For example, the reflecting filters of the first, second and third units may reflect 25%, 33% and 50% of the incident light, respectively. The last reflecting filter 1321 of the series desirably reflects all of the remaining light (about 25% of the original beam) to the last instrument of the series. As a result, each of the four Instruments should receive the same intensity of radiation 20 (light) to interrogate the cells in respective streams. Depending on the beam splitting devices used in the above system 1273, it may be desirable that the laser beam have a particular polarization. The tranmittance-to-reflectance ratio of dielectric filters can vary depending on the polarization of the light. Further, when dealing with linearly polarized light, dielectric filters (which are manufactured for use at a specified angle of 25 incidence) can be too sensitive to variations in the angle of incidence. Circularly or elliptically polarized light alleviates this problem to some extent because the polarization vector of the light is In a variety of different orientations with respect to the optical axis of a dielectric filter as the light interacts with the filter. Thus, elliptically or circularly polarized light simulates randomly polarized light, which provides more tolerance for variations in the angle of incidence on a 30 dielectric filter. Accordingly, if the laser described above generates a beam of light having a vertical polarization, for example, it may be advantageous to convert the light to circularly polarized light before it Is split. As will be understood by those skilled in the art, this can be accomplished by passing the beam through a 1/4-wave retardation plate (filter) of polarizing material having its optical axis rotated 45 degrees relative to the plane of the laser polarization. 35 The beam thus transmitted by the waveplate will have approximately circular polarization, and it can be more easily split to provide multiple beams to the optics systems of respective flow cytometer units. Moreover, by rotating the wave retardation plate to alter the angle between the laser polarization and the optical axis of the material used to make the waveplate, eccentricity can be 40 introduced into the approximately circular polarization of the beam (i.e., the polarization can be 133 made more elliptical). Changing the eccentricity of the elliptical polarization of the beam can change the transmittance-to-reflectance ratio of the dielectric filters by causing the polarization vector for a greater percentage of the light to have a particular angle with repspect to the optical axis of the dielectric filter. Accordingly, if the balance of light among the multiple cytometry units 5 is outside the desired range, one can rotate the waveplate to increase or decrease the eccentricity of the elliptically polarized light, thereby altering the transmittance-to-reflectance ratios of the various filters until a better balance is achieved. Similarly, if the waveplate is transmitting elliptically polarized light, one can influence the transmittance-to-reflectance ratio of one of the filters by rotating that filter. 10 Regardless of the method used to split the single beam into multiple separate beams. Balance of the power delivered to each cytometry unit can be achieved by selectively blocking a percentage of the light to bring all the cytometry units down to the same level of power. For example, the neutral density filter 447' of each epi-illumination system 415' can be selected to block more or less of the light to balance the illuminating power delivered by the beam splitting 15 and guidance system to each individual cytometry unit. If one channel of a multi-channel unit receives significantly more illumination from the beam splitting and guidance system, a neutral density filter 467' that transmits less light can be used in the epi-illumination system 415' of that channel to bring the illumination power for that channel more in line with the other channels. It is desirable, though not essential, that channel-to-channel variations in the illuminating power be 20 less than about 10%. It is even more desirable that the channel-to-channel variations be less than about 5%. It will also be appreciated that pulsed laser scanning, as described above, may be desirable for multi-channel flow cytometry. For example, the UV multiline laser can be replaced with a mode-locked pulsed laser operating at about 85 MHz to allow more flow cytometry 25 channels to be powered by a single laser. For example, the peak power provided in each pulse of a mode-locked laser emitting pulses having a width (duration) of about 12 picoseconds at a frequency of about 85 MHz is approximately 800 times the average power output of the laser. Thus, a mode-locked laser (e.g., a Vanguard 350 from Spectra-Physics) can provide enough Illumination energy to operate a few dozen cytometry units (e.g., 32 cytometry units) while 30 operating at only about 350 milliwatts. The use of fiber optics for supplying light to the units is also contemplated. In this embodiment, fibers are used to direct light from the laser to respective units, thus eliminating the need for the guidance system described above. 35 F. Common Deflector Plates In the embodiment shown in Figs. 106 and 108-116, the sorting system 119' of each flow cytometry unit 1003 is substantially identical to the sorting system 119 described in the first embodiment, except that the units desirably share two common deflector plates 1331 extending across the width of the housing 1009 at the front of the housing. There are advantages to using 40 a common set of deflector plates, including a consistent charge from one channel to the next, the 134 use of a common power supply, a larger plate area providing a more stable electric field and more uniform droplet deflection, and a consistent angle of deflection for collection of sorted samples. The deflector plates 1331 are mounted on a frame 1333 fastened to the housing 1009. Alternatively, separate plates could be provided for each unit. 5 G. Common Collection System In the embodiment shown in Figs. 107 and 116, a common collection system 2801 includes two intercepting devices for each cytometry unit as described above in connection with the collection system 2201 for the single unit. However, a common frame 2803 is provided to 10 hold all eight of the intercepting devices. Also, one of the two intercepting devices for each cytometry unit directs fluid into a common waste trough 2805 rather than a collection vessel. The waste trough makes it easier to discard sorted droplets that contain particles of little value (e.g., Y-chromosome bearing sperm cells for breeding dairy cows). If it is desirable to retain all the sorted droplets, the waste trough can be removed and collection vessels can be placed under 15 each intercepting device. The four collection vessels in the embodiment shown in Figs. 107 and 116 rest in openings in the surface of a collection tray 2807. A common water bath (not shown) may be provided under the surface of the collection tray to control the temperature of the contents of the collection vessels. 20 H. Multi-Channel Control The various flow cytometry units are controlled by the microprocessor 131', (or other suitable processing system) which desirably has a common input and a common output as discussed above. Desirably, the operational parameters of each flow cytometry unit 1003 can be set 25 independently of the other units so that such parameters can be varied as between units. These parameters may Include, for example, the frequency of droplet formation, the control and sorting strategies utilized by a particular unit, the criteria used by each unit to classify and sort particles in the fluid supplied to the unit, and other parameters. For example, in certain situations it may be desirable to supply one or more units with carrier fluid 17' at a first flow rate and other units a 30 second (different) flow rate. Similarly, it may be desirable to use one control sorting strategy (e.g., a "high efficiency" strategy) for one or more units while using a different strategy (e.g., a "low loss" strategy) for other units. By controlled variation of these parameters among the units, based on historical data and data collected on a real-time basis, the throughput of the units can be managed and the results of the system optimized. The capability of independent operation 35 also allows selected units to be operated in the event fewer than all of the units are needed or available. 1. Operation of Multi-Channel System The operation of the multi-channel system of this embodiment is similar to that described 40 previously, except that the multiple flow cytometry units are adapted to conduct flow cytometry 135 operations in parallel (i.e., during the same time period or overlapping time periods) for higher throughput. Prior to the start of a run, the fluid delivery system 1021 is flushed, if necessary, with cleaning solution from the tank 1173 by moving the valve V5 to its cleaning position. The system 5 is then conditioned by with buffer fluid using the syringe pump 1141. During this procedure, the valves VIA-V1D and V2A-V2D are moved to establish communication with the waste receptacle 1223 which is under vacuum. As a result, the cleaning solution and/or buffer fluid flows through the system to waste. This process cleans the system 1021, primes the syringe pump 1141 and removes air bubbles from the system. 10 With the three-way valve 1149 suitably positioned, the syringe pump 1141 is operated through an intake stroke to aspirate a quantity of carrier fluid 17' containing particles, e.g., sperm cells, following which the valve 1149 is moved to establish communication with the manifold 1177 and the syringe pump moves through a discharge stroke to pump a volume of carrier fluid into the sample reservoir 1207 to fill it. The temperature of the carrier fluid 17' is controlled by the 15 temperature control system 1257 to maintain the cells in the carrier fluid at the desired temperature. With the valves V1A-V1 D positioned to establish communication with the sample reservoir 1207, further operation of the syringe pump 1141 forces carrier fluid through the lines to the needles of respective nozzle assemblies for flow through the nozzles 101', as previously described. At the same time, and with the valves V2A-V2D positioned to establish 20 communication with the sheath fluid tank 1155, sheath fluid 19' is forced through the supply lines to respective flow bodies and through the nozzles, also as previously described. This process continues for an appropriate length of time sufficient to pump a suitable volume of fluid through the system 1001. The duration of a particular run will vary depending on the quantity of carrier fluid in the supply vessel, the rate at which the carrier fluid is pumped through the system, and 25 the number of channels in the system. For example, a run may continue for only a limited period of time (e.g., 15 minutes during which about one ml. of carrier fluid is delivered to each nozzle) or it may continue indefinitely, with the supply of fluid being replenished as needed. In the event a needle 157' becomes clogged, the appropriate valve V1 is moved to establish communication with the waste receptacle 1223. Sheath fluid 19' entering the flow body 30 133' will then flow under the force of the vacuum 1225 back through the needle 157' to waste, thus flushing and clearing the needle. If there is a need to shut off the flow to a particular nozzle, the valves V1 and V2 are simply switched to their waste positions. Although the system described herein with respect to both the single channel and multi channel configurations has been described with regard to particle separation, such as the 35 separation of X and Y cells, it is contemplated that such particles include any particles having different characteristics which may be arbitrarily noted as characteristic A and characteristic B. Further, it will be understood that in some embodiments, the sorting function can be eliminated entirely, so that the flow cytometry apparatus (single-channel or multi-channel) operates only to classify the particles and not to sort them.

136 While the multi-channel system is described above in the context of operating the flow cytometry units in parallel, it will be understood that the units could also be operated in series. For example, it is contemplated that particles in one stream could be sorted by one unit into multiple populations, and that one or more of such sorted populations could then be passed 5 through one or more other units in series to perform additional sorting operations to sort different particles using the same or different sorting strategies. J. Upriqlht Multi-Channel Embodiment Figs. 119 and 120 show another exemplary multi-channel flow cytometry system. This 10 system, generally designated 4001 comprises four cytometry units 4009 ganged together. The nozzle system 101', epi-illumination optics system 450', deflector plates 629', sample station 4051, contamination prevention mechanism 4031 and other components of each unit 4009 are mounted on a shared vertical mounting board 4011. Referring to Fig. 120, a single laser 4013 and a beam splitting and guidance system 4015, which is substantially similar to the beam 15 splitting and guidance system 1273 described above, provide illumination for each epi illumination system 450'. The laser 4013 passes through a hole 4019 (Fig. 119) in a common housing 4021 containing the beam splitting and guidance system 4115. The beam splitting and guidance system 4115 and epi-illumination systems 450' are on one side of the board 4011. The focusing lens assembly 491' of each epi-illumination system 450' extends through the board 20 4011 to the other side (similarly to the configuration show in the single channel system shown Figs. 26 & 27), on which the remainder of the components for the units 4009 are mounted. The units 4009 are all oriented so that their nozzle systems 101' direct the fluid streams 21' downward. Each unit 4009 also has a collection system 4031, which includes a collection vessel 4033 for collecting droplets 33 containing a desired population of particles and a waste 25 container 4035 for collecting other droplets 33. A water bath (not shown) or other temperature control may be used to control the temperature of the collection vessel 4033. The multiple flow cytometry units 4009 can also share a common power supply (not shown), a common input for controlling operation of the units (not shown), and a common output (not shown) allowing comparative evaluation of the operation of the units 4009 relative to one 30 another. As demonstrated by comparison of the two exemplary multi-channel embodiments 1001, 4001, the nature of the integrated platform and the sharing of features between or among multiple flow cytornetry units in a multi-channel system can be varied extensively without departing from the scope of the present invention. 35 Impact of Multi-Channel Processing on Overall Process The overall process described above can be performed with multi-channel sperm sorting to decrease the time required to sort the sperm cells. With few exceptions, the method does not change. One minor change is that sorted sperm cells will be collected in multiple collection vessels. The contents of the multiple collection vessels can be combined for concentration if 40 desired. Alternatively, the contents of each collection vessel can be concentrated separately. It 137 will be appreciated that the time required to sort a batch of sperm cells (e.g., an ejaculate) from collection to completion of the cryopreservation step can be significantly reduced by using multiple cytometry units to process the batch. For example, if four cytometry units operate in parallel to process the batch of sperm cells, the time required to complete sorting is reduced to 5 approximately one quarter of the time required to sort the batch using a single cytometry unit. Thus, by substituting the step of sorting sperm with four cytometry units operating in parallel with the step of sorting sperm with a single cytometry unit, the exemplary timeline for completion of the method from collection to completion of the freezing step can be reduced. The time can be reduced even further by increasing the number of cytometers operating in parallel to sort the 10 sperm cells in the sample, subject to the practical limitations involved In operating a parallel system having more than four such units. Thus, according to one embodiment of the present invention, the sorting step in the overall process described above is performed by sorting the sperm cells according to a specified DNA characteristic in a multi-channel flow cytometry apparatus. In yet another embodiment, a sperm processing method comprises the step of 15 sorting sperm cells according to a specified DNA characteristic in a multi-channel flow cytometry apparatus in which each channel collects in the range of about 2,000 - 10,000 sperm cells having a desired DNA characteristic per second. 20 Multi-Channel Sorting Example / Bull semen was collected from a sexually mature bull using an artificial vagina and the sample transported to a nearby staining facility in a temperature-controlled container at 37'C. Upon receipt, the semen was analyzed for concentration, visual motility, motility and progressive motility by the Hamilton-Thorn Motility Analyzer (IVOS), according to standard and well known 25 procedures (Farrell et al. Theriogenology, 49(4): 871-9 (Mar 1998)). Six tubes of 1 mL of 150 X 106 sperm/mL sperm suspension were prepared by suspending an aliquot of semen In 41 *C TCA #2 buffer containing 10mM pyruvate bringing the overall pH to 7.35. Then varying amounts of 10 mM Hoechst 33342 solution in water were added to the sperm samples to yield final dye concentrations of 200, 300, 400, 500, 600, & 700 30 pM Hoechst 33342. Each of the six samples was incubated at 41 0 C for approximately 30 minutes. The samples were analyzed by flow cytometry and the %CV of the X cell population was estimated by iterative computer algorithm for the 200, 300, and 400 IM Hoechst 33342 samples. The %CV for the 300 and 200 pM Hoechst 33342 were both ascertained to be within the acceptable range near 1.3 %CV. Accordingly, it was determined that a concentration of 250 35 pM Hoechst 33342 would be used to stain a batch of sperm cells for further processing. Two tubes containing 2mL each of 150 X 106 sperm/mL sperm suspension were prepared by suspending an aliquot of semen in 41 *C TCA #2 buffer containing 10mM pyruvate (again bringing the overall pH to 7.35). Then 10 mM Hoechst 33342 solution in water was added to each of the two sperm suspensions to yield a final dye concentration of 250pM Hoechst 40 33342. The sperm suspensions were maintained in a 41"C water bath for 30 min. After 30 138 minutes, the sperm suspensions were removed from the 41 *C water bath and 4AL of 25mg/mL FD&C #40 was added to one of the suspensions. The other was stored at ambient temperature to provide comparison samples for the assessment assays. The stained and quenched sperm suspension was loaded onto the sample port of one 5 channel of a four channel droplet sorting flow cytometer. Delbecco's PBS was used as the sheath fluid. The cytometer was equipped with a orienting nozzle as described above and having a 60 micron orifice. An semicircular baffle plate was installed perpendicular to the longitudinal axis of the nozzle as described above. The transducer was operated at 54 KHz and the droplet break-off location was controlled manually. An epi-illumination optics system as 10 described above was used to direct approximately 25% of the beam of a continuous wave laser to intersect the fluid stream at a perpendicular angle. The focusing and collection lens had a 0.65 numerical aperture. The beam was focused to a spot having a width less than 3 pm for slit scanning the sperm cells. Digital signal processing was used to extract the critical slope difference and pulse area for each detected pulse waveform. Classification parameters for 15 classification of X cells, Y cells, and undetermined cells in the two-dimensional CSD and pulse area feature space were manually entered into the processing system for classifying sperm cells according to chromosome content. Sperm were sorting according to X and Y chromosome content using a coincidence accept sort strategy for collection of X cells, assigning a 50/50 probability that each unclassified 20 sperm was an X cell or Y cell. The sample fluid rate was manually adjusted to maintain purity of collected X cell population (as indicated by the GUI) at 85% or better and to maintain the rate of ~ X cell collection above a minimum rate. After approximately fifteen million X sperm had been collected in a tube that had been soaked in sheath fluid for at least one hour and then coated with 0.5mL of 10% egg yolk in TCA #2 buffer at pH 7.0, the tube was removed and replaced with 25 an additional tube that has been similarly prepared. Immediately after removing a collection tube from the flow cytometer, a comparison sample from the stained, but not sorted, sperm suspension was prepared. The sorted and comparison samples were centrifuged for 7 min @ 750g in a 15 mL tube. The supernatants were removed using a transfer pipette to yield a concentration of approximately 40 million 30 sperm/mL. TCA #2 buffer pH 7.0 was added to the sperm suspensions to yield a final concentration of approximately 20 million sperm/mL. This process continued until the flow cytometer had produced four collection tubes (A2-A5). The sorted samples and 'non-sorted' comparison samples were assessed by IVOS. Sorted sample A3 and its non-sorted comparison sample were tested for % intact acrosomes by differential interference contrast microscopy. All 35 the sorted samples were counted by hemacytometer to determine the output rate of sorted sperm per hour. The % X chromosome bearing sperm was confirmed by flow cytometer reanalysis. Results of the IVOS assessment for the sorted and 'non-sorted' comparison samples are provided in Figs. 121 (motility) and 122 (progressive motility). The total number of sperm sorted into each collection tube is shown in Fig. 123. The rate of sperm sorted per hour for each 40 collection period is shown in Fig. 124. Percentage of X chromosome bearing sperm for each 139 sorted sample is listed in Fig. 125. Results of the assessment of the acrosome integrity were 72% intact acrosomes for the sorted sample and 78% for the non-sorted comparison sample. The results demonstrate the technical ability to yield more than 5,000 sorted X cells per second at greater than 85% purity per channel of multi-channel flow cytometry system for 5 sustained periods. The results also show the technical ability to yield more than 7,000 X cells per second at greater than 85% purity for sustained periods under ideal conditions. Further, the results indicate that samples of sorted sperm cells obtained by such high-speed flow cytometric sorting will suffer only slight declines in motility, indicating that the sorted sperm will have good fertility. 10 Multi-channel Sorting Example 1I Bull semen was collected from a sexually mature bull using an artificial vagina. The ejaculate was split into two aliquots. The first aliquot of 250pL of semen was suspended in 5mL 15 of 37*C Triladyl@. The second aliquot, which comprised the remained of the ejaculate, was suspended in two parts 370C carbonate buffer (pH 6.1-6.2). Both aliquots were transported at 370C in a temperature-controlled container to a processing facility. At the processing facility, the first aliquot was floated in -120mL of 370C water in a 200mL beaker and placed in a cold room to slowly cool to 5"C. The second aliquot was analyzed for concentration, motility and progressive 20. motility by the Hamilton-Thorn Motility Analyzer (IVOS), according to standard and well known procedures (Farrell et al. Theriogenology, 49(4): 871-9 (Mar 1998)). Three imL tubes of 150 X 106 sperm/mL sperm suspension were prepared by transferring sub-aliquots containing 150 million sperm from the second aliquot to empty tubes, centrifuging at 5OOg for 5 min, removing the supernatants, and re-suspending the sperm pellets 25 in 1mL of 280C TCA #2 buffer containing 10mM pyruvate pH 7.35. Ten mM Hoechst 33342 solution in water was added to each of the three tubes in various amounts to yield final dye concentrations of 100, 150, & 200 lM Hoechst 33342. Each of the three tubes was held at 28 0 C for approximately 60 minutes. Sperm from each of the three tubes was analyzed by flow cytometry and the CV of total fluorescence intensity of the X population was determined for the 30 100, 150, and 200 pM Hoechst 33342 staining conditions using an Interactive computer algorithm. The CVs for the 150 and 200 pM Hoechst 33342 were both within the acceptable range near 1.3%. Thus, it was determined to use staining conditions including 150 pM Hoechst 33342 concentration for sorting. One tube containing 5mL of 150 X 106 sperm/mL sperm suspension was prepared by 35 transferring a sub-aliquot containing 750 million sperm from the second aliquot, centrifuging at 5OOg for 5 min, removing the supernatant, and re-suspending the sperm pellet in 280C TCA #2 buffer containing 10mM pyruvate (pH 7.35). Ten mM Hoechst 33342 solution In water was added to the tube in an amount yielding a final dye concentration of 150pM Hoechst 33342. The tube was maintained in a 28*C water bath for 60 min. After 60 minutes, the tube was removed 40 from the 28"C water bath and I OpL of 25mg/mL FD&C #40 was added.

140 The now stained and quenched sperm suspension was loaded onto the sample port of one channel of a multi-channel droplet sorting flow cytometer system. The sperm suspension was maintained at 280C. Using substantially the same instrument settings as set forth in Multi channel Example 1, X & Y chromosome bearing sperm were separated by the flow cytometry 5 system using a coincidence abort sort strategy for a period necessary to place an enriched X cell population of approximately eighteen million sperm into a collection tube that had been prepared by soaking with sheath buffer for at least one hour and then adding 0.5mL of Triladyl@ cryo preservation media containing 10 mM pyruvate pH 6.6. The sperm cells were introduced into the flow cytometry system at a rate of between about 25,000 and 30,000 cells/second. An enriched 10 population of X cells was collected at a rate varying from 4,500 per second to 6,000 per second. When approximately eighteen million sperm had been sorted into a collection tube, the tube was removed and replaced with another tube that had been similarly prepared. Immediately after removal of a collection tube from the flow cytometer, the sorted sperm suspension was centrifuged for 7 min @ 700g. The supernatant was removed using a transfer pipette to yield a 15 concentration of approximately 100 million sperm/mL. Triladyl@ cryo-preservation media containing 10 mM pyruvate (pH 6.6) was added to the sperm suspensions to yield a final concentration. of approximately 50 million sperm/mL. This process continued until the flow cytometer had produced three collection tubes (D1-D3). Approximately 52 million sperm were sorted in 259 min yielding an overall collection rate of about 12 million enriched X sperm per hour 20 of sorting. The re-suspended sorted sample tubes were floated in -120mL of 28*C water in a 200mL beaker and placed in a 50C cold room to slowly cool. After the sorted samples reached 50C, the three tubes of sorted sperm were combined Into one tube. The pooled sample was analyzed by IVOS to determine the % motility, % progressive motility, and concentration. Additional Triladyl@ cryo-preservation media 25 containing 10 mM pyruvate pH 6.6 was added to the sample to yield a final concentration of approximately 50 million sperm per mL. The % X-chromosome bearing sperm In the sorted pooled sample was 87% as determined by flow cytometer re-analysis. A summary of the IVOS assessment compared to the non-sorted sample of the same ejaculate is illustrated In Fig. 126. The pooled sorted sample and the first aliquot were loaded into standard 0.25cc straws 30 In a 5*C cold room. The loaded straws were transferred to a programmable freezer and frozen by the following program: 5 min @ 5*C, cool from 5*C to -12*C @ 4 0 C/min, cool from -120C to 100 0 C @ 40*C/rnin, cool from -100*C to -140*C @ 2 0*C/min, hold at -140*C. After the straws had reached -1400C, they were quickly removed from the freezer and plunged into liquid nitrogen. 35 Thawed straws were analyzed by IVOS for % motility and % progressive motility after incubation at 370C for 30 and 120 minutes. Results from a set of two sorted and unsorted straws are summarized in Fig. 127 and Fig. 128. 40 141 Multi-channel Sorting Example Ill Bull semen was collected from a sexually mature bull using an artificial vagina and the ejaculate split into two aliquots. A first aliquot of 250pL of semen was suspended in 5mL of 37 0 C 5 Triladyl@. A second aliquot, which comprised the remainder of the ejaculate, was suspended in two parts 370C carbonate buffer (two parts 0.097 moles/L of NaHCO 3 , 0.173 moles/L of KHCO 3 , 0.090 moles/L CrH 8 07-H 2 0 in water) (pH 6.1-6.2). Both aliquots were transported at 370C in a temperature-controlled container to the processing facility. At the processing facility, the first aliquot was floated in -120mL of 370C water in a 200mL beaker and placed in a cold room to 10 slowly cool to 50C. The second aliquot was analyzed for concentration, motility and progressive motility by the Hamilton-Thorn Motility Analyzer (IVOS), according to standard and well known procedures (Farrell et al. Theriogenology, 49(4): 871-9 (Mar 1998)). Two tubes of 150 X 106 sperm/mL sperm suspension were prepared by transferring into each of two empty tubes a fraction containing 900 million sperm from the second aliquot, 15 centrifuging each tube at 500 X g for 5 minutes, removing the supernatant from each tube, and re-suspending each sperm pellet in 6mL of 280C TCA #2 buffer containing 10mM pyruvate (pH 7.35). 10mM Hoechst 33342 solution in water was added to each of the two tubes to yield final dye concentrations of 200pM Hoechst 33342 in one tube and 400pM Hoechst 33342 in the other tube. Each of the two tubes was held at 28*C for approximately 120 minutes. Sperm from each 20 of the tubes was analyzed by flow cytometry and the CV of total fluorescence intensity of the X population was determined for the 200pM and 400gM Hoechst 33342 staining conditions using an interactive computer algorithm. The CVs for the 200pM and 400pM Hoechst 33342 were both within the acceptable range of about 1.3%. The sperm suspension stained with a concentration of 200pM Hoechst 33342 was chosen for sorting. 10pL of 25mg/mL FD&C #40 was added to 25 this tube of stained sperm suspension just prior to sorting. The stained sperm suspension was loaded onto the sample port of one channel of a multi-channel droplet sorting flow cytometer system. The sperm suspension was maintained at 280C. Using substantially the same instrument settings as set forth in Multi-channel Example /, X & Y chromosome bearing sperm were separated by the flow cytometry system using a 30 coincidence abort sort strategy for a period of time necessary to place an enriched X chromosome bearing cell population of approximately eighteen million sperm into a collection tube that had been prepared by soaking with sheath buffer for at least one hour and then adding 0.5mL of Triladyl@ cryo-preservation media (pH 6.6). The sperm cells were introduced into the flow cytometry system at a rate of between about 25,000 and 30,000 cells/second. An enriched 35 population of X chromosome bearing cells was collected at a rate varying from 4,500 per second to 6,000 per second. When approximately eighteen million sperm had been sorted into a collection tube, the tube was removed and replaced with another tube that had been similarly prepared. Immediately after removal of a collection tube from the flow cytometer, the sorted sperm suspension was centrifuged for 7 min @ 700 X g. The supernatant was removed using a 40 transfer pipette to yield a concentration of approximately 100 million sperm/mL. Triladyl* cryo- 142 preservation media (pH 6.6) was added to the sperm suspensions to yield a final concentration of approximately 50 million sperm/mL. This process continued until the flow cytometer had produced two collection tubes (C1-C3). Approximately 35 million sperm were sorted in 193 minutes yielding an overall collection rate of 11 million enriched X chromosome bearing cells per 5 hour of sorting. The re-suspended sorted sample tubes were floated in -120mL of 2800 water in a 200mL beaker and placed in a 50C cold room to slowly cool. After the sorted samples reached 50C, the three tubes of sorted sperm were combined into one tube. The pooled sample was analyzed by IVOS to determine the % motility, % progressive motility and concentration. Additional Triladyl@ cryo-preservation media (pH 6.6) 10 was added to the sample to yield a final concentration of approximately 50 million sperm per mL. The % X-chromosome bearing sperm in the sorted pooled sample was 88% as determined by flow cytometer re-analysis. A summary of the IVOS assessment compared to the non-sorted sample of the same ejaculate is illustrated in Fig. 129. The pooled sorted sample and unsorted sample (i.e., the first aliquot from above) were 15 loaded into standard 0.25cc straws in the 5*C cold room. The loaded straws were transferred to a programmable freezer and frozen by the following program: 5 mi @ 51C cool from 5C to 120C @ 4 0 C/min, cool from -120C to -1000C t@ 4 0 C/min, cool from -100*C to -140*C @ 20*C/min, hold at -140 0 C. After the straws had reached -140"C, they were quickly removed from the freezer and plunged into liquid nitrogen. 20 Thawed straws were analyzed by IVOS for % motility and % progressive motility after incubation at 370C for 30 and 120 minutes. Results from a set of sorted and unsorted straws are summarized in Fig. 130 and Fig. 131. Multi-channel Sorting Example IV 25 Bull semen was collected from a sexually mature bull using an artificial vagina and the ejaculate split into two aliquots. The first aliquot of 25OpL of semen was suspended in 5 mL of 3700 Triladylo. The second aliquot, which comprised the remained of the ejaculate, was suspended in two parts 370C carbonate buffer (two parts 0.097 molesL of NaHC a 3 0.173 30 moles/L of KHCO 3 , 0.090 moles/L

C

6

H

8 0 7 -H20 in water)(pH 6.1-6.2) and held under C02. Both aliquots were transported at 37*C in a temperature-controlled container to the processing facility. At the processing facility, the first aliquot was floated in -120mL of 370C water in a 200mL beaker and placed in the cold room to slowly cool to 50C. The second aliquot was analyzed for concentration, motility and progressive motility by the Hamilton-Thorn Motility Analyzer (IVOS), 35 according to standard and well known procedures (Farrell et al. Theriogenology, 49(4): 871-9 (Mar 1998)). A 5 mL tube of 150 X 106 sperm/mL sperm suspension was prepared by transferring a fraction containing 750 million sperm from the second aliquot (pH 6.1-6.2) to an empty tube and adding 280C carbonate buffer (pH 7.35) to a final volume of 5 ml. To this sperm suspension, 10 40 mM Hoechst 33342 solution in water was added to yield a final dye concentration i 51M Hoechst 33342. The suspension was held at 41*C under C02 for approximately 40 minutes and 143 then placed at 28 0 C for sorting. Ten pL of 25mg/mL FD&C #40 was added to the tube of stained sperm suspension just prior to sorting. The stained sperm suspension was loaded onto the sample port of one channel of a multi-channel droplet sorting flow cytometer system. The sperm suspension was maintained at 5 28 0 C. X & Y chromosome bearing sperm were separated by the flow cytometry using a coincidence abort sort strategy for a time period necessary to place an enriched X chromosome bearing cell population of approximately eighteen million sperm into a collection tube that had been prepared by soaking with sheath buffer for at least one hour and then adding 0.5mL of Triladyle cryo-preservation media (pfl 6.6). The sperm cells were introduced into the flow 10 cytometry system at a rate of between about 25,000 and 30,000 cells/second. An enriched population of X chromosome bearing cells was collected at a rate varying from 4,500 per second to 6,000 per second. When approximately eighteen million sperm had been sorted into a collection tube, the tube was removed and replaced with another tube that has been similarly prepared. Immediately after removal of a collection tube from the flow cytometer, the sorted 15 sperm suspension was centrifuged for 7 min @ 700 X g. The supernatant was removed using a transfer pipette to yield a concentration of approximately 100 million sperm/mL. Triladyl cryo preservation media and pyruvate (pH 6.6) was added to the sperm suspensions to yield a final concentration of approximately 50 million sperm/mL. This process continued until the flow cytometer had produced two collection tubes (C2-C3). The re-suspended sorted sample tubes 20 were floated in -120mL of 28 0 C water in a 200mL beaker and placed in a soc cold room to slowly cool. After the sorted samples reached 5 0 C, the two tubes of sorted sperm were combined into one tube. The pooled sample was analyzed by IVOS to determine the % motility, % progressive motility and concentration. Additional Triladyl@ cryo-preseration media and pyruvate (pH 6.6) 25 was added to the sample to yield a final concentration of approximately 50 million sperm per mL. A summary of the IVOS assessment compared to the non-sorted sample of the same ejaculate is illustrated in Fig. 132. The pooled sorted sample and unsorted sample (i.e., the first aliquot from above) were loaded Into standard 0.25cc straws in the 5 0 C cold room. The loaded straws were transferred to 30 a programmable freezer and frozen by the following program: 5 mi @ 5C, cool from VC to 12 0 C @ 4 0 C/min, cool from -12*C to -100*C w 4 0C/min, cool from -1005C to -140C @ 20 C/min, hold at -140*C. After the straws had reached -140 0 C, they were quickly removed from the freezer and plunged into liquid nitrogen. Thawed straws were analyzed by IVOS for % motility and % progressive motility 35 immediately after thawing and after incubation at 37 0 C for 30 minutes. Results from a set of sorted and unsorted straws are summarized in Fig. 133 and Fig. 134. 40 144 CAPILLARY TUBE NOZZLE SYSTEM Fig. 135 illustrates an alternative nozzle system, generally designated 1335, similar to that described above except that a capillary tube 1337(of quartz or fused silica, for example) is connected to the nozzle 137 so that fluid exiting the nozzle orifice 103 is directed into and 5 through the tube. The optics system 109 of the flow cytometer is optically coupled to the side of the tube in a suitable manner, as by a chamber 1341 filled with a light-transmitting medium such as oil or gel having a known index of refraction. The use of a capillary tube, compared to the jetting of the fluid stream through open space, has the benefit of reducing the lensing of the stream 21 due to the acoustical energy supplied by the transducer 105, and enabling the 10 focusing lens 1343 to be positioned immediately adjacent the fluid stream for increasing resolution of the emission signals. After the particles have been interrogated and classified, they may be sorted using any conventional techniques known to those skilled in the art, as by use of a fluid switching device shown in Fig. 137 or other suitable devices such as photo-damage systems or droplet sorting 15 systems. SORTING TECHNIQUES OTHER THAN DROPLET SORTING Photo-damaqe Sortinq The flow cytometry improvements of this invention are applicable not only to droplet cell 20 sorting as described above, but also to other sorting techniques, such as sorting by photo damage (laser ablation). Photodamage sorting is discussed in United States Patent No. 4,395,397, which is incorporated herein by reference in its entirety. Fig. 136 schematically illustrates one embodiment of a single-channel flow cytometry photo-damage system, generally designated by the reference number 25 As shown in Fig. 136, the photo-damage sorting system 1351 is similar to the droplet sorting system of Fig. 2, and corresponding parts are designated by corresponding reference numbers with the addition of a double prime ("). In general, the system comprises the same components as the system of Fig. 2, except that the droplet sorting components are eliminated (e.g., the transducer 105, the charging device 627, the deflector plates 629, and associated 30 power sources 635)., Instead these components are replaced by a laser 1353 or similar device which is responsive to instructions received from the microprocessor 131" to ablate undesired particles in the fluid stream 21". As a result, the stream collected in a collection receptacle 1355 contains a desired population of particles. For example, if the particles being analyzed are sperm cells and the intended result is to collect sperm cells having a characteristic A (e.g., a 35 desired chromosome content), then the microprocessor receives signals from the epi-illumination system 415" which identifies cells not having characteristic A and selectively activates the laser to ablate such cells or otherwise render them ineffective. Different control sorting strategies can be employed in a photo-damage system, including the "high recovery" and "high purity" sorting strategies discussed above in the context 40 of a droplet sorter. In a photo-damage system, particles contained in the fluid stream are spaced 145 at various intervals along the stream and generally follow one after another in single file. The particles have different characteristics, some having a characteristic A, for example, and others having a characteristic B. The sequence of particles is random, so viewed as a continuous procession, the particles can be divided into different particle series, one following another, 5 including a first particle series consisting only of one or more particles having characteristic A, a second particle series consisting only of one or more particles having characteristic B and a third particle series consisting of two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. The latter (third) group generally corresponds to the closely spaced particles in a "coincident" droplet discussed previously, at 10 least for sorting strategy purposes. Thus, the two or more particles in the third group may be closely spaced in the sense that the spatial separation between the particles is insufficient to allow accurate discrimination/classification of the particles, or because such separation is insufficient to permit one particle in the series to be ablated by the laser without damaging the other particle(s) in the same series. In any event, the closely spaced particles in each (or at least 15 some) of the third series of particles can be ablated or not ablated, depending on the sorting strategy employed. It should be noted that multiple particles in a first series or multiple particles in a second series could be "closely spaced", but since the particles in any such series have the same characteristic (A or B), they are treated as a single-particle series, at least for sorting strategy purposes. 20 The photo-damage system can be a single-channel system or a multi-channel system, as described above. Fluid Switching Sortinq It is contemplated that the principles of this invention can also be applied to flow 25 cytometry systems using fluid switching techniques, as disclosed, for example, in U.S. Patents Nos. 6,432,246 (Adair), 4,756,427 (Gbhde, et al.), and 3,791, 517 (Friedman), which are incorporated herein by reference in their entireties. Fig. 137 is a partial view showing such a system, generally designated 1357. It is substantially identical to the system shown in Fig. 2 except that the nozzle system 101" includes a capillary tube 1369 (e.g., see Fig. 135), and the 30 sorting system comprises a fluid-switching device 1359 coupled to the capillary tube 1369 downstream from the interrogation location 115'. The construction and operation of the fluid switching device can incorporate any conventional fluid switching technology such as disclosed in the above-referenced patents. In general, the device functions to sort desired particles from undesired particles in response to instructions received from the processor by intermittently 35 diverting portions of the fluid stream containing the desired/undesired particles along separate flow paths 1361, 1365 for collection in vessels or the like. The switching is commonly achieved by selectively actuating a transducer 1367 in one of the flow paths. The various sorting strategies described above in regard to droplet sorting and photo damage sorting can also be employed in a fluid-switching system. In the fluid-switching system, 40 particles contained in the fluid stream are also spaced at various intervals along the stream and 146 generally follow one after another in single file. The particles have different characteristics, some having a characteristic A, for example, and others having a characteristic B, and the sequence of particles is random. Therefore, as discussed above in regard to the photo-damage system, the procession of particles can be divided into different particle series, one following another, 5 including a first particle series comprising one or more particles having characteristic A, a second particle series comprising one or more particles having characteristic B and a third particle series comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. The latter (third) group generally corresponds to the closely spaced particles in a "coincident" droplet discussed previously, at least for sorting 10 strategy purposes. Thus, the two or more particles in the third group may be closely spaced in the sense that the spatial separation between the particles is insufficient to allow accurate discrimination/classification of the particles, or because such separation Is insufficient to permit one particle in the series to be diverted by the fluid-switching device separate from the another particle in the same series. In any event, the closely spaced particles in each (or at least some) 15 of the third series of particles can be diverted to one collection location or another, depending on the sorting strategy employed. As explained above in connection with photo-damage sorting, multiple particles in a first series or multiple particles in a second series could be "closely spaced", but since the particles in any such series have the same characteristic (A or B), they are treated as a single-particle series for the purpose of sorting strategy. 20 The fluid switching system can be a single-channel system or a multi-channel system, as described above. Droplet Interference Sortinq It is also contemplated that the technology of this invention can be used in conjunction 25 with a droplet interference fluidic switching technique. For example, a high-speed droplet interference sorting system 1371, shown schematically in Fig. 138, may be used to sort particles by diverting selected segments of the coaxial carrier and sheath fluid stream. In contrast to some other sorting techniques, the droplet interference sorting technique does not require the coaxial carrier and sheath stream to be formed into droplets. Thus, there is 30 no need to couple the nozzle system 101"' used for delivery of the carrier and sheath fluids with a droplet generation system. By way of example only, passing the carrier and sheath fluids through a nozzle system at 60 psi to create a 50 micron diameter stream is one suitable arrangement for formation of a laminar coaxial fluid stream for delivery of particles to the droplet interference sorting system. Particles in the coaxial fluid stream are analyzed and classified by 35 the optics system 109' and processor 131"' as they move through the interrogation location 115"', as has been described above for the other sorting systems. Sorting occurs downstream from the interrogation location, at a location where the coaxial fluid stream intersects a high speed droplet interference stream 1373. The droplet interference stream 1373 is generated by a droplet generation system 1375 40 similar to the droplet generation system used for droplet sorting. A high-speed fluid stream 1379 147 passes through a high-speed nozzle system 1377 that is coupled to a piezoelectric transducer 1381 or other source of acoustical energy for causing the high-speed fluid stream to break into droplets 1383 downstream from the high-speed nozzle. For example, a particle-free fluid at 1500 psi may be passed through the high-speed nozzle to form a 70 micron diameter high-speed fluid 5 jet. The high-speed nozzle may be oscillated at 400 KHz to form high-speed droplets. The high speed droplets 1383 pass through an electric field generated by one or more electric deflection plates 1387 so that the path of the high-speed droplets may be controlled by selectively applying an electric charge to the droplets, as was done to control the path of droplets in the droplet sorting system. The high-speed droplet interference stream is directed so some high-speed 10 droplets intersect the coaxial fluid stream at a point 1399 downstream from the interrogation location. For example, uncharged droplets 1389 may be directed to collide with the fluid stream while charged droplets 1391 are deflected away from the coaxial fluid stream. When a high speed droplet collides with the coaxial fluid stream, a segment 1397 of the fluid stream and any particles contained therein are diverted from the path they would have otherwise taken. The 15 application of a charge or no charge to a high-speed droplet may be timed so the arrival of that droplet at the intersection 1399 with the coaxial fluid stream coincides with the arrival of a particular segment of the coaxial fluid stream. Thus, by selectively charging high-speed droplets depending on the classification of particles contained within the coaxial stream segments, one can sort particles by diverting all coaxial fluid stream segments that contain one or more selected 20 particles and not diverting other coaxial stream segments or vice-versa. Collection capillaries 1403 having a slight vacuum may be used to collect both the diverted 1397 and undiverted coaxial stream segments. The droplet interference sorting system may be set up so the high speed droplets merge with diverted coaxial stream segments or so the high-speed droplets remain separate from the diverted stream segments after collision with the coaxial stream 25 segments. Because there are no particles or cells in the high-speed droplet interference stream 1373, it Is possible to use very high pressures and very high droplet frequencies without damaging the particles or cells to be sorted. This allows sorting of stream segments each having less volume (e.g., four times less volume) than the volume of a droplet in the droplet sorting 30 system. This greatly increases the maximum throughput of the system while also reducing the dilution factor of the sorted particles. Moreover, because finely filtered liquid with no cells or particles is used to form the droplet interference stream, more consistent droplet formation is possible because the droplet formation nozzle is less likely to become clogged or suffer from protein buildup than the nozzle system used in the droplet sorting system. Another advantage is 35 that the distance between particle analysis at the interrogation location and the sorting point 1399 can be reduced (e.g., by a factor of four), allowing more accurate prediction of the time of arrival of a particular particle at the sorting point. Furthermore, the droplet interference system allows more flexibility in adjustment of nozzle size or pressure for the coaxial fluid stream. If desired, the droplet interference sorting system can be combined with the capillary tube nozzle system. A 148 multi-channel droplet interference sorting system may use a high-pressure fluidic pump to supply multiple droplet interference stream generating nozzles with fluid from a common fluid supply. When introducing elements of the present invention or the embodiment(s) thereof, the articles "a," "an," "the," and "said" are intended to mean that there are one or more of the 5 elements. The terms "comprising," "including," and "having" are intended to be inclusive and mean that there may be additional elements other than the listed elements. The term "or" is intended to include "and/or" and is intended to mean "one or another or both." Thus, an indication of "ABC or DEF" means (1) ABC, or (2) DEF, or (3) both ABC and DEF. The term "and/or" is intended to have the same meaning as "or" as defined above. Thus, the term "and/or" 10 Is intended to include "or" and is intended to mean "one or another or both." For example, an indication of "ABC and/or DEF" means (1) ABC, or (2) DEF, or (3) both ABC and DEF. In view of the above, it will be seen that the several objects of the invention are achieved and other advantageous results attained. As various changes could be made in the above constructions, products, and methods 15 without departing from the scope of the invention, it is intended that all matter contained in the above description and shown in the accompanying drawings shall be interpreted as illustrative and not in a limiting sense. 20 Comments on Inventive Features Those skilled in the art will recognize that the invention described above includes many inventive aspects, including at least the following: A. Multi-Channel Sorting Apparatus 25 Al. A multi-channel system for sorting particles according to one or more characteristics of the particles, said system comprising: multiple flow cytometry units each of which is operable to sort a desired population of particles in a mixture of particles by interrogating a stream of fluid containing said particles using 30 a beam of electromagnetic radiation, said units sharing an integrated platform comprising at least one of the following elements: (1) a common supply of particles; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common 35 processor for receiving and processing information from the units; and (6) a common fluid delivery system for delivering fluid containing said particles to said flow cytometry units. A2. The system of Al wherein said particles are cells. 40 A3. The system of Al wherein said particles are sperm cells.

149 A4. The system of Al wherein said system comprises at least element (2), and wherein one or more of said multiple flow cytometry units comprises a jet-in-air droplet sorting flow cytometry unit. 5 a A5. The system of Al wherein said integrated platform comprises at least elements (2) and (3). A6: The system of Al wherein said integrated platform comprises at least elements (4) and (5). 10 A7. The system of Al wherein said integrated platform comprises at least element (2), said common source comprising a single laser beam. A8. The system of A7 further comprising a beam splitting system for splitting the single 15 laser beam into multiple beams and directing the multiple beams into optics systems of respective flow cytometry units. A9. The system of A8 wherein said single laser beam comprises a plurality of pulses, each pulse having a peak power that is greater than the average power output of the laser. 20 Al0. The system of Al wherein said integrated platform comprises at least element (3), said flow cytometry units comprising interchangeable modules removably mounted in the housing. 25 Al 1. The system of Al wherein each flow cytometry unit comprises an epi-illumination optics system for interrogating a respective fluid stream. A12. The system of Al further comprising a collection system for collecting said desired population of particles from each unit. 30 Al 3. The system of Al wherein said integrated platform comprises at least element (5), and wherein said common output comprises an indication of the fluorescence intensity measured by each unit. 35 A14. The system of Al wherein said integrated platform comprises at least element (5), and wherein said common output comprises an indication of the rate at which each unit is separating particles. A15. The system of Al wherein said integrated platform comprises at least element (5), 40 and wherein said common output comprises an indication of particle staining variations.

I50 Al 6. The system of Al wherein said integrated platform comprises at least element (5), and wherein said common output comprises an indication of a decision boundary used by each unit for discriminating between particles. 5 Al 7. The system of Al wherein each of said flow cytometry units comprises a droplet sorting system. A18. The system of Al wherein said integrated platform comprises at least element (5), 10 and wherein said common output comprises an indication of a droplet break-off location of each unit. A19. The system of Al wherein at least one of said flow cytometry units comprises a photo-damage system. 15 A20. The system of Al wherein at least one of said flow cytometry units comprises a fluid-switching sorting system. A21. The system of Al wherein said flow cytometry units are adapted to operate in 20 parallel. A22. The system of Al wherein the integrated platform comprises at least a shared laser operable to emit a plurality of electromagnetic radiation pulses, wherein each pulse has a peak power exceeding the average power of the laser, and wherein one or more of said flow 25 cytometry units comprises: a flow channel for directing a fluid stream containing sample particles through a particle interrogation location; 30 a beam guidance system operable to direct a portion of the electromagnetic radiation in a pulse to the interrogation location; a timing circuit operable to produce a timing signal indicative of the arrival of electromagnetic radiation at the interrogation location; 35 a detector adapted to detect electromagnetic radiation from the interrogation location and operable to output a time-varying analog signal indicative of the intensity of the detected electromagnetic radiation; 151 an analog to digital converter adapted to receive the time-varying analog signal as input and to sample the analog signal to produce a digitized output; and an electronic processor operable to analyze the digitized output from the analog to digital 5 converter as a function of the timing signal. A23. The system of Al wherein the multiple flow cytometry units comprise three or more flow cytometry units. 10 A24. The system of Al wherein the multiple flow cytometry units comprise at least twelve flow cytometry units. A25. The system of claim Al, wherein the integrated platform comprises at least element (5), and wherein the common processor performs at least one of: (1) receiving and 15 processing said Information in real time; and (2) receiving and processing said information to permit evaluation of the operation of one unit relative to another unit. A26. The system of Al wherein each flow cytometry unit comprises a sensor operable to generate a time-varying output signal indicative of at least one characteristic of the particles, 20 wherein said integrated platform comprises at least element (5) and said information received by the common processor comprises the output signals from the respective sensors, and wherein the processor is operable to receive the output signals as a substantially continuous stream and to substantially continously process the output signals in real time. 25 A27. The system of Al wherein said Integrated platform comprises a common processor operable to send control signals to the flow cytometry units in real time during a sorting process to adjust their operation as a function of said information received by the common processor, and wherein the flow cytometry units are responsive to the control signals. 30 B. Multi-Channel Sorting Method B1. A multi-channel method of sorting particles according to one or more characteristics of the particles, said method comprising: 35 providing a plurality of flow cytometry units; operating said flow cytometry units to conduct a plurality of flow cytometry operations, said operations comprising forming separate fluid streams each containing a mixture of particles, and sorting desired populations of particles in said mixtures of particles by interrogating the 40 streams using beams of electromagnetic radiation; and 152 sharing at least one of the following elements while conducting said operations: (1) a common supply of particles for said streams; (2) a common source of electromagnetic radiation for said beams; (3) a common operations control input; (4) a common processor for receiving 5 and processing information from the units; (5) a common system for delivering fluid to said streams; and (6) a common housing for said flow cytometry units. B2. The method of B1 wherein said particles are cells. 10 B3. The method of BI wherein said particles are sperm cells. B4. The method of B1 wherein at least one of said multiple flow cytometry units comprises a jet-in-air droplet sorting flow cytometry unit. 15 B5. The method of BI further comprising at least sharing said common source of electromagnetic radiation in the form of a single laser beam, said method further comprising splitting the single laser beam into multiple beams and directing the multiple beams into optics systems of respective flow cytometry units. 20 B6. The method of B5 further comprising reflecting a percentage of beam light of the single beam toward the optics system of one of said flow cytometry units, and passing a percentage of beam light of the single beam for transmission to the optics system of another of said flow cytometry units. 25 B7. The method of B6 further comprising using a solid state laser to form said single laser beam. B8. The method of B7 further comprising mode-locking the solid state laser so that the single laser beam comprises a plurality of pulses, wherein each pulse has a peak power that is 30 greater than the average power output of the laser. B9. The method of BI further comprising sharing at least element (6), and wherein said method further comprises removably mounting said flow cytometry units in the common housing. 35 B10. The method of B1 further comprising at least sharing said common source of electromagnetic radiation in the form of a shared laser; the method further comprising the steps of: emitting a plurality of electromagnetic radiation (EMR) pulses from a laser, wherein the 40 peak power of each pulse exceeds the average power of the laser; 153 directing each pulse into a beam splitting and guidance system to intermittently illuminate each fluid stream and the particles contained therein by directing a portion of the energy in the pulses along a beam path from the laser to each interrogation location; detecting EMR from at least one interrogation location; generating a time-varying analog signal indicative of the intensity of the detected EMR from said interrogation location; 10 generating a timing signal indicative of the arrival of a pulse at said interrogation location; converting the time-varying analog signal into a digital signal; and 15 analyzing thedigital signal to determine characteristics of the particles in the fluid stream flowing through the respective interrogation location. B 11. The method of 81 further comprising using a first sorting strategy in a first operation of said operations and a second sorting strategy different from the first sorting strategy 20 in a second operation of said operations. B12. The method of B1 further comprising collecting a population of desired particles sorted by each flow cytometry unit, and combining the population collected from one unit with a population collected from a different unit to produce a blended population of desired particles. 25 813. The method of B1 further comprising varying the rate at which fluid is delivered to one or more of the flow cytometry units as a function of at least one of the following: (1) the purity of a first sorted population; and (2) the quantity of desired particles In a second population 30 814. The method of 81 further comprising conducting said flow cytometry operations in parallel. B15. The method of frh wherein the sharing step comprises sharing at least element (4), the method further comprising using the common processor to do at least one of the following: 35 (1) receive and process said information in real time; and (2) receive and process said information to permit evaluation of the operation of one unit relative to another unit. B16. The method of 81 wherein the sharing step comprises sharing at least element (4), the method further comprising using a sensor for each respective cytometry unit to generate a 40 time-varying output signal indicative of at least one characteristic of the particles and using the 154 common processor to receive the respective output signals as a substantially continous stream and to process the output signals in real time. B1 7. The method of B1 wherein the sharing step comprises sharing at least element (4), 5 the method further comprising sending a control signal to one or more of the flow cytometry units in real time during a sorting process to adjust the unit's operation as a function of the information received by the common processor. 10 C. [Reserved] D. Multi-channel Analyzer Di. A multi-channel system for classifying particles according to one or more 15 characteristics of the particles, said system comprising: a plurality of flow cytometry units each of which is operable to classify particles in a mixture of particles by interrogating a stream of fluid containing said particles using a beam of electromagnetic radiation, 20 said units sharing an integrated platform comprising at least one of the following elements: (1) a common supply of particles; (2) a common housing; (3) a common input for controlling operation of the units; (4) a common processor for receiving and processing information from the units; and (5) a common fluid delivery system for delivering fluid containing said particles to said flow 25 cytometry units. D2. The system of D1 wherein said Integrated platform further comprises a common source of electromagnetic radiation. 30 D3. The system of D1 wherein said particles are cells. D4. The system of D1 wherein said particles are sperm cells. D5. The system of D1 wherein said integrated platform comprises at least elements (3) 35 and (4). D6. The system of D5 wherein said integrated platform further comprises a common source of electromagnetic radiation.

155 D7. The system of D1 wherein said integrated platform further comprises a common source of electromagnetic radiation, said common source comprising a single laser beam. D8. The system of D7 further comprising a beam splitting system for splitting the single 5 laser beam into multiple beams and directing the multiple beams into optics systems of respective flow cytometry units. D9. The system of D1 wherein said integrated platform comprises at least element (2), said flow cytometry units comprising interchangeable modules removably mounted in the 10 housing. D10. The system of D1 wherein each flow cytometry unit comprises an epi-illumination optics system for interrogating a respective fluid stream. 15 D11. The system of D1 wherein said integrated platform comprises at least element (4), and wherein said processor is operable to output an indication of the fluorescence intensity measured by each unit. D12. The system of D1 wherein said integrated platform comprises at least element (4), 20 and wherein said processor is operable to output an indication of the rate at which each unit is separating particles. D13. The system of D1 wherein said integrated platform comprises at least element (4), and wherein said processor is operable to output an indication of particle staining variations. 25 D14. The system of D1 wherein said integrated platform comprises at least element (4), and wherein said processor is operable to output an indication of a decision boundary used by each unit for discriminating between particles. 30 D15. The system of D1 wherein said flow cytometry units are adapted to operate in parallel. D16. The system of D1 wherein said plurality of flow cytometry units are operable to sort the particles. 35 D1 7. The system of D16 wherein the integrated platform further comprises a common source of electromagnetic radiation, and wherein said plurality of flow cytometry units comprises a jet-in-air droplet sorting flow cytometry unit.

156 D18. The system of D1 wherein said integrated platform comprises at least element (4), and wherein the common processor is operable to perform at least one of the following: (1) receive and process said information in real time; and (2) receive and process said information to permit evaluation of the operation of one unit relative to another unit. 5 D19. The system of claim D1 wherein each flow cytometry unit comprises a sensor operable to generate a time-varying output signal indicative of at least one characteristic of the particles, wherein said integrated platform comprises at least element (4) and said information received by the common processor comprises outpt the signals from the respective sensors, and 10 wherein the processor is operable to receive the output signals as a substantially continous stream and to process the output signals in real time. D20. The system of D1 wherein said integrated platform comprises a common processor operable to send control signals to the flow cytometry units In real time during a sorting 15 process to adjust their operation as a function of said information received by the common processor, and wherein the flow cytometry units are responsive to the control signals. E. Multi-Channel Analyzing Method 20 El. A multi-channel method of classifying particles according to one or more characteristics of the particles, said method comprising: providing a plurality of flow cytometry units; 25 operating said flow cytometry units to conduct a plurality of flow cytometry operations, said operations comprising forming separate fluid streams each containing a mixture of particles, and classifying particles in said mixtures of particles by interrogating the streams using beams of electromagnetic radiation; and 30 sharing at least one of the following elements to conduct said operations: (1) a common supply of particles for said streams; (2) a common operations control input; (3) a common processor for receiving and processing Information from the units; (4) a common system for delivering fluid to said streams; and (5) a common housing for said flow cytometry units. 35 E2. The method of El further comprising sharing a common source of electromagnetic radiation for said beams. E3. The method of E2 wherein said plurality of flow cytometry units comprises a jet-in-air droplet sorting flow cytometry unit. 40 157 E4. The method of El further comprising operating said plurality of flow cytometers to sort said mixture of particles based on their classification. E5. The method of El wherein said particles are cells. 5 E6. The method of El wherein said particles are sperm cells. E7. The method of El further comprising sharing a common source of electromagnetic radiation for said beams in the form of a single laser beam, splitting the single laser beam into 10 multiple beams, and directing the multiple beams into optics systems of respective flow cytometry units. E8. The method of E7 wherein the sharing step comprises at least element (5), the method further comprising guiding said single laser beam into said common housing prior to 15 splitting the beam. E9. The method of E7 further comprising reflecting a percentage of beam light of the single beam toward the optics system of one of said flow cytometry units, and passing a percentage of beam light of the single beam for transmission to the optics system of another of 20 said flow cytometry units. E10. The method of El wherein the sharing step comprises at least element (5), the method further comprising removably mounting said flow cytometry units in the common housing. 25 El 1. The method of El comprising operating each flow cytometry unit to interrogate a respective fluid stream using an epi-illumination optics system. E12. The method of El further comprising operating said flow cytometry units In parallel. 30 E13. The method of El wherein said plurality of flow cytometry units comprise twelve or more flow cytometry units. E14. The method of El wherein the sharing step comprises sharing at least element (4), the method further comprising using the common processor to perform at least one of the 35 following: (1) receive and process said information in real time; and (2) receive and process said information to permit evaluation of the operation of one unit relative to another unit. E15. The method of El wherein the sharing step comprises sharing at least element (4), the method further comprising using a sensor for each respective cytometry unit to generate a 40 time-varying output signal indicative of at least one characteristic of the particles and using the 158 common processor to receive the respective output signals as a substantially continous stream and to process the output signals in real time. E16. The method of El wherein the sharing step comprises sharing at least element (4), 5 the method further comprising sending a control signal to one or more of the flow cytometry units in real time during a sorting process to adjust the unit's operation as a function of the Information received by the common processor. F. [Reserved] 10 G. Method of Splitting Single Laser for Multi-Channel Cytometry G1. A method of sorting particles using a system comprising a three or more flow cytometry units each of which Is operable to sort a desired population of particles from a mixture 15 of particles by interrogating a stream of fluid containing said particles using a beam of light, said method comprising: generating a single laser beam; 20 splitting the single beam into three or more light beams and directing the light beams into optics systems of the flow cytometry units; and operating the flow cytometry units to sort particles. 25 G2. The method of G1 wherein each cytometry unit interrogates the fluid stream with a light beam of about the same intensity. G3. The method of G1 wherein each unit requires a light beam having a power of W watts, and wherein said method further comprises generating said single laser beam having a 30 power of (W x N) + L, where N equals the number of flow cytometry units and L equals power loss in the system. G4. The method of G1 further comprising balancing the amount of beam light used by the cytometry units to interrogate respective fluid streams by using one or more filters to 35 attenuate the intensity of at least one of said three or more light beams. G5. The method of G4 further comprising adjusting the intensity of beam light entering respective units so that each unit receives the same amount of beam light within a tolerance of 10%. 40 159 G6. The method of GI wherein at least one of said flow cytometry units uses a droplet sorting process to sort said particles. G7. The method of GI wherein at least one of said flow cytometry units uses a photo 5 damage process to sort said particles. G8. The method of GI wherein at least one of said flow cytometry units uses a fluid switching sorting process to sort said particles. 10 G9. The method of GI wherein said flow cytometry units are mounted in a common housing, the method further comprising guiding said single laser beam into said common housing prior to splitting the beam. G10. The method of G9 further comprising reflecting a percentage of beam light of the 15 single laser beam toward the optics system of one of said flow cytometry units and passing a percentage of beam light of the single laser beam for transmission to the optics system of another of said flow cytometry units. GI1. The method of G1 wherein the step of splitting a single beam comprises splitting a 20 single beam into four separate beams. G12. The method of G1I wherein the splitting step comprises using a 50/50 beamsplitter to split the single beam into two beams, using a second 50/50 beamsplitter to split one of the two beams into two additional beams, and using a third 50/50 beamsplitter to split the 25 other of the two beams into two more additional beams. H. Apparatus for Sorting Using Sort Strategy H1. In a flow cytometry system for sorting a mixture of particles including particles 30 having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said parUcles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing 35 desired particles, the improvement comprising: a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the following: (1) 40 the purity of said at least one population with respect to either characteristic A particles or 160 characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 5 H2. The system of H1 wherein the particles are cells and characteristics A and B relate to physical characteristics of the cells. H3. The system of HI wherein the particles are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. 10 H4. The system of H3 wherein characteristic B is indicative of other than a live X cell (~X). H5. The system of H4 further comprising maintaining the purity of said at least one 15 population at more than 85% but less than 95%. H6. The system of H1 wherein the control increases the rate of fluid delivery when said purity is greater than a desired purity and decreases the rate of fluid delivery when said purity is less than said desired purity. 20 H7. The system of H1 wherein the control determines the purity of said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery so that the purity corresponds to the desired purity. 25 H8. The system of H7 wherein the control increases the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is greater than an acceptable quantity of characteristic A particles in the at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of characteristic A particles in said at least 30 one population is less than said acceptable quantity. H9. The system of H8 wherein the control determines the quantity of characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating an 35 acceptable quantity of characteristic A particles in said at least one population, and wherein the control varies the fluid delivery rate to obtain said acceptable quantity in said at least one population. HI. The system of H1 wherein said stream is formed to contain particles following 40 generally one after another in a series which comprises sequential sets of particles, including first 161 particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. 5 HI 1. The system of H10 wherein said sorting system is operable to use a sorting strategy in which said first particle sets are selected for collection in said at least one population and said second and third particle sets are not selected for collection in said at least one population. 10 H12. The system of H10 wherein said sorting system is operable to use a sorting strategy in which said first and third particle sets are selected for collection in said at least one population and said second particle set is not selected for collection in said at least one population. 15 H13. The system of H1 wherein said sorting system comprises a droplet sorting system. H14. The system of Hi wherein said sorting system comprises a photo-damage sorting system. 20 H15. The system of HI wherein said sorting system comprises a fluid-switching sorting system. 25 1. Method for Sorting Particles Using Sorting Strategy 11. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method comprising: 30 delivering a fluid containing said particles; forming the fluid into a stream and using flow cytometry to classify the particles in the stream according to said characteristics; 35 sorting the particles in the stream according to said classification and according to a sorting strategy thereby to provide at least one population containing desired particles; and varying the sorting strategy or varying the rate at which fluid Is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either 40 characteristic A particles or characteristic B particles; and (2) the quantity of characteristic

A

162 particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 12. The method of 11 wherein the particles are cells and characteristics A and B relate to 5 physical characteristics of the cells. 13. The method of 11 wherein said particles are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. 10 14. The method of 13 wherein characteristic B is indicative of other than a live X cell (-X). 15. The method of 13 further comprising maintaining said purity at more than 85% but less than 95%. 15 16. The method of II further comprising increasing the rate of fluid delivery when said purity is greater than a desired purity and decreasing the rate of fluid delivery when said purity is less than the desired purity. 17. The method of 11 further comprising increasing the rate of fluid delivery when the 20 quantity of characteristic A particles in said at least one population is greater than an acceptable quantity of characteristic A particles in the at least one population, and decreasing the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is less than said acceptable quantity. 25 18. The method of 11 further comprising forming the stream to contain particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at 30 least one of which has characteristic B. 19. The method of 18 further comprising sorting said particles according to a sorting strategy in which only first particles sets are selected for collection in said at least one population. 35 110. The method of 18 further comprising sorting said particles according to a sorting strategy in which first and third particle sets are selected for collection in said at least one population. 111. The method of 11 wherein said sorting comprises using a droplet sorting process. 40 163 112. The method of 11 wherein said sorting comprises using a photo-damage sorting process. 113. The method of 11 wherein said sorting comprises using a fluid-switching sorting 5 process. J. Droplet Sorter Including Sort Strategy J1. A system for sorting a mixture of particles including particles having a characteristic 10 A and particles having a characteristic B, said system comprising: a fluid delivery system for delivering a fluid stream containing said particles; a flow cytometry apparatus for receiving said stream, forming droplets containing said 15 particles, and sorting said droplets into different populations according to a sorting strategy, said droplets including first droplets each containing one or more particles having characteristic A, second droplets each containing one or more particles having characteristic B and third droplets each containing one or more particles having characteristic A and one or more particles having characteristic B; and 20 a control responsive to information received from the flow cytometry apparatus for controlling the flow cytometry apparatus to vary the sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of at least one droplet population with respect to either characteristic A 25 particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in at least one droplet population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. J2. The system of J1 wherein the control controls the fluid delivery system to maintain 30 the rate at which fluid is delivered as substantially constant, and wherein the control varies the sort strategy. J3. The system of J2 wherein the control varies the sort strategy in order to vary the percentage of third droplets in one of the droplet populations. 35 J4. The system of The system of J1 wherein the control controls the fluid delivery system to vary the rate at which fluid is delivered as a function of the purity of said at least one droplet population. 40 J5. The system of J4 wherein said purity is at least 85% and not more than 95%.

164 J6. The system of Ji wherein the control controls the fluid delivery system to vary the rate at which fluid is delivered as a function of the quantity of characteristic A particles in said at least one droplet population relative to the total quantity of characteristic A particles in said stream. 5 J7. The system of J6 wherein the rate at which the fluid is delivered is varied so that the quantity of characteristic A particles in said at least one droplet population represents at least about 60% of the total quantity of characteristic A particles in said stream. 10 J8. The system of Ji wherein said particles are sperm cells, and wherein characteristic A Is indicative of a live X sperm cell. J9. The system of J1 wherein the ratio of characteristic A particles to characteristic B particles in said mixture is a known ratio, and wherein said control is operable classify some of 15 the particles as having characteristic A or characteristic B and to vary the fluid delivery rate as a function of the ratio of classified particles to the known ratio. J10. The system of J1 wherein the control determines a purity of the sorted particles based on output signals from the flow cytometry apparatus, said system further comprising an 20 operator input to the control for indicating a desired purity, and wherein the control varies the rate so that the purity of said at least one droplet population generally corresponds to the desired purity. 25 K. Droplet Sorting Method Including Sort Strategy K1. A method of sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising: delivering a fluid stream containing said particles; 30 forming droplets containing said particles; sorting said droplets into different populations according to a sorting strategy, said droplets including first droplets each containing one or more particles having characteristic A, 35 second droplets each containing one or more particles having characteristic B and third droplets each containing one or more particles having characteristic A and one or more particles having characteristic B; and varying the sorting strategy or varying the rate at which fluid is delivered as a function of 40 at least one of the following: (1) the purity of at least one droplet population with respect to either 165 characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in at least one droplet population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 5 K2. The method of K1 further comprising maintaining the rate at which fluid is delivered as substantially constant, and varying the sorting strategy. K3. The method of K2 further comprising varying the sorting strategy in order to vary the percentage of third droplets in one of the droplet populations. 10 K4. The method of K1 further comprising varying the rate at which fluid is delivered as a function of the purity of at least one of the droplet populations. K5. The method of K4 further comprising maintaining said purity in the range of 85% to 15 95%. K6. The method of K1 further comprising varying the rate at which fluid is delivered as a function of the quantity of characteristic A particles in said at least one droplet population relative to the total quantity of characteristic A particles in said stream. 20 K7. The method of K6 wherein the rate at which the fluid is delivered is varied so that the quantity of characteristic A particles in said at least one of the droplet populations represents at least about 60% of the total quantity of characteristic A particles in said stream. 25 K8. The method of K1 wherein said particles are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. K9. The method of K1 further comprising increasing the rate when the purity of said at least one droplet population is greater than the desired purity and decreasing the rate when the 30 purity of said at least one droplet population is less than the desired purity. L. Variable Flow Rate Droplet Sorter Having Feedback Loop LI. A system for sorting a mixture of particles including particles having a characteristic 35 A and particles having a characteristic B, said system comprising: a variable rate fluid delivery system for delivering a fluid stream containing said particles; a flow cytometry apparatus for receiving said stream, forming droplets containing said 40 particles, and sorting said droplets into different populations according to a sorting strategy, said 166 droplets including first droplets each containing one or more particles having characteristic A, second droplets each containing one or more particles having characteristic B and third droplets each containing one or more particles having characteristic A and one or more particles having characteristic B; and 5 a control responsive to information received from the flow cytometry apparatus for controlling the fluid delivery system to vary the rate at which fluid is delivered from the fluid delivery system as a function of at least one of the following: (1) the purity of at least one of the droplet populations with respect to either characteristic A particles or characteristic B particles; 10 and (2) the quantity of characteristic A particles or characteristic B particles in at least one droplet population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. L2. The system of Li wherein the control controls the fluid delivery system to vary the 15 rate at which fluid is delivered as a function of the purity of at least one of the droplet populations. L3. The system of L2 wherein the purity is at least 85% and not more than 95%. L4. The system of LI wherein the control controls the fluid delivery system to vary the 20 rate at which fluid is delivered as a function of the quantity or percentage of characteristic A particles in at least one droplet population relative to the total quantity of characteristic A particles in said stream. L5. The system of L4 wherein the rate at which the fluid is delivered is varied so that the 25 quantity of characteristic A particles in said at least one of the droplet populations represents at least about 60% of the total quantity of characteristic A particles in said stream. L6. The system of LI wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. 30 L7. The system of LI wherein said cells are sperm cells, and wherein characteristic A Is indicative of a live X sperm cell. L8. The system of L7 wherein at least some of the droplets in said at least one droplet 35 population contain at least one live X cell and at least one Y cell in the same droplet, and wherein said purity of said at least one droplet population is measured by X/(X+Y). L9. The system of L8 wherein said control is operable to vary the rate of fluid delivery to maintain said purity at more than 85% but less than 95%. 40 167 cells. L 0. The system of L7 wherein characteristic B is indicative of cells which are not live X LI I. The system of L7 wherein said control is operable to vary the rate of fluid delivery 5 so that percentage of live X cells in said at least one droplet population is at least 60% of the total number of live X cells in said first, second and third pluralities of droplets. L12. The system of L1 wherein the purity of said at least one droplet population is maintained at less than 95%. 10 LI 3. The system of LI wherein the ratio of characteristic A particles to characteristic B particles in said mixture is a known ratio, and wherein said control is operable to classify some of the particles has having characteristic A or characteristic B and vary the fluid delivery rate as a function of the ratio of the classified particles to the known ratio. 15 LI 4. The system of LI wherein the particles having characteristic A are live X sperm cells and the particles having characteristic B are sperm cells which are not live X sperm cells, and wherein said control is operable to vary the fluid delivery rate as a function of the ratio of classified sperm cells to 50%. 20 LI 5. The system of Li wherein the control increases the rate when the purity of said at least one droplet population is greater than a desired purity and decreases the rate when the purity of said at least one droplet population Is less than the desired purity. 25 Li 6. The system of Li wherein the control determines a purity of the sorted particles based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate so that-the purity of said at least one droplet population generally corresponds to the desired purity. 30 M. Droplet Sorting Method Using Variable Flow Rate and Feedback MI. A method of sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising: 35 delivering a fluid stream containing said particles; forming droplets containing said particles; 168 sorting said droplets into different populations according to a sorting strategy, said droplets including first droplets each containing one or more particles having characteristic A, second droplets each containing one or more particles having characteristic B and third droplets each containing one or more particles having characteristic A and particles having characteristic 5 B; and varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of at least one of the droplet populations with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or 10 characteristic B particles in at least one droplet population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. M2. The method of M1 further comprising varying the rate at which fluid is delivered as a function of the purity of at least one of the droplet populations. 15 M3. The method of M2 wherein said purity is at least 85% and not more than 95%. M4. The method of M1 further comprising varying the rate at which fluid is delivered as a function of the quantity of characteristic A particles in at least one droplet population relative to 20 the total quantity of characteristic A particles in said stream. M5. The method of M4 further comprising varying the fluid delivery rate so that the quantity of characteristic A particles in said at least one of the droplet populations represents at least about 60% of the total quantity of characteristic A particles in said stream. 25 M6. The method of M1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. M7. The method of M1 wherein said cells are sperm cells, and wherein characteristic A 30 is Indicative of a live X sperm cell. M8. The method of M7 wherein at least some of said droplets in said at least one of the droplet populations contain at least one live X cell and at least one Y cell in the same droplet, and wherein said purity of said at least one droplet population is measured by X/(X+Y). 35 M9. The method of M8 further comprising varying the rate of fluid delivery to maintain said purity at more than 85% but less than 95%. M10. The method of M7 wherein characteristic B is indicative of cells which are not live 40 X cells.

169 M1 1. The method of M7 further comprising varying the rate of fluid delivery so that percentage of live X cells in said at least one droplet population is at least 60% of the total number of live X cells in said first, second and third pluralities of droplets. 5 M12. The method of M 11 further comprising maintaining the purity of said at least one droplet population at less than 95%. M13. The method of MI wherein the ratio of characteristic A particles to characteristic B 10 particles in said mixture is a known ratio, and said method further comprises varying the fluid delivery rate as a function of the ratio of classified particles to the known ratio. M14. The method of M1 wherein the particles having characteristic A are live X sperm cells and particles having characteristic B are not live X sperm cells, said method further 15 comprising varying the fluid delivery rate as a function of the ratio of classified sperm cells to 50%. M15. The method of M1 further comprising increasing the rate when the purity of said at least one droplet population is greater than the desired purity and decreasing the rate when the 20 purity of said at least one droplet population is less than the desired purity. N. Sperm Sorting System for High Purity Sort Strategy 25 N1. A system for sorting X and Y sperm cells, said system comprising: a variable rate fluid delivery system for delivering a fluid stream containing X and Y sperm cells; 30 a flow cytometry apparatus for (1) receiving said stream and forming droplets containing said particles, said droplets comprising first droplets each containing one or more X sperm cells, second droplets each containing one or more Y sperm cells, and third plurality of droplets each containing one or more X sperms cells and one or more Y sperm cells, (2) sorting said first droplets from said second and third droplets, (3) collecting said first droplets to provide at least 35 one population of X sperm cells, and (4) identifying a quantity of X sperm cells in the at least one population; and a control responsive to instructions received from the flow cytometer apparatus for varying the rate at which the fluid is delivered to the flow cytometer apparatus as a function of the 40 quantity of identified X sperm cells In said at least one population relative to the total number of X cells in said first, second and third droplets.

170 N2. The system of N1 wherein said flow cytometry apparatus is operable to identify the number of X cells collected in said at least one population, and wherein the control varies the rate at which fluid is delivered to the flow cytometer apparatus to maintain the quantity of X cells collected in said at least one population at or above an acceptable quantity relative to the total 5 number of X cells in said first, second and third droplets. N3. The system of N2 wherein said acceptable quantity is at least 60% of said total number of X cells. 10 N4. The system of N3 wherein said X cells are live X cells. N5. The system of N2 wherein the control is operable to increase the rate of fluid delivery when the quantity of X cells in said at least one population is above said acceptable quantity and to decrease the rate of fluid delivery when the quantity of X cells in said at least one 15 population is below said acceptable quantity. 0. Sperm Sorting Method Including High-Purity Sort Strategy 01. A method of sorting X and Y sperm cells, said method comprising: 20 delivering a fluid stream containing X and Y sperm cells to a first location and causing said stream to break into droplets at a second location, said droplets comprising first droplets each containing one or more X sperm cells, second droplets each containing one or more Y sperm cells, and third plurality of droplets each containing one or more X sperms cells and one or 25 more Y sperm cells; sorting said first droplets from said second and third droplets; collecting said first droplets to provide at least one population of X sperm cells; 30 identifying a quantity of X sperm cells collected in said at least one population; and varying the rate at which fluid is delivered to said first location as a function of the quantity of identified.X sperm cells collected in said at least one population relative to the total 35 number of X cells in said first, second and third droplets. 02. The method of 01 further comprising varying the rate at which fluid is delivered to said first location to maintain the quantity of X cells collected in said at least one population at or above an acceptable quantity relative to the total number of X cells in said first, second and third 40 droplets.

171 03. The method of 02 wherein said acceptable quantity is at least 60% of said total number of X cells. 5 04. The method of 03 wherein said X cells are live X cells. 05. The method of 01 further comprising increasing the rate of fluid delivery when the quantity or percentage of X cells collected in said at least one population is above said acceptable quantity and decreasing the rate of fluid delivery when the quantity or percentage of X 10 cells collected in said at least one population is below said acceptable quantity. P. Sperm Sorter for High-Recovery Sort Strategy 15 P1. System for sorting X and Y sperm cells, said system comprising: a variable rate fluid delivery system for delivering a fluid stream containing X and Y sperm cells; 20 a flow cytometer apparatus for (1) receiving said stream and forming droplets containing said particles, said droplets comprising first droplets each containing one or more X sperm cells, second droplets each containing one or more Y sperm cells, and third plurality of droplets each containing one or more X sperms cells and one or more Y sperm cells, (2) sorting said first and third droplets from said second droplets, (3) collecting said first and third droplets to provide at 25 least one population of X sperm cells, and (4) identifying a quantity of Y sperm cells in the at least one population; and a control responsive to instructions received from the flow cytometer apparatus for varying the rate at which the fluid is delivered to the flow cytometer apparatus as a function of the 30 quantity of identified Y sperm cells in said at least one population. P2. The system of P1 wherein said control varies the rate at which fluid is delivered to the flow cytometer system to maintain the purity of said at least one population at or above a desired purity. 35 P3. The system of P2 wherein said control is operable to increase the fluid delivery rate when the purity of said at least one population is greater than said desired purity and to decrease the fluid delivery rate when the purity is less than said desired purity. 40 P4. The system of P2 wherein said desired purity is no greater than 95%. P5. The system of P2 wherein said X sperm cells are live cells.

172 Q. Speerm Sorting Method Including High-Recovery Sort Strate.y Q1. A method of sorting X and Y sperm cells, said method comprising: delivering a fluid stream containing X and Y sperm cells to a first location and causing 5 said stream to break into droplets at a second location, said droplets comprising first droplets each containing one or more X sperm cells, second droplets each containing one or more Y sperm cells, and third plurality of droplets each containing one or more X sperms cells and one or more Y sperm cells; 10 sorting said first and third droplets from said second droplets; collecting said first and third droplets to provide at least one population of X sperm cells; identifying a quantity of Y sperm cells collected in said at least one population; and 15 varying the rate at which fluid is delivered to said first location as a function of the quantity of identified Y sperm cells collected in said at least one population. Q2. The method of Q1 further comprising varying the rate at which fluid is delivered to 20 maintain the purity of said at least one population with respect to X cells at or above a desired purity. Q3. The method of Q2 further comprising increasing the fluid delivery rate when the purity of said at least one population is greater than said desired purity and decreasing the fluid 25 delivery rate when the purity is less than said desired purity. Q4. The method of Q2 wherein said desired purity is no greater than 95%. Q5. The method of Q2 wherein said X sperm cells are live cells. 30 Q6. A method of sorting X and Y sperm cells using flow cytometry, said method comprising: delivering a fluid stream containing X and Y sperm cells to a first location and causing 35 said stream to break into droplets at a second location, said droplets comprising first droplets each containing one or more X sperm cells, second droplets each containing one or more Y sperm cells, and third plurality of droplets each containing one or more X sperms cells and one or more Y sperm cells; 40 sorting said first and third droplets from said second droplets; and 173 collecting said first and third droplets to provide at least one population of X sperm cells. 5 Q7. The method of Q6 wherein said X sperm cells are live cells and not dead X cells. Q8. A method of sorting X and Y sperm cells using flow cytometry, said method comprising: 10 delivering a fluid stream containing X and Y sperm cells and causing said stream to break into droplets; interrogating the fluid stream before it breaks into droplets to identify which sperm cells will reside in which droplets; 15 sorting droplets containing X sperm cells from droplets not containing X sperm cells; and collecting said droplets containing X sperm cells, including droplets containing at least one X sperm cell and at least one Y sperm cell. 20 Q9. The method of Q8 wherein said X sperm cells are live X cells and not dead X cells. R. Photodamage Sorting Having Sort Strategy 25 R1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system comprising a laser for ablating selected 30 particles in the stream according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: a control responsive to information received from the flow cytometry apparatus for controlling the laser to vary its sorting strategy or for controlling the fluid delivery to vary the rate 35 at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of unablated characteristic A particles or unablated characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 40 174 R2. The system of R1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. R3. The system of RI wherein said cells are sperm cells, and wherein characteristic A is 5 indicative of a live X sperm cell. R4. The system of R3 wherein characteristic B is indicative of other than a live X cell 10 R5. The system of R1 wherein the control increases the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreases the rate of fluid delivery when the purity Is less than the desired purity. R6. The system of RI wherein the control determines said purity based on output 15 signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery to obtain the desired purity. R7. The system of R1 wherein said stream is formed into a stream containing particles 20 following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. 25 R8. The system of R7 wherein said laser ablates only the second particle sets. R9. The system of R8 wherein said control maintains the purity of said at least one population at more than 85% but less than 95%. 30 R10. The system of R7 wherein characteristic B is indicative of other than a live X cell (-X) and said laser is operable to ablate the second particle sets and the third particle sets in the stream. 35 R1 1. The system of R10 wherein the control increases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is greater than an acceptable quantity of unablated characteristic A particles in the at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. 40 175 R12. The system of R10 wherein the control determines the quantity of unablated characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating an acceptable quantity of unablated characteristic A particles in said at least one 5 population, and wherein the control varies the fluid delivery rate to obtain the acceptable quantity of unablated characteristic A particles in said at least one population. S. Photodamage Sorting Method Including Sort Strategy 10 Si. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method comprising: delivering a fluid containing said particles; 15 forming the fluid into a stream and using flow cytometry to classify the particles In the stream according to said characteristics; sorting the particles in the stream by ablating selected particles according to said 20 classification and according to a sorting strategy thereby to provide at least one population containing desired particles; and varying the sorting strategy or varying the rate at which fluid Is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either 25 characteristic A particles or characteristic B particles; and (2) the quantity of unablated characteristic A particles or unablated characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 30 S2. The method of S1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. S3. The method of S1 wherein said cells are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. 35 S4. The method of S1 further comprising increasing the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreasing the rate of fluid delivery when the purity is less than the desired purity.

176 S5. The method of S1 further comprising forming said fluid into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third 5 particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. S6. The method of S5 further comprising ablating the second particles sets and not the first and third particle sets. 10 S7. The method of SB further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. S8. The method of S5 further comprising ablating the second and third particle sets and 15 not the first particle sets. S9. The method of S8 further comprising increasing the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is greater than an acceptable quantity of unablated characteristic A particles in the at least one population, and 20 decreasing the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. T. Photodamage Sorter Having Variable Flow Rate and Feedback 25 T1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a variable rate fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the 30 particles according to said characteristics, and a sorting system comprising a laser for ablating selected particles in the stream according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: 35 a control responsive to information received from the flow cytometry apparatus for controlling the laser to vary the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of unabated characteristic A particles or unablated characteristic B particles in said at least one population relative to the total quantity 40 of characteristic A particles or characteristic B particles in said stream.

177 T2. The system of T1 wherein the particles are cells and characteristics A and B relate to physical characteristics of the cells. T3. The system of T2 wherein said cells are sperm cells and characteristic A is 5 indicative of a live X sperm cell. T4. The system of T3 wherein characteristic B is indicative of other than a live X cell (-X) and said laser ablates only the second particle sets. 10 T5. The system of T4 further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. T6. The system of T2 wherein characteristic B is indicative of other than a live X cell (-X), and wherein said laser ablates the second and third particles sets. 15 T7. The system of T1 wherein the control increases the rate of fluid delivery when the purity of the at least one population is greater than the desired purity and decreases the rate of fluid delivery when the purity is less than the desired purity. 20 T8. The system of T1 wherein the control determines a purity of the at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery to obtain the desired purity. 25 T9. The system of TB wherein the control increases the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is greater than an acceptable quantity of characteristic A particles In said at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of characteristic A particles in the at least one population is less than an acceptable quantity of characteristic A particles in the at least one 30 population. T1 0. The system of T8 wherein the control determines the total number of characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating an 35 acceptable quantity of characteristic A particles in the at least one population, and wherein the control varies the rate so that the quantity of characteristic A particles in the at least one population to obtain said acceptable quantity or percentage. T1 1. The system of T1 wherein said stream is formed into a stream containing particles 40 following generally one after another in a series which comprises sequential sets of particles, 178 including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. 5 T1 2. The system of Ti 1 wherein characteristic A is indicative of a live X sperm cell (X), wherein characteristic B is indicative of other than a live X cell (-X), wherein the laser ablates the second particles sets and third particle sets and not the first particle set, and wherein the control varies the rate at which the fluid is delivered to the flow cytometer apparatus as a function of the 10 number of live X sperm cells in the at least one population. T1 3. The system of T1 1 wherein characteristic A is indicative of a live X sperm cell (X), wherein characteristic B is indicative of other than a live X cell (-X), wherein the laser ablates the second particle sets and not the first and third particle sets, and wherein the control varies the 15 rate at which the fluid is delivered to the flow cytometer system as a function of the number of -X sperm cells in said at least one population. U. Photodamage Sorting Method Including Variable Flow Rate Sort Strategy 20 U1. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method comprising: delivering a fluid containing said particles; 25 forming the fluid into a stream and using flow cytometry to classify the particles in the stream according to said characteristics; sorting the particles in the stream by ablating selected particles according to said 30 classification and according to a sorting strategy thereby to provide at least one population containing desired particles; and varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or 35 characteristic B particles; and (2) the quantity of unablated characteristic A particles or unablated characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. U2. The method of Ul wherein the particles are cells and characteristics A and B relate 40 to physical characteristics of the cells.

179 U3. The method of U2 wherein said cells are sperm cells and characteristic A is indicative of a live X sperm cell. 5 U4. The method of U3 wherein characteristic B is indicative of other than a live X cell (-X) and said laser ablates only the second particle sets. U5. The method of U4 further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. 10 U6. The method of U2 wherein characteristic B is indicative of other than a live X cell (-X), and wherein said laser ablates the second and third particles sets. U7. The method of U1 wherein the control Increases the rate of fluid delivery when the 15 purity of the at least one population is greater than the desired purity and decreases the rate of fluid delivery when the purity is less than the desired purity. U8. The system of U1 wherein the control determines a purity of the at least one population based on output signals from the flow cytometry apparatus, said system further 20 comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery to obtain the desired purity. U9. The system of U8 wherein the control increases the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is greater than an acceptable 25 quantity of characteristic A particles in said at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of characteristic A particles in the at least one population is less than an acceptable quantity of characteristic A particles in the at least one population. 30 U10. The system of U8 wherein the control determines the total number of characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating an acceptable quantity of characteristic A particles in the at least one population, and wherein the control varies the rate so that the quantity of characteristic A particles in the at least one 35 population to obtain said acceptable quantity or percentage. U1 1. The system of U1 wherein said stream is formed into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second 40 particle sets each comprising one or more particles having characteristic B, and third particle sets 180 each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. U12. The system of U1 1 wherein characteristic A is indicative of a live X sperm cell (X), 5 wherein characteristic B is indicative of other than a live X cell (-X), wherein the laser ablates the second particles sets and third particle sets and not the first particle set, and wherein the control varies the rate at which the fluid is delivered to the flow cytometer apparatus as a function of the number of live X sperm cells in the at least one population. 10 U13. The system of U1 1 wherein characteristic A is indicative of a live X sperm cell (X), wherein characteristic B is indicative of other than a live X cell (-X), wherein the laser ablates the second particle sets and not the first and third particle sets, and wherein the control varies the rate at which the fluid is delivered to the flow cytometer system as a function of the number of -X sperm cells in said at least one population. 15 V. Fluid Switching Particle Sorter Including Sort Strategy V1. In a flow cytometry system for sorting a mixture of particles including particles 20 having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a fluid switching sorting system for sorting selected particles in the stream according to said classification and according to a sorting strategy to 25 provide at least one population containing desired particles, the improvement comprising: a control responsive to information received from the flow cytometry apparatus for controlling the fluid switching sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the 30 following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 35 V2. The system of V1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. V3. The system of V1 wherein said cells are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. 40 V4. The system of V3 wherein characteristic B is indicative of other than a live X cell

(-X).

181 V5. The system of V1 wherein the control increases the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreases the rate of fluid delivery when the purity is less than the desired purity. 5 V6. The system of V1 wherein the control determines said purity based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery to obtain the desired purity. 10 V7. The system of VI wherein said stream is formed into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets 15 each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. V8. The system of V7 wherein said laser ablates only the second particle sets. 20 V9. The system of V8 wherein said control maintains the purity of said at least one population at more than 85% but less than 95%. V10. The system of V7 wherein characteristic B is indicative of other than a live X cell (-X) and said laser is operable to ablate the second particle sets and the third particle sets in the 25 stream. V11. The system of V1 0 wherein the control increases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is greater than an acceptable quantity of unablated characteristic A particles In the at least one population, and 30 wherein the control decreases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. V12. The system of V10 wherein the control determines the quantity of unablated characteristic A particles in said at least one population based on output signals from the flow 35 cytometry apparatus, said system further comprising an operator input to the control for indicating an acceptable quantity of unablated characteristic A particles in said at least one population, and wherein the control varies the fluid delivery rate to obtain the acceptable quantity of unablated characteristic A particles in said at least one population. 40 182 W. Method of Fluid Switching Sorting Including Sort Strategy W1. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method comprising: 5 delivering a fluid containing said particles; forming the fluid into a stream and using flow cytometry to classify the particles in the stream according to said characteristics; 10 sorting the particles in the stream by diverting selected particles in the stream according to said classification and according to a sorting strategy thereby to provide at least one population containing desired particles; and 15 varying the sorting strategy or varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 20 W2. The method of W1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. W3. The method of W1 wherein said cells are sperm cells, and wherein characteristic A 25 is indicative of a live X sperm cell. W4. The method of W1 further comprising increasing the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreasing the rate of fluid delivery when the purity is less than the desired purity. 30 W5. The method of W1 further comprising forming said fluid into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, Including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third 35 particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. W6. The method of WS further comprising ablating the second particles sets and not the first and third particle sets. 40 183 W7. The method of W6 further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. W8. The method of W5 further comprising ablating the second and third particle sets 5 and not the first particle sets. W9. The method of W8 further comprising increasing the rate of fluid delivery when the quantity of unablated characteristic A particles In said at least one population is greater than an acceptable quantity of unablated characteristic A particles in the at least one population, and 10 decreasing the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. X. Fluid Switching Sorter including Variable Flow Rate Sort Strategy 15 X1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles 20 according to said characteristics, and a fluid switching sorting system for sorting selected particles in the stream according to said classification to provide at least one population containing desired particles, the improvement comprising: a control responsive to information received from the flow cytometry apparatus for 25 controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 30 X2. The system of X1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. X3. The system of X1 wherein said cells are sperm cells, and wherein characteristic A is 35 indicative of a live X sperm cell. X4. The system of X3 wherein characteristic B is indicative of other than a live X cell (-X). 40 X5. The system of X1 wherein the control increases the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreases the rate of fluid delivery when the purity is less than the desired purity.

184 X6. The system of X1 wherein the control determines said purity based on output signals from the flow cytometry apparatus, said system further comprising an operator Input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery 5 to obtain the desired purity. X7. The system of X1 wherein said stream is formed into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second 10 particle sets each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. X8. The system of X7 wherein said laser ablates only the second particle sets. 15 X9. The system of X8 wherein said control maintains the purity of said at least one population at more than 85% but less than 95%. X10. The system of X7 wherein characteristic B is indicative of other than a live X cell 20 (-X) and said laser is operable to ablate the second particle sets and the third particle sets in the stream. X11. The system of X1 0 wherein the control increases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is greater than an 25 acceptable quantity of unablated characteristic A particles in the at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. X12. The system of XIO wherein the control determines the quantity of unablated 30 characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating an acceptable quantity of unablated characteristic A particles In said at least one population, and wherein the control varies the fluid delivery rate to obtain the acceptable quantity of unablated characteristic A particles in said at least one population. 35 Y. Fluid Switching Sorting Method Including Variable Flow Rate and Feedback Y1. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method 40 comprising: 185 delivering a fluid containing said particles; forming the fluid into a stream and using flow cytometry to classify the particles in the 5 stream according to said characteristics; sorting the particles in the stream by diverting selected particles in the stream according to said classification thereby to provide at least one population containing desired particles; and 10 varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 15 Y2. The method of Y1 wherein the particles are cells, and wherein characteristics A and B relate to physical characteristics of the cells. Y3. The method of Y1 wherein said cells are sperm cells, and wherein characteristic A is 20 indicative of a live X sperm cell. Y4. The method of YI further comprising increasing the rate of fluid delivery when the purity of said at least one population is greater than a desired purity and decreasing the rate of fluid delivery when the purity is less than the desired purity. 25 Y5. The method of Y1 further comprising forming said fluid into a stream containing particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third 30 particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. Y6. The method of Y5 further comprising ablating the second particles sets and not the first and third particle sets. 35 Y7. The method of Y6 further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. Y8. The method of Y5 further comprising ablating the second and third particle sets and 40 not the first particle sets.

186 Y9. The method of Y8 further comprising increasing the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is greater than an acceptable quantity of unablated characteristic A particles in the at least one population, and 5 decreasing the rate of fluid delivery when the quantity of unablated characteristic A particles in said at least one population is less than said acceptable quantity. Z. [Reserved] 10 AA AID converter for PMT output signals and DSP analyzing and classifying AM. In a flow cytometry system for sorting a mixture of particles including particles 15 having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing 20 desired particles, the Improvement comprising: an analog to digital converter synchronously sampling a time-varying analog output from said flow cytometry apparatus and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the 25 corresponding digital information are indicative of characteristic A or characteristic B; a digital signal processor analyzing and classifying the digital information and providing a sorting signal to said sorting system as a function of the analyzed and classified digital information. 30 AA1A. The system of AA1 wherein the time-varying analog output comprises a series of waveform pulses, each of which Is representative of characteristic of a particle, wherein the digital signal processor detects portions of the digital information corresponding to the waveform pulses and classifies said detected portions, and wherein the digital signal processor provides 35 said sorting signal as a function of said detected and classified portions. AA1 B. The system of AA1 further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a 40 function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of 187 characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. AA2. The system of AA1B wherein the particles are cells and characteristics A and B 5 relate to physical characteristics of the cells. AA3. The system of AA B wherein the particles are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. 10 AA4. The system of AA3 wherein characteristic B is indicative of other than a live X cell (-X). AA5. The system of AA4 further comprising maintaining the purity of said at least one population at more than 85% but less than 95%. 15 AA6. The system of AA1 wherein the control increases the rate of fluid delivery when said purity is greater than a desired purity and decreases the rate of fluid delivery when said purity is less than said desired purity. 20 AA7. The system of AA1 wherein the control determines the purity of said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator input to the control for indicating a desired purity, and wherein the control varies the rate of fluid delivery so that the purity corresponds to the desired purity. 25 AA8. The system of AA7 wherein the control increases the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is greater than an acceptable quantity of characteristic A particles in the at least one population, and wherein the control decreases the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is less than said acceptable quantity. 30 AA9. The system of AA8 wherein the control determines the quantity of characteristic A particles in said at least one population based on output signals from the flow cytometry apparatus, said system further comprising an operator Input to the control for indicating an acceptable quantity of characteristic A particles in said at least one population, and wherein the 35 control varies the fluid delivery rate to obtain said acceptable quantity in said at least one population. AA 0. The system of AA1 wherein said stream is formed to contain particles following generally one after another in a series which comprises sequential sets of particles, including first 40 particle sets each comprising one or more particles having characteristic A, second particle sets 188 each comprising one or more particles having characteristic B, and third particle sets each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. 5 AA11. The system of AA1 0 wherein said sorting system is operable to use a sorting strategy in which said first particle sets are selected for collection in said at least one population and said second and third particle sets are not selected for collection in said at least one population. 10 AA12. The system of AA1O wherein said sorting system is operable to use a sorting strategy in which said first and third particle sets are selected for collection in said at least one population and said second particle set is not selected for collection In said at least one population. 15 yse 3. The system of AA1 wherein said sorting system comprises a droplet sorting system. AA14. The system of AA1 wherein said sorting system comprises a photo-damage sorting system. 20 AA15. The system of AA1 wherein said sorting system comprises a fluid-switching sorting system. AA16. The system of AA1 wherein said digital signal processor includes instructions for 25 detecting pulses corresponding to the digital information, instructions for extracting features in the detected pulses, and instructions for discriminating the detected pulses as a function of their extracted features. AA1 7. The system of AA 6 wherein said digital signal processor includes instructions for 30 defining a decision boundary discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. AA18. The system of AA17 wherein said digital signal processor adjusts the relative location of the decision boundary with respect to the extracted features representing 35 characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 40 189 AA1 9. The system of AA1 wherein said digital signal processor comprises a data management processor for assembling the digital information into a continuous stream. AA20. The system of AA1 wherein said digital signal processor comprises a pulse 5 detection processor for detecting waveform pulses represented by the digital information, and wherein said digital signal processor classifies the digital information as a function of the detected waveform pulses. AA21. The system of AA20 further comprising a filter for filtering the analog output at a 10 frequency equal to or less than one half the continuous sampling rate of the converter, wherein the converter converts the filtered analog output into corresponding digital Information, and wherein said digital signal processor classifies the digital information as a function of a discrimination boundary. 15 AA22. The system of AA21 wherein the continuous sampling rate is about 105 MHz or higher. AA23. The system of AA1 wherein said digital signal processor comprises a feature extraction and discrimination processor for defining a decision boundary discriminating between 20 extracted features representing characteristics A and extracted features representing characteristic B, and wherein the feature extraction and discrimination processor extracts features represented by said digital information and classifies the features as a function of the decision boundary. 25 AA24. The system of AA1 wherein said digital signal processor comprises a sort processor responsive to the classifying for providing the sort signals to said sorting system. AA25. The system of AA1 wherein the processor innumerates the number of classified particles having characteristic A or having characteristic B. 30 AA26. The system of AA1 wherein said digital signal processor classifies the digital information as a function of reducing a coefficient of variation of a population of the particles having characteristic A to be substantially equal to or less than a preset amount or as a function of minimizing a coefficient of variation of a population of the particles having characteristic B to 35 be substantially equal to or less than a preset amount. AA27. The system of AA26 wherein the preset amount is about 1.5% or less. AA27a. The system of AA26 wherein the preset amount is about 1.3% or less. 40 190 AA28. The system of AA1 wherein said digital signal processor classifies the digital information such that a population of the particles having characteristic A and a population of the particles having characteristic B correspond to a computer model of three populations including a first model population of particles having characteristic A, a second model population of particles 5 having characteristic B and a third model population of unaligned particles, said model estimating population statistics for each of the first, second and third model populations. AA29. The system of AA28 wherein the third model population comprises two populations of unaligned particles, and wherein the model estimates the population statistics for 10 the two populations. AA30. The system of AA1 wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses represented by the digital Information, and wherein said digital signal processor classifies the digital information as a function of a coefficient 15 of variation of a population of the particles having characteristic A or as a function of a coefficient of variation of a population of the particles having characteristic B. AA30a. The system of AA30 further comprising a filter for filtering the analog output at a frequency equal to or less than one half the continuous sampling rate of the converter, wherein 20 the converter converts the filtered analog output into corresponding digital information, and wherein said digital signal processor classifies the digital information as a function of a coefficient of variation of a population of the particles having characteristic A or as a function of a coefficient of variation of a population of the particles having characteristic B. 25 AA30b. The system of AA1 wherein said digital signal processor comprises a feature extraction and discrimination processor for defining a decision boundary discriminating between extracted features representing characteristics A and extracted features representing characteristic B, and wherein the feature extraction and discrimination processor extracts features represented by said digital information and classifies the features as a function of a 30 coefficient of variation of a population of the particles having characteristic A or as a function of a coefficient of variation of a population of the particles having characteristic B. AA31. A method of using a flow cytometry system to sort a mixture of particles including particles having a characteristic A and particles having a characteristic B, said method 35 comprising: delivering a fluid containing said particles; forming the fluid into a stream and using flow cytometry to detect the particles in the 40 stream according to said characteristics; 191 sorting the particles in the stream and according to a sorting strategy thereby to provide at least one population containing desired particles; 5 converting an analog output from said flow cytometry into corresponding digital information wherein the analog output is indicative of characteristic A or characteristic B; and analyzing and classifying the digital information and sorting the particles as a function of the analyzed and classified digital information. 10 AA31A. The method of AA31 further comprising varying the sorting strategy or varying the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at 15 least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. AA32. The method of AA31 wherein the particles are cells and characteristics A and B relate to physical characteristics of the cells. 20 AA33. The method of AA31 wherein the particles are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. AA34. The method of AA33 wherein characteristic B is indicative of other than a live X 25 cell (-X). AA35. The method of AA33 further comprising maintaining said purity at more than 85% but less than 95%. 30 AA36. The method of AA31 further comprising increasing the rate of fluid delivery when said purity is greater than a desired purity and decreasing the rate of fluid delivery when said purity is less than the desired purity. AA37. The method of AA31 further comprising increasing the rate of fluid delivery when 35 the quantity of characteristic A particles in said at least one population is greater than an acceptable quantity of characteristic A particles in the at least one population, and decreasing the rate of fluid delivery when the quantity of characteristic A particles in said at least one population is less than said acceptable quantity.

192 AA38. The method of AA31 further comprising forming the stream to contain particles following generally one after another in a series which comprises sequential sets of particles, including first particle sets each comprising one or more particles having characteristic A, second particle sets each comprising one or more particles having characteristic B, and third particle sets 5 each comprising two or more closely spaced particles at least one of which has characteristic A and at least one of which has characteristic B. AA39. The method of AA38 further comprising sorting said particles according to a sorting strategy in which only first particles sets are selected for collection in said at least one 10 population. AA40. The method of AA38 further comprising sorting said particles according to a sorting strategy in which first and third particle sets are selected for collection in said at least one population. 15 AA41. The method of AA31 wherein said sorting comprises using a droplet sorting process. AA42. The method of AA31 wherein said sorting comprises using a photo-damage 20 sorting process. AA43. The method of AA31 wherein said sorting comprises using a fluid-switching sorting process. 25 AA44. The method of AA31 further comprising detecting waveform pulses represented by the digital information, extracting features of the waveform pulses from the digital information, and discriminating the detected waveform pulses as a function of their extracted features. AA45. The method of AA44 further comprising defining a decision boundary 30 discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. AA46. The method of AA45 further comprising adjusting the relative location of the decision boundary with respect to the extracted features representing characteristic A and with 35 respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 40 193 AA47. The method of AA31 wherein said converting comprises synchronously sampling the analog output. AA48. The method of AA31 wherein classifying the digital information comprises 5 classifying the digital information as a function of minimizing a coefficient of variation of a population of the particles having characteristic A to be substantially equal to or less than a preset amount or as a function of minimizing a coefficient of variation of a population of the particles having characteristic B to be substantially equal to or less than a preset amount. 10 AA49. The method of AA48 wherein the preset amount is about 1.5% or less. AA50. The method of AA31 wherein classifying the digital information comprises classifying the digital information such that a population of the particles having characteristic A and a population of the particles having characteristic B correspond to a computer model of three 15 populations including a first model population of particles having characteristic A, a second model population of particles having characteristic B and a third model population of unaligned particles, said model estimating population statistics for each of the first, second and third model populations. 20 AA51. The method of AA31 wherein classifying the digital information comprises classifying the digital information as a function of a coefficient of variation of a population of the particles having characteristic A or as a function of a coefficient of variation of a population of the particles having characteristic B. 25 BB. Determining initial detection parameters BB1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid 30 delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: 35 an analog to digital converter synchronously sampling a time-varying analog output from said flow cytometry apparatus and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are indicative of characteristic A or characteristic B; 40 194 a digital signal processor determining background characteristics of said time-varying analog output from said digital information; detecting waveform pulses represented by said digital information as a function of said 5 determined background characteristics; and providing a sorting signal to said sorting system as a function of the detected waveform pulses. 10 BB2. The system of claim BB1 wherein said digital signal processor employs an iterative procedure for determining a pulse detection threshold for defining the background characteristics, said iterative procedure including: computing background statistic estimates from the digital information; 15 using the computed estimates to apply a pulse detection logic to said digital information in order to identify pulses indicative of characteristic A or characteristic B; recomputing the estimates without using the digital information corresponding to the 20 identified pulses; and repeating the above procedure until the background statistic estimates converge or a fixed maximum number of iterations occurs. 25 BB3. The system of BB1 wherein said digital signal processor includes instructions for detecting waveform pulses represented by the digital information, instructions for extracting features in the detected pulses and instructions for discriminating the detected pulses as a function of their extracted features. 30 BB4. The system of BB3 wherein said digital signal processor Includes instructions for defining a decision boundary discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. BB5. The system of BB4 wherein said digital signal processor adjusts the relative 35 location of the decision boundary with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the 40 total quantity of characteristic A particles or characteristic B particles in said stream.

195 BB6. The system of BB1 further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of 5 at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 10 8B7. The system of 81 wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses represented by the digital information, and wherein said digital signal processor classifies the digital information as a function of the detected waveform pulses. 15 BB8. The system of BB7 further comprising a filter for filtering the analog output at a frequency equal to or less than one half a sampling rate of the converter, and wherein the converter converts the filtered analog output into corresponding digital information. 20 CC. Generating initial discrimination parameters CC1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for 25 receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: 30 an analog to digital converter synchronously sampling a time-varying analog output from said flow 6ytometry apparatus and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are indicative of characteristic A or characteristic B; and 35 a digital signal processor generating initial discrimination parameters from the digital information, discriminating the digital information as a function of the initial discrimination parameters, and providing a sorting signal to said sorting system as a function of the discriminated digital information. 40 196 CC2. The system of claim CC1 wherein the digital signal processor employs at least one of the following algorithms to generate the initial discrimination parameters: k-Means, Fuzzy k Means and Agglomerative Hierarchical. 5 CC3. The system of CCI wherein said digital signal processor includes instructions for detecting waveform pulses represented by the digital information, instructions for extracting features in the detected waveform pulses and instructions for discriminating the detected waveform pulses as a function of their extracted features. 10 CC4. The system of CC3 wherein said digital signal processor includes instructions for defining a decision boundary discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. CC5. The system of CC4 wherein said digital signal processor adjusts the relative 15 location of the decision boundary with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the 20 total quantity of characteristic A particles or characteristic B particles in said stream. CC6. The system of CCI further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of 25 at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles, and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 30 DD. Synchronously sampling waveform pulses to Classify DD1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising: 35 a fluid delivery system for delivering a fluid containing said particles, and a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics; an analog to digital converter synchronously sampling a time-varying analog output 40 comprising a series of waveform pulses from said flow cytometry apparatus and providing an 197 output including digital information corresponding to said waveform pulses wherein said waveform pulses and the corresponding digital information are indicative of characteristic A or characteristic B; and 5 a digital signal processor analyzing the digital information and classifying the particle as a function of the analyzed digital -information corresponding thereto. DD2. The system of claim DD1 wherein said digital processor employs a detection threshold for defining the waveform the pulses, and wherein said detection threshold is a function 10 of a background mean estimate and a standard deviation of the digital information computed within a moving window of samples ending with the current sample. DD3. The system of claim DD1 wherein the digital control employs a statistical anomaly detection analysis, and wherein the digital information statistically anomalous from background 15 characteristics of the digital information is considered part of a digital pulse. DD4. The system of DD1 wherein said digital signal processor includes instructions for detecting pulses corresponding to the digital information, instructions for extracting features in the detected pulses and instructions for discriminating the detected pulses as a function of their 20 extracted features. DD5. The system of DD4 wherein said digital signal processor Includes instructions for defining a decision boundary discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. 25 DD6. The system of DD5 wherein said digital signal processor adjusts the relative location of the decision boundary with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of at least one population with respect to 30 either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. DD7. The system of DDI further comprising a filter for filtering the analog output at a 35 frequency equal to or less than one half a sampling rate of the converter, and wherein the converter converts the filtered analog output into corresponding digital information. DD8. The system of DD1 further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or 40 for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of 198 at least one of the following: (1) the purity of at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 5 DD9. The system of DDI wherein the processor innumerates the number of classified particles having characteristic A or having characteristic B. DD10. The system of DD1 further comprising a pulsed illumination device in 10 synchronization with synchronous sampling for illuminating the particles to produce the corresponding waveform pulses. DD1 1. The system of DDIO wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses represented by the digital information, and 15 wherein said digital signal processor classifies the digital information as a function of a coefficient of variation of a. population of the particles having characteristic A or as a function of a coefficient of variation of a population of the particles having characteristic B. 20 EE. Feature Extraction EE1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles 25 according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: an analog to digital converter synchronously sampling a time-varying analog output from 30 said flow cytometry apparatus and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are indicative of characteristic A or characteristic B; a digital signal processor extracting features from the digital information and providing a 35 sorting signal to said sorting system as a function of the extracted features. EE2. The apparatus of claim EE1 wherein the extracted feature corresponds to one or more of the following features: pulse area, pulse peak, pulse inner area, pulse width, pulse gaussianity, pulse lagging peak or pulse slope. 40 199 EE3. The apparatus of claim EE2 wherein the extracted feature comprises an approximation of a derivative of the pulse or slope of the pulse at a point of the pulse relative to an average peak height of the pulse. 5 EE4. The apparatus of claim EE3 wherein said point along the pulse corresponds to a point at which there is a difference between a first derivative of a pulse produced by particles having characteristic A and a first derivative of a pulse produced by particles having characteristic B. 10 EE5. The apparatus of claim EE3 wherein the time-varying analog output corresponds to a fluorescence emission pulse from the particles, and wherein said point along the pulse corresponds to a point at which a difference between a first derivative of a pulse produced by particles having characteristic A and a first derivative of a pulse produced by particles having characteristic B is at or near a maximum. 15 EE6. The apparatus of claim EE3 wherein the time-varying analog output corresponds to a fluorescence emission pulse from the particles, and wherein said point along the pulse is a function of a peak height of the fluorescence emission pulses. 20 EE7. The apparatus of EE1 wherein said digital signal processor includes instructions for detecting waveform pulses represented by the digital information, instructions for extracting features in the detected waveform pulses and instructions for discriminating the detected waveform pulses as a function of their extracted features. 25 EE8. The apparatus of EE7 wherein said digital signal processor includes instructions for defining a decision boundary discriminating between the extracted features representing characteristics A and the extracted features representing characteristic B. EE9. The apparatus of EE8 wherin said digital signal processor adjusts the relative 30 location of the decision boundary with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the 35 total quantity of characteristic A particles or characteristic B particles in said stream. EE1 0. The apparatus of EE1 further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a 40 function of at least one of the following: (1) the purity of said at least one population with respect 200 to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 5 EE1 1. The apparatus of EE1 wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses represented by the digital information and for classifying the detected waveform pulses. EE12. The apparatus of EE1 I further comprising a filter for filtering the analog output at 10 a frequency equal to or less than one half a sampling rate of the converter, and wherein the converter converts the filtered analog output into corresponding digital information. FF. Discriminating waveform pulses 15 FF1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles according to said characteristics, and a sorting system for sorting the particles according to said 20 classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: an analog to digital converter synchronously sampling a time-varying analog output comprising waveform pulses from said flow cytometry apparatus and providing an output 25 including digital information corresponding to said waveform pulses wherein said waveform pulses and the corresponding digital information are Indicative of characteristic A or characteristic B; a digital signal processor discriminating the digital information as indicative of 30 characteristic A or as indicative of characteristic B and providing a sorting signal to said sorting system as a function of the discriminated digital information. FF2. The apparatus of FF1 wherein said digital signal processor includes instructions for detecting waveform pulses represented by the digital information, instructions for extracting 35 features in the detected waveform pulses, and Instructions for discriminating the detected waveform pulses as a function of their extracted features. FF3. The apparatus of FF2 wherein said digital signal processor includes instructions for defining a decision boundary discriminating between the extracted features representing 40 characteristics A and the extracted features representing characteristic

B.

201 FF4. The apparatus of FF3 wherein said digital signal processor adjusts the relative location of the decision boundary with respect to the extracted features representing characteristic A and with respect to the extracted features representing characteristic B as a 5 function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. 10 FF5. The apparatus of FF1 wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses corresponding to the digital information, and wherein said digital signal processor classifies the digital information as a function of the detected waveform pulses. 15 FF6. The apparatus of FF5 further comprising a filter for filtering the analog output at a frequency equal to or less than one half a sampling rate of the converter, and wherein the converter converts the filtered analog output into corresponding digital information. FF7. The apparatus of FF1 further comprising a control responsive to information 20 received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of characteristic A particles or characteristic B particles in said at least one population relative to the 25 total quantity of characteristic A particles or characteristic B particles in said stream. FF8. The apparatus of FF1 further comprising a pulsed illumination device in synchronization with synchronous sampling for illuminating the particles to produce the corresponding waveform pulses. 30 FF9. The apparatus of FF8 wherein said digital signal processor comprises a pulse detection processor for detecting waveform pulses represented by the digital information, and wherein said digital signal processor classifies the digital information as a function of a coefficient of variation of a population of the particles having characteristic A or as a function of a coefficient 35 of variation of a population of the particles having characteristic B. GG. LED array break-off sensor GG1. An apparatus for use with a continuous stream of fluid which is breaking into 40 droplets at a break-off location, comprising: 202 a light source positioned on one side of the stream to illuminate the stream; a linear photoarray positioned on the other side of the stream adapted to be oriented 5 along an axis substantially parallel to the stream, said photoarray adapted to detect light from the light source which passes through the stream and said photoarray adapted to provide an output signal corresponding to the detected light; a control for receiving the output signal and providing a location signal corresponding to 10 a location of the break-off location. GG2. The apparatus of GG1 further comprising a display for providing a display indicating the location of the break-off location. 15 GG3. The apparatus of GG1 further comprising a transducer applying a force to stream for varying the location of the break-off location, said transducer varying an amplitude of the force as a function of an input signal, and wherein the location signal from the detector is provided to the transducer as the input signal. 20 GG4. The apparatus of GG3 further comprising a look up table for specifying variations of the amplitude of the force applied to the stream as a function of the location of the break-off location. 25 HH. Flow Cytometry Break-off Sensor HH1. In a flow cytometry system for sorting a mixture of particles including particles having a characteristic A and particles having a characteristic B, said system comprising a fluid delivery system for delivering a fluid containing said particles, a flow cytometry apparatus for receiving said fluid, forming it into a stream and using flow cytometry to classify the particles 30 according to said characteristics, and a sorting system for sorting the particles according to said classification and according to a sorting strategy to provide at least one population containing desired particles, the improvement comprising: a light source positioned at the second location on one side of the stream to illuminate 35 the stream; a linear photoarray positioned at the second location on the other side of the stream adapted to be oriented along an axis substantially parallel to the stream, said photoarray adapted to detect light from the light source which passes through the stream and said photoarray 40 adapted to provide an output signal corresponding to the detected light; 203 a control for receiving the output signal indicative of a position of the second location, said control varying operation of said transducer as a function of the output signal. 5 HH2. The apparatus of HH1 further comprising a control responsive to information received from the flow cytometry apparatus for controlling the sorting system to vary its sorting strategy or for controlling the fluid delivery system to vary the rate at which fluid is delivered as a function of at least one of the following: (1) the purity of said at least one population with respect to either characteristic A particles or characteristic B particles; and (2) the quantity of 10 characteristic A particles or characteristic B particles in said at least one population relative to the total quantity of characteristic A particles or characteristic B particles in said stream. HH3. The apparatus of HHI further comprising a display for providing a display indicating the location of the break-off location. 15 HH4. The apparatus of HH1 further comprising a transducer applying a force to stream for varying the location of the break-off location, said transducer varying an amplitude of the force as a function of an input signal, and wherein the location signal from the detector is provided to the transducer as the input signal. 20 HH5. The apparatus of HH4 further comprising a look up table for specifying variations of the amplitude of the force applied to the stream as a function of the location of the break-off location. 25 II. Droplet Sorter Having Epi-illumination Optics Ill. Apparatus for sorting particles contained in a fluid stream according to one more characteristics of the particles, said system comprising: 30 flow cytometry apparatus for delivering a fluid stream containing said particles to a first location and for causing the stream to break into droplets at a second location, said flow cytometry apparatus being operable using flow cytometry to classify the particles according to said characteristics and to sort said droplets according to the classification of particles contained in the droplets; 35 said flow cytometry apparatus comprising an epi-illumination optics system including a focusing lens, said optics system being operable to direct a laser beam through said focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from 40 the cells directed along said beam axis in a rearward direction.

204 112. The apparatus of ill wherein said particles are cells. 113. The apparatus of Ill wherein said particles are sperm cells. 5 114. The system of 113 wherein said beam is focused by said optics system as a spot on the fluid stream at said first location, said spot having a generally elliptical shape with a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said 10 width being less than the length of the head of a sperm cell passing through the spot. 115. The apparatus of 113 wherein said optics system includes a single photodetector to the rear of said focusing lens for detecting said emissions. 15 116. The apparatus of Ill wherein said flow cytometry apparatus further comprises a nozzle having an interior surface configured to exert a force on the particles tending to bring them into a desired orientation prior to passing through said beam. 117. The apparatus of 114 wherein said nozzle Is rotatable about a longitudinal axis of the 20 nozzle to adjust said desired particle orientation relative to the beam axis. 118. The apparatus of IlI wherein said flow cytometry apparatus comprises a nozzle oriented to direct the fluid stream in an upward, non-vertical direction. 25 119. The apparatus of Ill wherein said nozzle has an exterior surface coated with a non reflective, non-emissive coating. 1110. The apparatus of Ill wherein said optics system includes a single photodetector to the rear of said focusing lens for detecting said emissions. 30 1111. The apparatus of Ill wherein said flow cytometry apparatus comprises a nozzle having a nozzle orifice, and a capillary tube extending from the orifice through which said fluid stream is delivered to said first location. 35 1112. The apparatus of 119 wherein said first location is inside said capillary tube. Ill3. The system of Ill wherein said flow cytometry apparatus comprises a plurality of flow cytometry units operable to analyze multiple fluid streams simultaneously, each flow cytometry unit comprising said epi-illumination optics system. 40 205 JJ. Method of Sorting Particles Using Epi-illumination Optics JJ1. A method of sorting particles contained in a fluid stream according to one more characteristics of the particles, said method comprising: 5 delivering a fluid stream containing said particles to a first location and causing the stream to break into droplets at a second location; and using a flow cytometry process to classify the particles according to said characteristics 10 and to sort said droplets according to the classification of particles contained in the droplets, said flow cytometry process comprising directing a laser beam through a focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from the 15 cells directed along said beam axis In a rearward direction. JJ2. The method of JJ1 wherein said particles are cells. JJ3. The method of JJ1 wherein said particles are sperm cells. 20 JJ4. The method of JJ3 wherein the step of delivering a fluid stream comprises directing said stream through a nozzle orifice having a diameter of 50 to 70 microns at a pressure of 20-40 psi and at a rate of 30,000 to 50,000 sperm cells per second. 25 JJ5. The method of JJ3 further comprising focusing said beam on said fluid stream as a spot of generally elliptical shape having a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 30 JJ6. The method of JJ5 wherein the head of said sperm cell includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. 35 JJ7. The method of JJ3 further comprising generating a plurality of separate fluid streams each containing sperm cells and, for each such stream, carrying out steps (a) (b). JJ8. The method of JJ7 further comprising using a common laser beam to illuminate said fluid streams. 40 206 JJ9. The method of JJ1 further comprising exerting a force on the particles tending to bring them into a desired orientation prior to passing through said beam. JJIO. The method of JJ4 further comprising flowing the fluid stream through a nozzle 5 configured for exerting said force, and rotating the nozzle about a longitudinal axis of the nozzle to adjust said desired particle orientation relative to the beam axis. JJI1. The method of JJI wherein said flow cytometry process further comprises using only one photodetector to detect the emission of electromagnetic radiation. 10 KK. Photodamage Sorter Having Epi-illumination Optics KK1. Apparatus for sorting particles contained in a fluid stream according to one more characteristics of the particles, said system comprising: 15 a flow cytometry apparatus for delivering a fluid stream containing said particles to a first location, classifying the particles according to said characteristics, and sorting said particles according to said classification into at least one population containing desired particles; and 20 a laser for ablating particles in said stream, said flow cytometry apparatus comprising an epi-illumination optics system including a focusing lens, said optics system being operable to direct a laser beam through said focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so that said 25 cells pass through the beam, resulting in emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction. KK2. The apparatus of KK1 wherein said particles are cells. 30 KK3. The apparatus of KK2 wherein said cells are sperm cells. KK4. The apparatus of KK1 wherein said flow cytometry apparatus further comprises a nozzle having an interior surface configured to exert a force on the particles tending to bring them into a desired orientation prior to passing through said beam. 35 KK5. The apparatus of KK4 wherein said nozzle is rotatable about a longitudinal axis of the nozzle to adjust said desired particle orientation relative to the beam axis. KK6. KKI (copy claims AA2 etc.) 40 207 LL. Method of Sorting Particles Using Epi-illumination Optics and Photodamage LL1. A method of sorting particles contained in a fluid stream according to one more characteristics of the particles, said method comprising: 5 using a flow cytometry process to classify particles in a fluid stream according to said characteristics and to sort said particles according to said classification of particles; and ablating particles in said fluid stream, 10 said flow cytometry process comprising directing a laser beam through a focusing lens in a forward direction along a beam axis intersecting the fluid stream so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction. 15 MM. Sperm Sorter Having Ei-illumination Optics MM1. A system for sorting sperm cells according to chromosomal DNA characteristics, comprising: 20 flow cytometry apparatus for delivering a fluid stream containing said cells to a first location and for causing the stream to break into droplets at a second location, said flow cytometry apparatus being operable to classify the cells according to said DNA characteristics and to sort said droplets according to the classification of cells contained in the droplets, 25 said flow cytometry apparatus comprising an epi-illumination optics system including a focusing lens, said optics system being operable to direct a laser beam through said focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from 30 the cells directed along said beam axis in a rearward direction. MM2. The system of MM1 wherein said optics system further comprises a photodetector on said beam axis to the rear of said focusing lens operable to detect and convert at least some of said emissions into electrical signals indicative of said DNA characteristics. 35 MM3. The system of MM1 wherein said droplets are sorted into first droplets each of which contains at least one live X sperm cell and second droplets each of which contains at least one Y cell.

208 MM4. The system of MM3 wherein at least some of the first droplets contain a live X cell and a live Y cell. MM5. The system of MM1 wherein said flow cytometry apparatus comprises a nozzle 5 having an interior surface configured to exert a force on the cells tending to bring them into a desired orientation prior to passing through said beam. MM6. The system of MM5 wherein said nozzle is rotatable about a longitudinal axis of the nozzle to adjust said desired cell orientation relative to the beam axis. 10 MM7. The system of MM1 wherein said beam axis intersects the fluid stream at an angle of incidence which is skewed relative to a longitudinal axis of the stream at said first location. 15 MM8. The system of MMI wherein said beam is focused by said optics system as a spot on the fluid stream at said first location, said spot having a generally elliptical shape with a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 20 MM9. The system of MM8 wherein the head of said sperm cell includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. 25 MM10. The system of MM1 wherein said flow cytometry apparatus comprises a plurality of flow cytometry units operable to analyze multiple fluid streams simultaneously, each flow cytometry unit comprising said epi-illumination optics system. MM11. The system of MM1 wherein said flow cytometry apparatus comprises a nozzle 30 oriented to direct the fluid stream in an upward, non-vertical direction. MM12. The system of MM1 wherein said optics system includes only one photodetector for detecting said emissions. 35 MM1 3. The system of MMI further comprising a collector for collecting at least said first droplets. MM14. The system of MM1 wherein said flow cytometry apparatus comprises a nozzle having a nozzle orifice, and a capillary tube extending from the orifice through which said fluid 40 stream is delivered to said first location.

209 MM15. The system of MM14 wherein said first location is inside said capillary tube. MM16. The system of MM15 wherein said optics system is optically coupled to said 5 capillary tube for transmission of the beam into the stream flowing through the tube. NN. Method of Sorting Sperm Using Epi-llumination Optics NN1. A method of sorting animal sperm cells according to their chromosomal DNA 10 characteristics, comprising the steps of: (a) delivering a fluid stream containing said cells to a first location and causing the stream to break into droplets at a second location; 15 (b) directing a laser beam through a focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction; 20 (c) detecting and converting at least some of said emissions into electrical signals indicative of said DNA characteristics; (d) processing said electrical signals and classifying the cells according to said DNA characteristics; and 25 (e) sorting said droplets according to the classification of cells contained In the droplets. NN2. The method of NNI wherein said droplets are sorted into first droplets each of which contains at least one live X sperm cell and second droplets each of which contains at least 30 one Y cell. NN3. The method of NN2 wherein at least some of said first droplets contain a live X cell and a live Y cell. 35 NN4. The method of NN1 wherein step (a) comprises directing said stream through a nozzle orifice having a diameter of 50 to 70 microns at a pressure of 20-40 psi and at a rate of 30,000 to 50,000 sperm cells per second. NN5. The method of NN1 further comprising exerting a force on the cells tending to 40 bring them into a desired orientation prior to passing through said beam.

210 NN6. The method of NN5 wherein said sperm cells have heads with wide faces and narrow edges, and wherein said desired orientation is one where the beam strikes said wide faces. 5 NN7. The method of NN6 wherein said fluid delivery step comprises directing said stream through a nozzle, and wherein said method further comprises rotating the nozzle about a longitudinal axis of the nozzle to adjust said desired cell orientation relative to the beam axis. 10 NN8. The method of NN1 further comprising focusing said beam on said fluid stream as a spot of generally elliptical shape having a length along'a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 15 NN9. The method of NN8 wherein the head of said sperm cell includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. 20 NN10. The method of The method of NN5 wherein step (d) comprises deflecting at least said first droplets. NN1 1. The method of NN1 further comprising directing at least some of said emissions through a filtering system including a spatial filter having an aperture with length and width 25 dimensions, at least one of said dimensions being adjustable to vary the size of the aperture. NN12. The method of NN1 further comprising directing said fluid stream along an upward, non-vertical trajectory. 30 NN13. The method of NNI further comprising generating a plurality of separate fluid streams each containing sperm cells and, for each such stream, carrying out steps (a), (b), (c) and (d). NN13A. The method of NN13 further comprising using a common laser beam to 35 illuminate said fluid streams. NN14. The method of NN13 wherein said fluid streams contain fluid from a common supply of fluid.

211 NN1 5. The method of NN1 wherein said fluid stream is delivered to said first location through a capillary tube. 5 00. Sperm Analyzer Having Epi-illumination Optics 001. Apparatus for classifying animal sperm cells by chromosomal DNA characteristics, comprising: a nozzle system for delivering a fluid stream containing sperm cells to a first location and 10 for exerting a force on the sperm cells tending to bring them into a desired orientation before the stream reaches said first location; an epi-illumination optics system for directing a beam of electromagnetic radiation in a forward direction along a beam axis which intersects said fluid stream at said first location at an 15 angle of incidence other than 0 degrees stream so that said cells pass through the beam, resulting In emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction; a photodetector operable to detect and convert at least some of said emissions into 20 electrical signals indicative of said DNA characteristics; and a processor for processing said electrical signals and classifying the cells according to said DNA characteristics. 25 002. The apparatus of 001 wherein said nozzle system is part of a droplet cell sorting system. 003. The apparatus of 001 wherein said nozzle system is part of a photo-damage cell sorting system. 30 004. The apparatus of 001 wherein said nozzle system Is part of a fluid-switching cell sorting system. 005. The apparatus of 001 wherein said optics system further comprises a 35 photodetector on said beam axis to the rear of said focusing lens operable to detect and convert at least some of said emissions into electrical signals indicative of said DNA characteristics 006. The apparatus of 001 wherein said flow cytometry apparatus comprises a nozzle having an interior surface configured to exert a force on the cells tending to bring them into a 40 desired orientation prior to passing through said beam.

212 007. The apparatus of 006 wherein said nozzle is rotatable about a longitudinal axis of the nozzle to adjust said desired cell orientation relative to the beam axis. 5 008. The apparatus of 001 wherein said beam axis intersects the fluid stream at an angle of incidence which is skewed relative to a longitudinal axis of the stream at said first location. 009. The apparatus of 001 wherein said beam is focused by said optics system as a 10 spot on the fluid stream at said first location, said spot having a generally elliptical shape with a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 15 0010. The apparatus of 009 wherein the head of said sperm cell Includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. 0011. The apparatus of 001 wherein said flow cytometry apparatus comprises a 20 plurality of flow cytometry units operable in parallel to analyze multiple fluid streams simultaneously, each flow cytometry unit comprising said epi-illumination optics system. 0012. The apparatus of 001 wherein said nozzle system comprises a nozzle oriented to direct the fluid stream in an upward, non-vertical direction. 25 0013. The apparatus of 001 wherein said optics system includes only one photodetector for detecting said emissions. 0014. The apparatus of 001 wherein said flow cytometry apparatus comprises a 30 nozzle having a nozzle orifice, and a capillary tube extending from the orifice through which said fluid stream is delivered to said first location. 0015. The apparatus of 0014 wherein said first location is inside said capillary tube. 35 0016. The apparatus of 0015 wherein said optics system is optically coupled to said capillary tube for transmission of the beam into the stream flowing through the tube.

213 PP. Method of Analyzing Sperm Using Epi-illumination Optics PPI. A method of classifying animal sperm cells by chromosomal DNA characteristics, comprising the steps of: 5 (a) delivering a fluid stream containing sperm cells to a first location and exerting a force on the sperm cells tending to bring them into a desired orientation before the stream reaches said first location; (b) directing a beam of electromagnetic radiation in a forward direction along a beam 10 axis which intersects said fluid stream at said first location at an angle of incidence other than 0 degrees stream so that said cells pass through the beam, resulting in emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction; (c) detecting and converting at least some of said emissions into electrical signals 15 indicative of said DNA characteristics; and (d) processing said electrical signals and classifying the cells according to said DNA characteristics. 20 PP2. The method of PP1 further comprising sorting said cells according to said DNA characteristics. PP3. The method of PP1 further comprising using a photo-damage sorting process to sort said cells. 25 PP4. The method of PP1 further comprising using a fluid-switching sorting process to sort said cells. PP5. The method of PP1 further comprising using a droplet sorting process to sort said 30 cells. PP6. The method of PP1 wherein step (a) comprises directing said stream through a nozzle orifice having a diameter of 50 to 70 microns at a pressure of 20-40 psi and at a rate of 30,000 to 50,000 sperm cells per second. 35 PP7. The method of PP1 further comprising exerting a force on the sperm cells tending to bring them into a desired orientation prior to passing through said beam.

214 PP8. The method of PP7 wherein said sperm cells have heads with wide faces and narrow edges, and wherein said desired orientation is one where the beam strikes said wide faces. 5 PP9. The method of PP8 wherein said fluid delivery step comprises directing said stream through a nozzle, and wherein said method further comprises rotating the nozzle about a longitudinal axis of the nozzle to adjust said desired cell orientation relative to the beam axis. PPI0. The method of PP1 further comprising focusing said beam on said fluid stream as 10 a spot of generally elliptical shape having a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 15 PP 11. The method of PP1 0 wherein the head of said sperm cell includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. PP12. The method of PP1 further comprising directing at least some of said emissions 20 through a filtering system including a spatial filter having an aperture with length and width dimensions, at least one of said dimensions being adjustable to vary the size of the aperture. PP13. The method of PP1 further comprising directing said fluid stream along an upward, non-vertical trajectory. 25 PP14. The method of PP1 further comprising generating a plurality of separate fluid streams each containing sperm cells and, for each such stream, carrying out steps (a), (b), (c) and (d). 30 PPI5. The method of PP14 further comprising using a common laser beam to illuminate said fluid streams. PP16. The method of PP14 wherein said fluid streams contain fluid from a common supply of fluid. 35 PP17. The method of PP1 wherein said fluid stream is delivered to said first location through a capillary tube. 40 215 QQ. Particle Analyzer Having Skewed Angle of Incidence Epi-illumination Optics QQ1. Apparatus for analyzing particles contained in a fluid stream, comprising: an epi-illumination optics system for directing a beam of electromagnetic radiation in a 5 forward direction along a beam axis which intersects said fluid stream at an angle of incidence which is skewed relative to a longitudinal axis of the fluid stream; said epi-illumination system including a focusing lens on said beam axis path for focusing said beam of electromagnetic radiation on the fluid stream as a spot, said particles 10 being adapted to pass through said spot resulting in emissions of electromagnetic radiation from the particles directed along said beam axis in a rearward direction; and a photodetector to the rear of the focusing lens for detecting and converting at least some of said emissions into electrical signals to be processed to obtain information regarding 15 said particles. QQ2. The apparatus of QQ1 wherein said angle of incidence is in the range of 5 to 45 degrees. 20 003. The apparatus of QQ1 wherein said angle of incidence is in the range of 15 to 30 degrees. QQ4. The apparatus of QQ1 wherein said particles are cells, and wherein said information relates to DNA characteristics of the cells. 25 QQ5. The apparatus of QQ1 wherein said particles are sperm cells, and wherein said information relates to the X/Y chromosomal DNA characteristics of the cells. QQ6. The apparatus of QQ5 further comprising a nozzle system for directing said fluid 30 stream and for exerting a force on the sperm cells tending to bring them into a desired orientation before the stream passes through said beam. QQ7. The apparatus of QQ1 wherein said nozzle system comprises a nozzle, and wherein said beam strikes said fluid stream at a location less than 1.0 mm from the nozzle. 35 QQ8. The apparatus of QQI further comprising a droplet cell sorting system for sorting said particles according to said information. QQ9. The apparatus of QQ1 further comprising a photo-damage cell sorting system for 40 sorting said particles according to said information.

216 QQ10. The apparatus of QQ1 further comprising a fluid-switching cell sorting system for sorting said particles according to said information. 5 RR. Method of analyzing Particles Using Skewed Epi-illumination Optics RR1. A method of analyzing particles contained in a fluid stream, comprising: directing a beam of electromagnetic radiation in a forward direction along a beam axis 10 which intersects said fluid stream at an angle of incidence which is skewed relative to a longitudinal axis of the fluid stream; focusing said beam of electromagnetic radiation on the fluid stream as a spot, said particles. being adapted to pass through said spot resulting in emissions of electromagnetic 15 radiation from the particles directed along said beam axis in a rearward direction; detecting and converting at least some of said emissions into electrical signals Indicative of characteristics of the particles; and 20 processing said electrical signals to obtain information regarding said characteristics. RR2. RR1 (add claims similar to QQ2-etc.) 25 SS. Cell Analyzer Having Epi-illumination Optics and Elliptical Spot Focus SS1. Apparatus for analyzing DNA characteristics of cells In a fluid stream, each cell comprising a DNA region having a length in the direction of stream flow, said apparatus comprising: 30 an epi-illumination optics system for directing a beam of electromagnetic radiation in a forward direction along a beam axis so that the beam intersects said fluid stream; said optics system including a focusing lens on said beam axis for focusing the beam on the fluid stream as a generally elliptical spot having a length along a major axis extending 35 generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, the width of the beam spot being less than the length of said DNA region, said cells being adapted to pass through said spot resulting in an emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction, including emissions from said DNA regions indicative of said DNA 40 characteristics; 217 a photodetector to the rear of the focusing lens for detecting and converting at least some of said emissions from said DNA regions into electrical signals indicative of said DNA characteristics; and 5 a system for processing said electrical signals, identifying said DNA characteristics, and classifying the cells according to said DNA characteristics. SS2. The apparatus of SS1 wherein said spot width is less than about 3.0 pm. 10 SS3. The apparatus of SS2 wherein said spot length is greater than about 80pm. SS4. The apparatus of SSI wherein said cells are sperm cells and said DNA characteristics are indicative of the sex of the sperm cells. 15 SS5. The apparatus of SS1 further comprising a nozzle system for exerting a force on the cells in the stream tending to bring them into a desired orientation before the stream passes through said beam. SS6. The apparatus of SS1 further comprising a droplet cell sorting system for sorting 20 said particles according to said DNA characteristics. SS7. The apparatus of SS1 further comprising a photo-damage cell sorting system for sorting said particles according to said DNA characteristics. 25 SS8. The apparatus of SS1 further comprising a fluid-switching cell sorting system for sorting said particles according to said DNA characteristics. SS9. Apparatus for analyzing chromosomal DNA characteristics of animal sperm cells in a fluid stream having a direction of flow, each sperm cell having a head with a nucleus 30 comprising a localized chromosome region containing at least one chromosome, said nucleus having a length in the direction of stream flow, said apparatus comprising: an optics system for focusing a beam of electromagnetic radiation on the fluid stream as a generally elliptical spot having a length along a major axis extending generally at right angles to 35 the direction of stream flow and a width along a minor axis extending generally parallel to the direction of stream flow, the width of the beam spot being less than the length of said nucleus, said sperm cells being adapted to pass through said spot resulting in a emissions of electromagnetic radiation from the sperm cells, including emissions from said chromosome regions indicative of chromosomal characteristics of the regions; 40 218 a photodetector for detecting and converting at least some of said emissions from the chromosome regions into electrical signals indicative of said chromosomal characteristics; and a processor for processing said electrical signals, identifying said chromosomal 5 characteristics, and classifying the sperm cells according to said chromosomal characteristics. SS10. The apparatus of claim SS9 wherein said chromosomal characteristics are indicative of the sex of the sperm cells. 10 SS1 1. The apparatus of claim SSI0 wherein said sperm cells are bovine sperm cells. SS12. The apparatus of claim SSIO wherein said chromosome region is localized within an area of the nucleus extending no more than about 20% of the nucleus length on either side of a longitudinal center of the nucleus. 15 SS13. The apparatus of claim SSIO wherein said chromosome region is localized within an area of the nucleus extending no more than about 10%-15% of the nucleus length on either side of a longitudinal center of the nucleus. 20 SS14. The apparatus of claim SS9 further comprising an analog to digital converter synchronously sampling a time-varying analog output from said photodetector and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are indicative of said chromosomal characteristics; and wherein said processor comprises a digital signal processor 25 analyzing and classifying the digital information. SS1 5. The apparatus of claim SS9 wherein said spot width is less than about 3.0 pm. SS1 6. The apparatus of claim SS1 5 wherein said spot length is about 8Opm. 30 SS17. The apparatus of claim SS9 further comprising a nozzle system for exerting a force on the sperm cells in the stream tending to bring them into a desired orientation before the stream passes through said beam. 35 SS18. The apparatus of claim SS9 further comprising a droplet cell sorting system for sorting said sperm cells according to said chromosomal DNA characteristics. SS19. The apparatus of claim SS9 further comprising a photo-damage sperm cell sorting system for sorting said sperm cells according to said chromosomal DNA characteristics. 40 219 SS20. The apparatus of claim SS9 further comprising a fluid-switching sperm cell sorting system for sorting said sperm cells according to said chromosomal DNA characteristics. 5 TT. Method of analyzing cells Using Epi-illumination Optics and Elliptical Spot Focus TT1. A method of analyzing DNA characteristics of cells in a fluid stream, each cell comprising a DNA region having a length in the direction of stream flow, said method comprising: directing a beam of electromagnetic radiation in a forward direction along a beam axis so 10 that the beam intersects said fluid stream; focusing said beam of electromagnetic radiation on the fluid stream as a generally elliptical spot having a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the 15 direction of fluid stream flow, the width of the beam spot being less than the length of said DNA region, said cells being adapted to pass through said spot resulting In an emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction; detecting and converting said emissions into electrical signals indicative of said DNA 20 characteristics; and processing said electrical signals, including differentiating between electrical signals from emissions from the DNA region of a sperm head and electrical signals from emissions from other regions of the sperm cell; and 25 classifying the cells according to said DNA characteristics. TT2. The method of TT1 wherein said cells are sperm cells. 30 TT3. The method of TT1 further comprising exerting a force on the cells in the stream tending to bring them Into a desired orientation before the stream passes through said beam. TT4. The method of TT1 further comprising droplet sorting said cells according to said DNA characteristics. 35 TT5. The method of TT1 further comprising photo-damage sorting said particles according to said DNA characteristics. TT6. The method of TTI further comprising fluid-switching sorting said particles 40 according to said DNA characteristics.

220 TT7. A method of analyzing chromosomal DNA characteristics of animal sperm cells in a fluid stream having a direction of flow, each sperm cell having a head with a nucleus comprising a localized chromosome region containing at least one chromosome, said nucleus 5 having a length in the direction of stream flow, said method comprising: focusing a beam of electromagnetic radiation on the fluid stream as a generally elliptical spot having a length along a major axis extending generally at right angles to the direction of stream flow and a width along a minor axis extending generally parallel to the direction of stream 10 flow, the width of the beam spot being less than the length of said nucleus, said sperm cells being adapted to pass through said spot resulting in a emissions of electromagnetic radiation from the sperm cells, including emissions from said chromosome regions indicative of chromosomal characteristics of the regions; 15 detecting and converting at least some of said emissions from the chromosome regions into electrical signals indicative of said chromosomal characteristics; processing said electrical signals, including identifying said chromosomal characteristics; and 20 classifying the sperm cells according to said chromosomal characteristics. TT8. The method of claim TT7 wherein said chromosomal characteristics are indicative of the sex of the sperm cells. 25 TT9. The method of claim TT8 wherein said sperm cells are bovine sperm cells. TT10. The method of claim TT8 wherein said chromosome region is localized within an area of the nucleus extending no more than about 20% of the nucleus length on either side of a 30 longitudinal center of the nucleus. TT11. The method of claim T110 wherein said chromosome region is localized within an area of the nucleus extending no more than about 10%-15% of the nucleus length on either side of a longitudinal center of the nucleus. 35 TT12. The method of claim TT7 wherein said electrical signals comprise a time-varying analog output, and further comprising synchronously sampling the time-varying analog output and providing an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are 40 indicative of said chromosomal characteristics; wherein said processing comprises analyzing the 221 digital information; and wherein said classifying comprises classifying analyzed digital information. TT1 3. The method of claim TT7 wherein said spot width is less than about 3.0 pm. 5 TT1 4. The method of claim TT1 3 wherein said spot length is greater than about 180 pm. TTI 5. The method of claim TT7 further comprising exerting a force on the sperm cells in the stream tending to bring them into a desired orientation before the stream passes through said 10 beam. TT16. The method of claim TT7 further comprising droplet sorting droplet said sperm cells according to said chromosomal DNA characteristics. 15 TT17. The method of claim TT7 further comprising a photo-damage sorting said sperm cells according to said chromosomal DNA characteristics. TT18. The method of claim TT7 further comprising fluid-switching sorting sperm cells according to said chromosomal DNA characteristics. 20 UU. Sperm Sorter Having Only One Photodetector UU1. Apparatus for classifying and sorting sperm cells according to chromosomal DNA characteristics of the cells, said apparatus comprising: 25 a nozzle system for delivering a fluid stream containing said cells to a first location and for causing the stream to break into droplets at a second location, said nozzle system comprising a nozzle having an interior surface configured to exert a force on the cells tending to bring them into a desired orientation before reaching said first location; 30 an optics system for directing a beam of electromagnetic radiation to intersect the fluid stream at said first location so that cells in the stream pass through said beam resulting in emissions of electromagnetic radiation from the cells; 35 only one photodetector for detecting and converting at least some of said emissions into electrical signals; and a system for classifying the cells according to said DNA characteristics and for sorting said droplets according to the classification of cells contained in the droplets. 40 222 UU2. The apparatus of UU1 wherein said optics system is an epi-illumination system. W. Orienting Nozzle 5 WI. A nozzle for use in flow cytometry apparatus for sorting animal sperm cells in a fluid stream by chromosome content, said nozzle comprising: a nozzle body having an interior surface and an orifice through which said fluid stream is adapted to flow; 10 said interior surface of the nozzle comprising first, second and third axially tapered regions for progressively accelerating the speed of said fluid stream in a downstream direction toward said nozzle orifice, at least two of said regions having generally elliptical cross sectional shapes oriented in different directions for applying torsional forces to said fluid stream tending to 15 bring the sperm cells into a desired orientation. W2. The nozzle of WI wherein said generally elliptical cross sectional shape of one of said at least two regions is oriented at about 90 degrees relative to the generally elliptical cross sectional shape of the other of said at least two regions. 20 W3. The nozzle of W2 wherein said generally elliptical cross sectional shapes of the first and second regions are oriented in substantially the same direction to define a first torsional zone, and wherein the generally elliptical cross sectional shape of the third region, constituting a second torsional zone, is oriented at about 90 degrees relative to the generally elliptical cross 25 sectional shapes of the first and second regions. W4. The nozzle of W3 wherein the first torsional zone has an axial length of 3.0-4.5 mm and the second torsional zone has an axial length of 3.5-5.0 mm. 30 W5. The nozzle of WI wherein the third region tapers at an angle of 42-48 degrees. W6. The nozzle of WI wherein all of said regions have generally elliptical cross sectional shapes. 35 W7. The nozzle of WI wherein said nozzle body has an exterior surface with a non reflective coating thereon. W8. The nozzle of VV1 further comprising a mount for mounting said nozzle in a position pointing upward to direct said fluid stream along an upward trajectory. 40 223 VV9. The nozzle of VV8 wherein said nozzle body is rotatable on said mount on a longitudinal axis of the body. 5 WW. Method of Orienting Sperm Cells WWI. A method of orienting animal sperm cells in flow cytometry apparatus, said method comprising: introducing a fluid containing sperm cells into a fluid stream; 10 directing the fluid stream containing said sperm cells under a pressure in the range of 20 to 40 psi through a nozzle having one or more tapered regions for accelerating the speed of said fluid stream in a downstream direction toward a nozzle orifice having a diameter in the range of 50-70 microns, one or more of said tapered regions having a generally elliptical cross sectional 15 shape for applying a torsional force to said fluid stream tending to bring the cells into a desired orientation as they pass through said orifice at a rate in the range of 30,000 to 50,000 sperm cells per second. WW2. The method of WW1 wherein said nozzle has three or more tapered regions for 20 progressively accelerating the fluid stream toward the nozzle orifice. WW3. The method of WW2 wherein said nozzle has two torsional zones defined by interior surfaces of the nozzle in said three or more tapered regions. 25 WW4. The method of WW3 wherein said nozzle has a flow axis through said orifice, and wherein at least some of said interior nozzle surfaces have generally elliptical shapes which are rotated relative to one another about said axis. WW5. The method of WW1 further comprising directing said stream along an upward 30 non-vertical trajectory. WW6. The method of WWI further comprising rotating the nozzle body on a central longitudinal axis of the body while directing said stream. 35 XX. Particle Sorter Having Upward Pointing Nozzle XXI. Apparatus for sorting particles using flow cytometry, comprising: 224 a nozzle system for delivering a fluid stream containing said particles through a nozzle orifice along an upward, non-vertical trajectory; an optics system for directing a beam of electromagnetic radiation to intersect said fluid 5 stream at said first location resulting in emissions of electromagnetic radiation from the particles; a photodetector operable to detect and convert at least some of said emissions into electrical signals indicative of said particle characteristics; 10 a processor for processing said electrical signals and classifying the particles according to said characteristics; and a sorting system for sorting said particles according to the classification of the particles. 15 XX2. The apparatus of XXI wherein said sorting system comprises a droplet sorting system. XX3. The apparatus of XX1 wherein said sorting system comprises a photo-damage sorting system. 20 XX4. The apparatus of XX1 wherein said sorting system comprises a fluid-switching sorting system. XX5. The apparatus of XXI wherein said nozzle system comprises a nozzle having a 25 non-reflective coating thereon. XX6. The apparatus of XX1 wherein said upward trajectory at the nozzle orifice is at an angle in the range of 5-85 degrees off horizontal. 30 XX7. The apparatus of XX1 wherein said upward trajectory at the nozzle orifice is at an angle in the range of 15-75 degrees off horizontal. XX8. The apparatus of XX1 wherein said upward trajectory at the nozzle orifice is at an angle in the range of 30-65 degrees off horizontal. 35 XX9. The apparatus of XX1 wherein said upward trajectory at the nozzle orifice is at an angle in the range of 45-60 degrees off horizontal.

225 YY. Method of Sorting Particles Using Upward Pointing Nozzle YY1. Method of sorting particles using flow cytometry, comprising: delivering a fluid stream containing said particles through a nozzle orifice along an 5 upward, non-vertical trajectory to a first location; directing a beam of electromagnetic radiation to intersect said fluid stream at said first location resulting in emissions of electromagnetic radiation from the particles; 10 detecting and converting at least some of said emissions into electrical signals indicative of said particle characteristics; processing said electrical signals and classifying the particles according to said characteristics; and 15 sorting said particles according to the classification of the particles. YY2. The method of YY1 wherein said sorting step comprises sorting by using a droplet sorting process. 20 YY3. The method of YY1 wherein said sorting step comprises sorting by using a photo damage sorting process. YY4. The method of YY1 wherein said sorting step comprises sorting by using a fluid 25 switching sorting process. ZZ. Process Parameters ZZ1. A method of separating a desired cell population from a mixture of cells using flow 30 cytometry, said population having a light detectable characteristic, said method comprising: directing a stream of fluid containing said cells through a nozzle orifice having a diameter of from about 50 to 70 pm at a pressure in the range of about 20 to 40 psi and at a cell rate of about 30,000 to 50,000 cells per second; 35 ' causing the fluid stream to break into droplets at a frequency of about 20 to 100 KHz; and sorting the droplets using flow cytometry to separate said desired cell population from 40 said mixture of cells.

226 ZZ2. The method of ZZ1 wherein said cells are sperm cells. ZZ3. The method of ZZ2 wherein said desired cell population contains live X cells. 5 AAA. Business Method AAA1. A method of doing business including the handling of semen having cells therein, said method comprising: 10 obtaining a supply the semen; using a programmable machine to conduct a plurality of integrated flow cytometry operations, said operations comprising: (a) receiving said supply of semen; (b) forming multiple 15 streams containing said cells; and (c) sorting said cells into a first population of cells having characteristic A and a second population of cells having characteristic B; and distributing the first or the second population for commercial use. 20 AAA2. The method of AAA1 wherein said cells are sperm cells, and wherein characteristic A is indicative of a live X sperm cell. AAA3. The method of AAA2 wherein the semen is bovine semen, and wherein the first population is sold for use in artificially inseminating cows. 25 AAA4. The method of AAA3 wherein said programmable machine is operable to conduct said operations in parallel. 30 BBB. Business Method BBB1. A method of doing business including the handling of a sample of semen having cells therein, said method comprising: obtaining a supply of semen; 35 using a programmable machine to conduct a plurality of integrated flow cytometry operations, said operations comprising: (a) receiving said supply of semen; and (b) sorting said cells from an initial portion of said supply into different populations, including a first population containing cells having characteristic A and a second population containing cells having 40 characteristic B; and 227 sorting said cells from the remaining portion of said supply into different groups, including a first group containing cells having characteristic A and a second group containing cells having characteristic B, only if the cells initially sorted from the initial portion meet or exceed a preset 5 standard. BBB2. The method of BBB1 further comprising distributing the first or the second population for commercial use. 10 BBB3. The method of BBB1 wherein the preset standard is a minimum recovery rate of cells having characteristic A or characteristic B or a minimum purity for at least one of the populations. BBB4. The method of BBB1 further comprising conducting said plurality of integrated 15 flow cytometry operations in parallel. CCC. Business Method CCC1. A method of doing business including the handling of a sample of semen having 20 cells therein, said method comprising: obtaining a supply of semen; using a machine to conduct a plurality of integrated flow cytometry operations, said 25 operations comprising: (a) receiving said supply of semen; and (b) sorting said cells from a first portion of said supply into different populations, Including a first population containing cells having characteristic A and a second population containing cells having characteristic B, and sorting said cells from a second portion of said supply into different populations, including a first population containing cells having characteristic A and a second population containing cells 30 having characteristic B; and blending one of the populations of the first portion with one of the populations of the second portion to obtain a blended population. 35 CCC2. The method of CCC1 wherein the first population of the first portion has an unacceptable purity, wherein the first population of the second portion has an acceptable purity, and wherein the blended population has an acceptable purity. 40 228 DDD. ropet ntfence Sorting W/ Epi-illumination DDDI. A droplet interference system for sorting sperm cells according to chromosomal DNA characteristics, comprising: 5 flow cytometry apparatus for delivering a fluid stream containing said cells to a first location and for causing selected stream segments of the fluid stream to be hit by a droplet from a droplet interference fluid stream at a second location, thereby separating the selected segments and cells contained therein from the fluid stream, said flow cytometry apparatus being operable to classify the cells according to said DNA characteristics and to sort the stream 10 segments according to the classification of cells contained in the stream segments, said flow cytometry apparatus comprising an epi-illumination optics system including a focusing lens, said optics system being operable to direct a laser beam through said focusing lens in a forward direction along a beam axis intersecting the fluid stream at said first location so 15 that said cells pass through the beam, resulting in emissions of electromagnetic radiation from the cells directed along said beam axis in a rearward direction. DDD2. The system of DDDI wherein said optics system further comprises a photodetector on said beam axis to the rear of said focusing lens operable to detect and convert 20 at least some of said emissions into electrical signals indicative of said DNA characteristics. DDD3. The system of DDD1 wherein the cells are sperm cells and the DNA characteristics comprises sex chromosome content of the sperm cells. 25 DDD4. The system of DDD3 wherein said beam is focused by said optics system as a spot on the fluid stream at said first location, said spot having a generally elliptical shape with a length along a major axis extending generally at right angles to the direction of fluid stream flow and a width along a minor axis extending generally parallel to the direction of fluid stream flow, said width being less than the length of the head of a sperm cell passing through the beam spot. 30 DDD5. The system of DDD4 wherein the head of said sperm cell includes a DNA region having a length in the direction of stream flow, and wherein said beam spot width is less than the length of said DNA region. 35 DDD6. The system of DDD1 wherein said flow cytometry apparatus comprises a nozzle having an interior surface configured to exert a force on the cells tending to bring them into a desired orientation prior to passing through said beam. DDD7. The system of DDD6 wherein said nozzle is rotatable about a longitudinal axis of 40 the nozzle to adjust said desired cell orientation relative to the beam axis.

229 DDD8. The system of DDD1 wherein said flow cytometry apparatus comprises a plurality of flow cytometry units operable to analyze multiple fluid streams simultaneously, each flow cytometry unit comprising said epi-illumination optics system. 5 DDD9. The system of DDD1 wherein said optics system includes only one photodetector for detecting said emissions. DDD10. The system of DDD1 wherein said flow cytometry apparatus comprises a 10 nozzle having a nozzle orifice, and a capillary tube extending from the orifice through which said fluid stream is delivered to said first location. DDD11. The system of DDD10 wherein said first location is inside said capillary tube. 15 DDD12. The system of DDD1 I wherein said optics system is optically coupled to said capillary tube for transmission of the beam into the stream flowing through the tube. A'. Cryopreservation 20 a. (add cryoprotectant then cool) Al'. A method of cryopreserving sperm cells comprising the steps of: adding a cryoprotectant to a quantity of sperm cells; 25 cooling said quantity of sperm cells and said cryoprotectant to a holding temperature in a range of about 0 - 8*C; maintaining said sperm cells and said cryoprotectant substantially at said holding temperature for a period of less than 60 minutes; and 30 supercooling said quantity of sperm cells to a temperature of -40*C. A2'. The method of claim A1'wherein said holding temperature is in a range of about 2 6 0 C. 35 A3'. The method of claim A' wherein said holding temperature is in a range of about 4 5 0 C. A4'. The method of claim Al' wherein the step of adding a cryoprotectant comprises 40 adding glycerol.

230 A5'. The method of claim Al' wherein the step of adding a cryoprotectant comprises adding about 6% glycerol (v/v). 5 A6'. The method of claim Al wherein said holding period is less than about 40 minutes. A7'. The method of claim A1'wherein said holding period is about 30 minutes. A8'. The method of claim A1'wherein the cooling step comprises cooling said quantity of 10 sperm at a substantially constant cooling rate. A9'. The method of claim A8' wherein the cooling rate is selected so that said quantity of sperm cells is cooled from a temperature above a glass transition temperature below which sperm cells are subject damage from cold shock to the holding temperature in about 90 minutes. 15 A10'. The method of claim A8' wherein the substantially constant cooling rate is in the range of about 0.1 - 0.3 *C per minute. Al 1'. The method of claim A8' wherein the substantially constant cooling rate is in the 20 range of about 0.15 - 0.25 "C per minute. A12'. The method of claim Al1' wherein said holding period is less than about 40 minutes in length. 25 A13'. The method of claim Al' wherein the cooling step is performed by using a programmable freezer to cool the sperm cells at a programmed rate. A14'. The method of claim A13' wherein said holding period is less than 40 minutes in length. 30 A15'. The method of claim A14' wherein the programmed cooling rate comprises a constant cooling rate of about 0.2 *C per minute. A16'. The method of claim Al wherein the step of supercooling said quantity of sperm 35 comprises cooling the sperm cells at a first cooling rate to a temperature that approaches a critical temperature zone at which ice crystal formation and changes in osmotic pressure damage sperm cells and cooling the sperm at a second cooling rate faster than said first cooling rate to a temperature that is less than about -30 *C.

231 A17'. The method of claim A16' wherein said first cooling rate is in the range of about 1 5 *C per minute. Al 8'. The method of claim Al 6' wherein said first cooling rate is in the range of about 2 5 4 *C per minute. Al 9'. The method of claim Al 6' wherein said first cooling rate is about 3 *C per minute. A20'. The method of claim A16' wherein said second cooling rate is in the range of 10 about 8-12*C per minute. A21'. The method of claim A16' wherein said second cooling rate is about 10*C per minute. 15 A22'. The method of claim A16' wherein the sperm cells are cooled to a temperature of about -15 *C at said first cooling rate. A23'. The method of claim A22' wherein the sperm cells are cooled from about -15*C to a temperature of about --80 *C at said second cooling rate. 20 A24'. The method of claim A16' wherein the sperm cells are cooled to a temperature of about -18 *C at said first cooling rate. A25'. The method of claim A24' wherein the sperm cells are cooled from about -18*C to 25 a temperature of about -80 0C at said second cooling rate. A26'. The method of claim A16' wherein the sperm cells are cooled at said first rate and said second rate in a programmable freezer. 30 A27'. The method of claim Al' wherein the step of adding a cryoprotectant to a quantity of sperm cells comprises adding a cryoprotectant to a sheath fluid and using said sheath fluid in a flow cytometer that analyzes sperm cells. A28'. The method of claim A27' further comprising the step of using said flow cytometer 35 to sort said sperm cells into a population of sperm cells having a desired characteristic to obtain said quantity of sperm cells. A29'. The method of claim Al' wherein the steps of cooling said quantity of sperm, maintaining said sperm cells at the holding temperature, and supercooling said quantity of sperm 40 cells are all completed in less than 220 minutes.

232 A30'. The method of claim Al' wherein the steps of cooling said quantity of sperm, maintaining said sperm cells at the holding temperature, and supercooling said quantity of sperm cells are all completed in less than about 190 minutes. 5 A31'. The method of claim Al wherein the steps of cooling said quantity of sperm, maintaining said sperm cells at the holding temperature, and supercooling said quantity of sperm cells are all completed in less than about 150 minutes. 10 A32'. The method of claim Al'further comprising the step of loading said quantity of sperm cells into an artificial insemination straw after the cryoprotectant has been added to said quantity of sperm cells. A33'. The method of claim Al' wherein said quantity of sperm cells constitutes a first 15 quantity of sperm cells, the method further comprising the steps of obtaining a sorted population of sperm cells comprising more than 500 x 106 sperm cells from a flow cytometer to thereby obtain a plurality of quantities of sperm cells including said first quantity of sperm cells, loading each of said plurality of quantities of sperm cells into an artificial insemination straw, and performing the steps of cooling, maintaining, and supercooling on each of said plurality of 20 quantities of sperm cells in a batch process to obtain a batch of artificial insemination straws containing cryopreserved sperm cells. A34'. The method of claim A33' wherein said sorted population of sperm cells comprises more than 800 x 108sperm cells. 25 A35'. The method of claim A33' wherein the steps of the method are completed in less than about 240 minutes. A36'. The method of claim A33' wherein the steps of the method are completed in less 30 than about 210 minutes. A37'. The method of claim A33' wherein the steps of the method are completed in less than about 170 minutes. 35 A38'. The method of claim Al'further comprising the step of staining said quantity of sperm cells with a DNA selective fluorescent dye before the cooling step. A39'. The method of claim A38' wherein said DNA selective dye comprises Hoechst 33342. 40 233 A40'. The method of claim A39' wherein said step of staining said quantity of sperm comprises the step of incubating said quantity of sperm cells for a period of time in a solution comprising Hoechst 33342 at a temperature that exceeds 40*C. 5 b. cold temperature sorting A41'. A method of cryopreserving sperm cell comprising the steps of: cooling a quantity of sperm cells to a holding temperature in the range of about 0 - 8 0 C; 10 adding a cryoprotectant to said quantity of sperm cells; and maintaining said sperm cells and said cryoprotectant substantially at said holding temperature for a period of less than 60 minutes. 15 A42'. The method of claim A41' wherein said period is In the range of about 30 minutes to less than 60 minutes. A43'. The method of claim A41' wherein the step of adding a cryoprotectant comprises adding glycerol. 20 A44'. The method of claim A41' wherein the step of adding a cryoprotectant comprises adding about 7% glycerol (v/v/). 25 B'. Nozzle with Baffle B1'. A nozzle for use in flow cytometry apparatus for analyzing particles in a fluid stream, said fluid stream comprising a sheath stream surrounding a core stream containing said particles, said nozzle comprising: 30 a nozzle having an interior surface defining a flow path for said fluid stream, and an orifice for exit of the fluid stream from the nozzle; and a baffle in the nozzle positioned in said flow path upstream from said orifice for deflecting the fluid stream as it moves along said flow path, 35 the baffle and interior surface of the nozzle being configured to orient the particles In a desired orientation as they exit the orifice.

234 82'. The nozzle of claim B1' wherein said baffle is configured for deflecting said core stream away from a central longitudinal axis of the nozzle and toward said interior surface of the nozzle. 5 B3'. The nozzle of claim B1' wherein said nozzle has a first cross sectional flow area upstream of said baffle and a second cross sectional flow area different from said first cross sectional flow area at the baffle. B4'. The nozzle of claim B3' wherein said second cross sectional flow area is smaller 10 than said first cross sectional flow area. B5'. The nozzle of claim 83' wherein said first and second cross sectional flow areas have different shapes. 15 B6'. The nozzle of claim B5' wherein said second cross sectional flow area is generally semi-cylindrical. B7'. The nozzle of claim B1' wherein said interior surface of the nozzle is shaped to define at least two axially tapered regions downstream from said baffle for progressively 20 accelerating the speed of the fluid stream in a downstream direction toward the nozzle orifice. B8'. The nozzle of claim B7' wherein said baffle is configured for deflecting said core stream toward a portion of said interior surface of the nozzle defining at least one of said at least two axially tapered regions. 25 B9'. The nozzle of claim B8' wherein said at least two axially tapered regions have generally elliptical cross sectional shapes oriented in different directions for applying torsional forces to said fluid stream that tend to bring the particles into said desired orientation. 30 B10'. The nozzle of claim B9' wherein said generally elliptical cross sectional shape of one of said at least two regions is oriented at about 90 degrees relative to the generally elliptical cross sectional shape of the other of said at least two regions. BI 1'. The nozzle of claim 81' wherein the nozzle has an exterior surface with a non 35 reflective coating thereon. 812'. The nozzle of claim B1' further comprising a mount for mounting said nozzle in a position pointing upward to direct said fluid stream along an upward trajectory.

235 B13'. The nozzle of claim B13' wherein the nozzle is rotatable on said mount about a longitudinal axis of the nozzle. B14'. The nozzle of claim 81' wherein said baffle comprises a baffle member for 5 deflecting said fluid stream and a holder for holding said baffle member in fixed position in said nozzle. B15'. The nozzle of claim B14' wherein said baffle member comprises a baffle plate. 10 316'. The nozzle of claim B15' wherein said baffle plate has a first leg extending generally transversely relative to said fluid stream and a second leg extending generally in the direction of said fluid stream. SB17'. The nozzle of claim B15' wherein said holder comprises a generally cylindrical 15 shell holding said baffle plate and positioned in said nozzle. B18'. The nozzle of claim B16' wherein said interior surface of the nozzle has a region of generally elliptical cross section downstream from said baffle, and wherein said first and second legs of the baffle member intersect along a line which is substantially parallel with a major axis of 20 said generally elliptical cross section. B19'. The nozzle of claim B16' wherein said interior surface of the nozzle has a region of generally elliptical cross section downstream from said baffle, and wherein said first and second legs of the baffle member intersect along a line which is substantially perpendicular to a major 25 axis of said generally elliptical cross section. 820'. The nozzle of claim B15' wherein the baffle plate is generally perpendicular to a longitudinal axis of the nozzle. 30 B21'. The nozzle of claim 820' wherein the baffle plate has a semi-circular shape. B22'. The nozzle of claim B20' wherein the baffle plate has a semi-elliptical shape. B23'. The nozzle of claim B20' wherein the interior surface of the nozzle is shaped to 35 define a shoulder and the holder comprises an o-ring seal capable of pressing the baffle plate against the shoulder to hold the baffle plate in a desired position. B24'. The method of claim B20' wherein the baffle holder holds the baffle plate in a position in which the baffle plate intersects the longitudinal axis of the nozzle. 40 236 B25'. The nozzle of claim 81' wherein said particles comprise sperm cells. C. Nozzle with Baffle (Method) 5 C1'. A method of orienting particles in a flow cytometry apparatus, said method comprising: causing a fluid stream having a core stream of sample fluid containing said particles and a sheath stream of sheath fluid surrounding the core stream to flow through a nozzle having an 10 interior surface that generally tapers from an upstream portion of the nozzle to an orifice at the downstream end of the nozzle; and deflecting the core stream as it flows through the nozzle to subject the particles in the core stream to hydrodynamic forces that tend to cause the particles to assume a desired 15 orientation. C2'. The method of claim Cl' wherein the nozzle has a longitudinal axis and the step of deflecting the core stream comprises deflecting the core stream away from the longitudinal axis toward said interior surface. 20 C3'. The method of claim C1 wherein the nozzle has a longitudinal axis and the step of deflecting the path of the core stream comprises deflecting the core stream from a path that generally coincides with the longitudinal axis to a deflected path, at least a portion of the deflected path being offset from the longitudinal axis of the nozzle. 25 C4'. The method of claim Cl' wherein the nozzle has a longitudinal axis, the method further comprising introducing the core stream into the sheath stream at a location that is offset from the longitudinal axis. 30 C5'. The method of claim C1 wherein the deflecting step comprises using a baffle to deflect the core stream. C6'. The method of claim Cl' wherein the deflecting step comprises using a baffle plate to deflect the core stream and using a baffle holder to hold the baffle plate in position in the 35 nozzle. C7'. The method of claim C6' wherein the baffle plate intersects the longitudinal axis of the nozzle.

237 C8'. The method of claim C1' wherein the nozzle has an interior surface that is shaped to define at least one torsional zone for subjecting the particles to hydrodynamic orienting forces. C9'. The method of claim C8' wherein that at least one torsional zone comprises a 5 tapered region of the nozzle having a generally elliptical cross section. C10'. The method of claim C8' wherein said interior surface is shaped to define multiple torsional zones. 10 C1'. The method of claim C10' wherein each of said multiple torsional zones comprises a tapered region of the nozzle having a generally elliptical cross section. C12'. The method of claim C1I' wherein the generally elliptical cross section for a first of the multiple torsional zones is oriented in a different direction that the generally elliptical cross 15 section for a second of the multiple torsional zones. C13'. The method of claim C1' wherein the step of deflecting the core stream comprises using a baffle to deflect the core stream, the method further comprising the step of causing the fluid stream to flow through a first cross sectional flow area and then a second cross sectional 20 flow area downstream from the first cross sectional flow area, wherein the first and second cross sectional flow areas have different shapes. C14'. The method of claim C15' wherein the second cross sectional flow area is smaller than the first cross sectional flow area. 25 D'. Nozzle with Asymmetric niection Needle (Apparatus) D1'. A nozzle system for use in a flow cytometer for analyzing particles in a fluid stream, said fluid stream comprising a sheath stream surrounding a core stream containing said 30 particles, said nozzle system comprising: a nozzle having a longitudinal axis, an interior surface defining a flow path for said fluid stream, and an orifice at the downstream end of the nozzle for exit of the fluid stream from the nozzle, said interior surface being shaped to define at least one torsional zone comprising an 35 axially tapered region having a generally elliptical cross section for orienting said particles in a desired orientation as the fluid stream flows through the torsional zone toward the orifice; and a conduit from a particle source to the nozzle, said conduit being positioned to introduce said core stream into the nozzle at a location that is offset with respect to the longitudinal axis of 40 the nozzle.

238 D2'. The nozzle system of claim Dl' wherein said location is upstream from said at least one torsional zone. 5 D3'. The nozzle system of claim D1' wherein said at least one torsional zone constitutes a first torsional, said nozzle further comprising a second torsional zone. D4'. The nozzle system of claim D3' wherein said location is upstream from the first torsional zone and at least a portion of the second torsional zone. 10 D5'. The nozzle system of claim D3' wherein the second torsional zone comprises an axially tapered region of the nozzle having a generally elliptical cross section. D6'. The nozzle system of claim D5' wherein the major axis of the generally elliptical 15 cross section of the first torsional zone is oriented in a different direction than the major axis of the generally elliptical cross section of the second torsional zone. D7'. The nozzle system of claim D6' wherein the generally elliptical cross section of the first torsional zone is oriented at an angle of about 90 degrees with respect to the generally 20 elliptical cross section of the second torsional zone. D8'. The nozzle system of claim D7' wherein said location is upstream from the first torsional zone and at least a portion of the second torsional zone. 25 E'. Asymmetric Sample Introduction (Method) El'. A method of orienting particles In a flow cytometer comprising: causing a sheath fluid to flow through a nozzle having a longitudinal axis and at least one 30 torsional zone comprising an axially tapered region of the nozzle having a generally elliptical cross section; and introducing a core fluid stream containing particles into the sheath fluid stream at a location that is offset from said longitudinal axis for flow of the sheath fluid stream and core fluid 35 stream through the at least one torsional zone. E2'. The method of claim El wherein the step of causing the fluid stream through at least one torsional zone comprises causing the core stream to flow along a flow path, a portion of said flow path being offset from the longitudinal axis of the nozzle, and subjecting said particles 239 to hydrodynamic orientation forces generated by said torsional zone while said particles are moving along said offset portion of the flow path. E3'. The method of claim El wherein said at least one torsional zone constitutes a first 5 torsional zone, the method further comprising the step of causing the sheath fluid stream and core fluid stream to flow through a second torsional zone for orienting the particles in a desired orientation. E4'. The method of claim E3 wherein said second torsional zones comprises a tapered 10 region in the nozzle having generally elliptical cross sectional area. E5'. The method of claim E4 wherein the major axis of the generally elliptical cross sectional area of the first torsional zone is oriented in a different direction than the major axis of the generally elliptical cross sectional area of the second torsional zone. 15 E6'. The method of claim E4 wherein the major axis of the generally elliptical cross sectional area of the first torsional zone is perpendicular to the major axis of the generally elliptical cross sectional area of the second torsional zone. 20 F'. Concentration of Sorted Sperm by Secondary Centrifugation F1'. A method of processing animal sperm cells comprising the steps of: collecting sperm cells from a male animal; 25 sorting the sperm cells into one of multiple populations of sperm cells on the basis of one or more specified DNA characteristics; obtaining a quantity of sperm cells having a desired DNA characteristic from one of said 30 multiple populations of sperm cells, said quantity of sperm cells being contained in a volume of collection fluid; subjecting said volume of collection fluid to a first centrifugation process to form a first pellet of sperm cells and a supernatant overlying the first pellet; 35 separating the first pellet from the supernatant; subjecting the supernatant to additional centrifugation to form a second pellet of sperm cells that remained in the supernatant after the first centrifugation; and 40 240 adding a volume of resuspension fluid to the first and second pellets to obtain a suspension of sperm cells having the desired DNA characteristic, the amount of said volume of resuspension fluid being selected to result in a desired concentration of sperm cells in the suspension. 5 F2'. The method of claim Fl' wherein the first centrifugation process comprises centrifuging at a speed sufficient to generate a g-force in the range of 550-800g. F3'. The method of claim F2' wherein the first centrifugation process comprises 10 centrifuging said volume of collection fluid at said speed for a period in the range of 7 - 10 minutes. F4'. The method of claim F1' wherein said one or more specified DNA characteristics comprises whether the sperm cell contains an X or a Y sex chromosome. 15 F5'. The method of claim Fl' further comprising obtaining a plurality of quantities of sperm cells having a desired DNA characteristic and distributing said plurality of quantities of sperm cells to animal breeders through a commercial distribution system. 20 G'. Filtration with low pressure Gl'. A method of processing animal sperm cells comprising the steps of: collecting sperm cells from a male animal; 25 sorting the sperm cells to obtain a quantity of sperm cells having a desired characteristic, said quantity of sorted sperm cells being contained in a first volume of fluid having a first concentration of sperm cells therein; and 30 subjecting the sperm cells to a concentration step in which the concentration of said sperm cells is increased to a second concentration greater than said first concentration, wherein said concentration step comprises flowing at least a portion of the first volume of fluid through a first filter at a pressure differential across the first filter of less than about 20 in. 35 mercury, said filter having filter pores sufficiently small to inhibit passage of said sperm cells therethrough, and retaining a second volume of unfiltered fluid containing said sperm cells. G2'. The method of claim G1' wherein the pressure differential across the filter during said flowing is substantially constant. 40 241 G3'. The method of claim G1' further comprising the step of Intermittently reducing the pressure differential across the filter for a period and then substantially restoring the pressure differential. 5 G4'. The niethod of claim G3' wherein the step of reducing the pressure differential comprises the step of reducing the pressure differential to about zero. G5'. The method of claim G1' wherein the filter pores have a size of in the range of about 0.2 - 1.0 microns. 10 G6'. The method of claim G1' wherein about 80%-90% of said first volume of fluid flows through said first filter. G7'. The method of claim G1' wherein said second volume of unfiltered fluid is sufficient 15 to prevent caking of the sperm cells on said first filter. G8'. The method of claim G 1' further comprising flowing at least a portion of said second volume of unfiltered fluid through a second filter having filter pores sufficiently small to inhibit, passage of said sperm cells therethrough, retaining a third volume of unfiltered fluid containing 20 said sperm cells, and flushing said second filter with a resuspension fluid to remove sperm cells from the second filter for addition to said third volume to arrive at said second concentration. G9'. The method of claim G8' wherein about 80% of the second volume of unfiltered fluid flows through said second filter. 25 G10'. The method of claim G8' wherein said third volume of unfiltered fluid is sufficient to prevent caking of the sperm cells on said second filter. G11'. The method of claim G8' wherein said second filter is a thin filter having a 30 thickness in the range of about 50 - 500 microns. G12'. The method of claim G8' wherein said second filter is a thin filter having a thickness in the range of about 75 - 250 microns. 35 G13'. The method of claim G8' wherein said second filter is a thin filter having a thickness in the range of about 100 - 150 microns. G14'. The method of claim G1' wherein said first filter is a thin filter having a thickness in the range of about 50 - 500 microns. 40 242 G1 5'. The method of claim G1' wherein said first filter is a thin filter having a thickness in the range of about 75 - 250 microns. G16'. The method of claim G1' wherein said first filter is a thin filter having a thickness in 5 the range of about 100 - 150 microns. H'. Overall Temperature Control (High Temperature Staining) H1'. A method of processing sperm cells comprising the steps of: 10 collecting a semen sample containing sperm cells from a male animal; transporting the semen sample to a sperm processing facility; 15 conducting an initial quality control check on the semen; staining the sperm cells in said semen sample with a DNA selective fluorescent dye that selectively binds to DNA in the sperm cells by exposing said sperm cells to a DNA selective fluorescent dye to form a staining mixture, and subjecting the staining mixture to a temperature of 20 at least about 40 0 C; using a flow cytometer to sort the sperm cells on the basis of a specified DNA characteristic; 25 obtaining a quantity of sperm cells having a desired DNA characteristic suspended in a volume of fluid; adjusting the concentration of sperm cells in said suspension by performing a concentration process to achieve a desired concentration; and 30 supercooling said quantity of sperm cells. H2'. The method of claim Hi' further comprising maintaining the temperature of the sperm cells from the time they are collected until the beginning of the staining step at 35 temperatures in the range of about 20 - 37*C and insulating the sperm cells from temperature fluctuations during that time. H3'. The method of claim H2' wherein the step of insulating the sperm cells comprises keeping the semen sample in an insulated container during transportation to the processing 40 facility.

243 H4'. The method of claim H1'further comprising the step of placing the stained sperm cells in an environment having a temperature in the range of about 18 - 25 0 C before they are introduced into said flow cytometer to cool the sperm cells from the temperature they attained 5 during the staining step before beginning the sorting step. H5'. The method of claim H1 wherein the supercooling step comprises cooling the sperm cells from a temperature that exceeds 20*C to a temperature in the range of about 0 8*C, and adding a protein source and cryoprotectant to said sperm cells before the temperature 10 of the sperm cells has been cooled below 20*C. H6'. The method of claim H5' further comprising using a programmable freezer to: (a) cool the sperm cells to a holding temperature in the range of about 0 - 8*C; (b) maintain the sperm at said holding temperature for a period of less than about 60 minutes to allow the sperm 15 cells to substantially equilibrate with the cryoprotectant; (c) cool the sperm at a first cooling rate to a temperature that approaches a critical temperature zone in which ice crystal formation and changes in osmotic pressure damage sperm cells; and (d) cool the sperm cells through said critical temperature zone at a second cooling rate faster than said first cooling rate. 20 H7'. The method of claim H6' further comprising cooling the sperm cells from said holding temperature to about -15*C at said first cooling rate. H8'. The method of claim H7' further comprising cooling the sperm cells from about 180C to at least about - 30 0 C at said second cooling rate. 25 H9'. The method of claim H6' further comprising cooling the sperm cells from said holding temperature to about -1 8*C at said first cooling rate. H10'. The method of claim H6' further comprising using the programmable freezer to 30 cool the sperm cells to said holding temperature at a cooling rate in the range of about 0.1 - 0.3 *C per minute. H11'. The method of claim H10' further comprising using the programmable freezer to cool the sperm cells from said holding temperature to a temperature of about -1 5*C at said first 35 rate of about 1 - 5 0C per minute. H12'. The method of claim H6' further comprising using the programmable freezer to cool the sperm cells from a temperature of about -18*C to at least about - 30 0 C at said second cooling rate of about 8 - 12*C per minute. 40 244 H13'. The method of claim H12' further comprising using the&programmable freezer to cool the sperm cells from said holding temperature to a temperature of at least about -15 0 C at said first cooling rate of about 1 - 5 *C per minute. 5 H14'. The method of claim H6' wherein the sperm cells are maintained at said holding temperature for a period of about 30 minutes. HIS'. The method of any one of claims H1'-H14' wherein the staining mixture further comprises an antioxidant. 10 HI 6'. The method of claim H15' wherein the antioxidant is selected from the group consisting of pyruvate, vitamin K, lipoic acid, and a combination thereof. H17'. The method of any one of claims HI' or H5'-H16' further comprising placing the 15 stained sperm cells in an environment having a temperature of at least about 37 0 C until they are introduced into a flow cytometer. H18'. The method of any one of claims Hi' or H5'-H16'further comprising placing the stained sperm cells in an environment having a temperature of at least about 40*C until they are 20 introduced into a flow cytometer. H19'. The method of claim Hi' wherein the step of obtaining a quantity of sperm cells comprises obtaining a population of live sperm cells having said desired DNA characteristic at a rate of at least 5,000 sperm cells per second. 25 H20'. The method of claim H19' wherein the purity of said population is at least 85%. if. Overall Temperature Control (without High-Temp staining) 30 J1'. A method of processing sperm cells comprising the steps of: collecting a semen sample containing sperm cells from a male animal; transporting the semen sample to a sperm processing facility; 35 performing an initial quality control check on the semen sample; staining sperm cells in said semen sample with DNA selective fluorescent dye; 245 sorting the sperm cells with a flow cytometer to obtain one or more populations of sperm cells having a desired DNA characteristic; obtaining a quantity of sperm cells having the desired DNA characteristic suspended in a 5 fluid; adjusting the concentration of said quantity of sperm cells to attain a desired concentration of sperm cells having the desired DNA characteristic in a fluid suspension; 10 adding a cryoprotectant to a quantity of sperm cells having said desired characteristic while said quantity of sperm cells has a temperature in excess of a glass transition temperature below which sperm cells are subject to damage from cold shock; cooling said quantity of sperm cells and cryoprotectant said from said glass transition 15 temperature to a holding temperature in the range of about 0 - 8*C; maintaining said quantity of sperm cells and cryoprotectant in a temperature range of about 0 - 80C for period of less than 60 minutes; and 20 supercooling said quantity of sperm to a temperature below -400C. J2'. The method of claim J1' wherein said cryoprotectant is added while said quantity of sperm cells has a temperature in excess of about 20*C. 25 J3. The method of claim JI' wherein the stained sperm cells are placed in an environment having a temperature in the range of about 20 - 250C until they are sorted in a flow cytometer. J4'. The method of claim Ji' further comprising using a programmable freezer to cool 30 said quantity of sperm at a first cooling rate from said holding temperature to a temperature that approaches a critical temperature zone in which ice crystal formation and changes in osmotic pressure damage sperm cells, and then to cool said quantity of sperm cells through said critical temperature zone at a second cooling rate that is faster than said first cooling rate. 35 J5'. The method of claim J1'wherein the step of maintaining said quantity of sperm cells comprises holding said quantity of sperm cells at said holding temperature for a period of less than about 40 minutes.

246 J6'. The method of claim J1' wherein the step of maintaining said quantity of sperm cells comprises holding said quantity of sperm cells at said holding temperature for a period of about 30 minutes. 5 J7'. The method of any one of claims J1'-J6' wherein the staining step further comprises adding an antioxidant to the sperm cells. J8. The method of claim J7' wherein the antioxidant is selected from the group consisting of pyruvate, vitamin K, lipoic acid, and a combination thereof. 10 J9. The method of claim Ji' wherein the step of obtaining a quantity of sperm cells having a desired DNA characteristic comprises obtaining a population of live sperm cells having said desired DNA characteristic at a rate of at least 5,000 sperm cells per second. 15 J 10'. The method of claim J9' wherein the purity of said population of sperm cells is at least 85%. K1. Overall Temperature Control (cold staining) 20 K1'. A method of processing sperm cells comprising the steps of: collecting a semen sample containing sperm cells from a male animal; transporting the semen sample to a sperm processing facility; 25 performing an Initial quality control check on the semen sample; cooling the sperm cells to a temperature in the range of about 0 - 8*C before any substantial dilution of the sperm cells is performed; 30 forming a mixture comprising a solution containing the sperm cells and a DNA selective dye and subjecting the mixture to a temperature in the range of 0 - 8 0 C to stain the sperm cells; sorting the sperm cells with a flow cytometer to obtain one or more populations of sperm 35 cells having a desired DNA characteristic; obtaining a quantity of sperm cells having the desired DNA characteristic suspended in a fluid; 247 adjusting the concentration of said quantity of sperm cells to attain a desired concentration of sperm cells having the desired DNA characteristic in a fluid suspension; adding a cryoprotectant to said quantity of sperm cells; 5 holding said quantity of sperm cells and said cryoprotectant at a holding temperature in the range of about 0 - 8'C for a period in the range of about 30 minutes to 3 hours; and supercooling said quantity of sperm cells to a temperature below 400. 10 K2. The method of claim K1' further comprising the step of substantially avoiding warming the cells at any time during the process. K3. The method of claim K1 wherein the step of cooling the sperm cells to a 15 temperature in the range of 0 - 8* comprises placing a container holding the sperm cells into a water bath that is substantially the same temperature as the pre-cooled sperm cells and placing the water bath in an environment having a temperature less than about 8 0 C. K4'. The method of claim K3' wherein the cooling step further comprises monitoring 20 the temperature of the sperm cells as they cool and adding ice to the water bath after the sperm cells have cooled to a temperature less than about 10'C. KS. The method of claim K1 wherein said holding period is in the range of about 1 2 hours. 25 K6'. The method of claim K1' wherein said holding period is in the range of about 90 minutes. K7'. The method of claim KI' wherein said holding period is in the range of about 30 30 minutes to less than 60 minutes. K8'. The method of claim KI' wherein the step of supercooling said quantity of sperm cells comprises using a programmable freezer to cool said quantity of sperm at a first cooling rate from said holding temperature to a temperature that approaches a critical temperature zone 35 in which ice crystal formation and changes in osmotic pressure damage sperm cells and then to cool said quantity of sperm cells through said critical temperature zone at a second cooling rate that is faster than said first cooling rate. K9'. The method of claim K1' wherein the step of adding a cryoprotectant comprises 40 adding glycerol.

248 K1 0'. The method of claim KI' wherein the step of adding a cryoprotectant comprises adding 7% glycerol (v/v). 5 K1 1'. The method of claim K1' where in the step of obtaining a quantity of sperm cells having a desired DNA characteristic comprises obtaining a population of live sperm cells having said desired DNA characteristic at a rate of at least 5,000 sperm cells per second. K12'. The method of claim K1' wherein the purity of said population of sperm cells is 10 at least 85%. L'. Collection System (Apparatus) Li'. A collection system for collecting a stream of droplets sorted by a droplet sorting 15 flow cytometer that produces a stream of droplets moving along a trajectory that includes a horizontal component, the system comprising an intercepting device for intercepting droplets in said stream as they move along said trajectory, and a collection vessel disposed to collect said intercepted droplets. 20 L2'. The collection system of claim Li' wherein the intercepting device comprises an impact surface disposed across said trajectory against which said droplets are adapted to impact. L3'. The collection system of claim L2' wherein the impact surface is disposed across 25 said trajectory at a location at which said droplets have an upward velocity component. L4'. The collection system of claim L2' wherein at least some of the droplets contain particles and the impact surface is coated with a substance that reduces damage to said particles upon impact with the impact surface. 30 L5'. The collection system of claim L4' wherein said substance comprises one or more substances selected from the group consisting of egg yolk, bovine serum albumin, and phosphate buffered saline. 35 L6'. The collection system of claim L4' wherein said particles are sperm cells. L7'. The collection system of claim L2' wherein said intercepting device is configured for guiding said intercepted droplets to the collection vessel.

249 L8'. The collection system of claim L7' wherein the intercepting device comprises a guide below said impact surface for guiding said droplets down to said collection vessel. L9'. The collection system of claim L7' wherein the intercepting device comprises a 5 hollow enclosure defining said impact surface and having an entry window for entry of droplets moving along said trajectory into said enclosure for impact against said impact surface. 110'. The collection system of claim Li' wherein said stream of droplets constitutes a first stream of droplets, said intercepting device constitutes a first intercepting device, said 10 collection vessel constitutes a first collection vessel, and said cytometer also produces a second stream of droplets moving along a second trajectory that is different from said first trajectory, said collection system further comprising a second intercepting device for intercepting droplets moving along said second trajectory and a second collection vessel for collecting droplets intercepted by the second intercepting device. 15 L1i'. The collection system of claim 10' wherein said first intercepting device has a window therein through which said second stream is adapted to pass, and wherein said second intercepting device is positioned behind said first intercepting device for intercepting droplets in the second stream passing through said window. 20 L12'. The collection system of claim 10' wherein said second intercepting device is configured for guiding said intercepted droplets in the second stream to the second collection vessel. 25 L13'. The collection system of claim LI' wherein said droplets contain particles, the collection system further comprising a substance coating the impact surfaces of the intercepting devices for reducing damage to said particles upon impact. L14'. The collection system of claim L13' wherein said particles comprise live sperm 30 cells. L15'. The collection system of claim L13' wherein said substance comprises a substance selected from the group consisting of: egg yolk, bovine serum albumin, and phosphate buffered saline. 35 L16'. The collection system of claim L' in combination with a flow cytometer positioned to direct a droplet stream into the intercepting device. 40 250 M'. Collection System (Method) M1'. A method of collecting droplets sorted by a droplet sorting flow cytometer that produces a stream of droplets moving along a trajectory that includes a horizontal component, said method comprising the steps of: 5 intercepting said droplets as they move along said trajectory; and collecting said intercepted droplets in a first collection vessel. 10 M2'. The method of claim M1' wherein said collecting step comprises guiding said intercepted droplets into said first collection vessel. M3'. The method of claim M2' wherein said intercepting step comprises positioning an impact surface across said trajectory at a location at which said droplets have an upward 15 velocity component. M4'. The method of claim M3' further comprising adjusting the position of said impact surface to accommodate different droplet trajectories. 20 M5'. The method of claim Ml' wherein said flow cytometer produces first and second streams of droplets moving along respective first and second trajectories, each trajectory having a horizontal component, said method further comprising intercepting said droplets in said second stream as they move along said second trajectory, and collecting said intercepted droplets of the second stream in a second collection vessel. 25 M6'. The method of claim M5' wherein said first and second trajectories lie substantially in one plane. M7'. The method of claim M5' wherein droplets in said first stream are intercepted by 30 positioning a first impact surface across said first trajectory at a location at which said droplets have an upward velocity component, and wherein droplets in said second stream are Intercepted by positioning a second impact surface across said second trajectory at a location at which said droplets have an upward velocity component. 35 M8'. The method of claim M7' wherein said second impact surface is positioned at a different elevation than said first impact surface. Mg'. The method of claim MI'wherein said droplets contain particles and the step of intercepting the said droplets comprises using an intercepting device to intercept said droplets, 251 the method further comprising contacting said intercepting device with a composition to reduce damage to said particles. M10'. The method of claim M9' wherein said particles comprise live sperm cells. 5 M1 1'. The method of claim M0' wherein said composition comprises a substance selected from the group consisting of: egg yolk, bovine serum albumin, and phosphate buffered saline. 10 M12'. The method of claim M10' wherein the step of contacting said intercepting device with a composition comprises soaking said intercepting device in said composition for a period that is sufficient for the composition be absorbed by and/or adhere to the intercepting device. M13'. The method of claim M12' wherein said period is in the range of about 30 - 90 15 minutes. M14'. The method of claim M13' wherein said period is in the range of about 30 - 60 minutes. 20 M15'. The method of claim M14' wherein said period is about 60 minutes. M16'. The method of any of claims M10'-M15' wherein the step of collecting said droplets comprises collecting said droplets in a collection vessel, the method further comprising the step of contacting the collection vessel with a composition to reduce damage to said 25 particles. MIT. The method of claim M16'further wherein the step of contacting the collection vessel with a composition to reduce damage to the particles comprises contacting the collection vessel with the same composition used to contact the intercepting device. 30 M18'. The method of claim M16' wherein the step of contacting the collection vessel with a composition to reduce damage to said particles comprises soaking the collection vessel in said composition for a period that is sufficient for the composition to be absorbed by and/or adhere to the collection vessel. 35 M19'. The method of claim M18' wherein said period is in the range of about 30 - 90 minutes. M20'. The method of claim M18' wherein said period is about 60 minutes. 40 252 N'. Synergistic Combinations a. Multi-channel FCM (with sort strategy) 5 Nal'. A method of processing animal sperm cells comprising the steps of: sorting the sperm cells into different populations of sperm cells on the basis of one or more specified DNA characteristics using a flow cytometry process comprising delivering a sample fluid containing the sperm cells to a plurality of flow cytometry units each of which is 10 operable to sort the sperm cells on the basis of said one or more DNA characteristics, and operating said units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of 15 the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; and varying the rate at which sample fluid is delivered to one or more of the flow cytometry units as a function of at least one of the following: (1) the purity of a first sorted population of 20 sperm cells having a desired DNA characteristic; and (2) the quantity of sperm cells having said desired DNA characteristic in a second sorted population. Na2'. The method of claim Nat further comprising operating said flow cytometry units in parallel. 25 Na3'. The method of claim Na1 wherein said one or more specified DNA characteristics comprises whether a sperm cell contains an X or a Y sex chromosome. b. Multi-channel FCM with Digital Processing 30 Nbl'. A method of processing animal sperm cells comprising the steps of: sorting the sperm cells into different populations of sperm cells on the basis of one or more specified DNA characteristics using a flow cytometry process comprising delivering a sample fluid containing the sperm cells to a plurality of flow cytometry units each of which is 35 operable to sort the sperm cells on the basis of said one or more DNA characteristics, and operating said units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of 253 the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; and using one or more analog to digital converters to synchronously sample a time-varying 5 output from each flow cytometry unit and provide an output including digital information corresponding to said time-varying analog output wherein said time-varying analog output and the corresponding digital information are indicative of said specified DNA characteristic. Nb2'. The method of claim Nbl' wherein said one or more specified DNA characteristics 10 comprises whether a sperm cell has an X or a Y sex chromosome. C. Multi-channel FCM (w/ high-temperature staining) Ncl'. A method of processing animal sperm cells comprising the steps of: 15 forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; and sorting the sperm cells into different populations of sperm cells on the basis of one or more specified DNA characteristics using a flow cytometry process comprising delivering a 20 sample fluid containing the sperm cells to a plurality of flow cytometry units each of which is operable to sort the sperm cells on the basis of said one or more DNA characteristics, and operating said units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a 25 common processor for receiving and processing information from the units to permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units. Nc2'. The method of claim Ncl'wherein the dye is a UV excitable or a visible light 30 excitable dye. Nc3'. The method of claim Nc2' wherein the dye is selected from the group consisting of a bisbenzimide, SYBR-14, and a conjugate, an analog, or a derivative thereof. 35 Nc4'. The method of any one of claims Nc 1-Nc3' wherein the staining mixture is subjected to the temperature for a period of time sufficient to allow the dye to bind the DNA such that X and Y bearing sperm cells can be differentially sorted based upon fluorescence. Nc5'. The method of claim Nc4' wherein the period of time is in the range of about 1 40 160 minutes.

254 Nc6'. The method of any one of claims Nc1'-Nc5' wherein the staining mixture further comprises an antioxidant. 5 Nc7'. The method of claim Nc' wherein said one or more characteristics comprises whether a sperm cell contains an X or a Y sex chromosome. d. Multi-channel (with rapid cryopreservation) 10 Nd1'. A method of processing animal sperm cells comprising the steps of: sorting the sperm cells into different populations of sperm cells on the basis of one or more specified DNA characteristics using a flow cytometry process comprising delivering a sample fluid containing the sperm cells to a plurality of flow cytometry units each of which is 15 operable to sort the sperm cells on the basis of said one or more DNA characteristics, and operating said units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of 20 the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; obtaining a quantity of sperm cells having a desired DNA characteristic from one or more of the sorted populations of sperm cells; 25 adding a cryoprotectant to said quantity of sperm cells; cooling said quantity of sperm cells and the cryoprotectant to a holding temperature of about 0-8*C; 30 maintaining said sperm cells and said cryoprotectant substantially at said holding temperature for a period of less than 60 minutes; and supercooling said quantity of sperm cells to a temperature of -40"C. 35 Nd2'. The method of claim Ndl'wherein the step of adding a cryoprotectant comprises adding glycerol. Nd3'. The method of claim Ndl' wherein said one or more specified DNA characteristics 40 comprises whether a sperm cell has an X or a Y sex chromosome.

255 Nd4'. The method of claim Ndl' wherein the step of cooling said quantity of sperm cells to said holding temperature comprises using a cooling rate that is selected so that said quantity of sperm cells is cooled from a temperature above a glass transition temperature below which 5 sperm cells are subject to damage from cold shock to said holding temperature in about 90 minutes. Nd5'. The method of claim Nd4' wherein the cooling rate is a substantially constant cooling rate in the range of about 0.1 -0.3 *C per minute. 10 Nd6'. The method of claim Ndl wherein the step of supercooling said quantity of sperm comprises cooling the sperm cells at a first cooling rate to a temperature that approaches a critical temperature zone at which ice crystal formation and changes in osmotic pressure damage sperm cells and cooling the sperm at a second cooling rate faster than said first cooling rate to a 15 temperature that is less than about -30 *C. Nd7'. The method of Ndl' further comprising: forming a staining mixture containing the sperm cells and a DNA selective fluorescent 20 dye, and subjecting the staining mixture to a temperature of at least about 40*C. e. Sort Strategy (with high-temperature staining) Nel'. A method of processing animal sperm cells comprising the steps of: 25 forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; delivering a fluid stream of said staining mixture containing the sperm cells to a first location and causing said stream to break into droplets at a second location, said droplets 30 comprising first droplets each containing one or more sperm cells having a desired sex chromosome, second droplets each containing one or more sperm cells having an undesired sex chromosome, and third droplets each containing one or more sperm cells having the desired sex chromosome and one more sperm cells having the undesired sex chromosome; 35 sorting said first droplets from said second and third droplets; collecting said first droplets to provide at least one population of sperm cells having a desired sex chromosome; 256 identifying a quantity of sperm cells having the desired sex chromosome in said at least one population; and varying the rate at which fluid is delivered to said first location as a function of the 5 quantity of sperm cells identified as having the desired sex chromosome in said at least one population relative to the total number of sperm cells having the desired sex chromosome in said first, second, and third droplets. Ne2'. A method of processing animal sperm cells comprising the steps of: 10 forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; delivering a fluid stream of said staining mixture containing the sperm cells to a first 15 location and causing said stream to break into droplets at a second location, said droplets comprising first droplets each containing one or more sperm cells having a desired sex chromosome, second droplets each containing one or more sperm cells having an undesired sex chromosome, and third droplets each containing one or more sperm cells having the desired sex chromosome and one more sperm cells having the undesired sex chromosome; 20 sorting said first droplets and third droplets from said second droplets; collecting said first and third droplets to provide at least one population of sperm cells having a desired sex chromosome; 25 identifying a quantity of sperm cells having the undesired sex chromosome in said at least one population; and varying the rate at which fluid is delivered to said first location as a function of the 30 quantity of sperm cells identified as having the undesired sex chromosome in said at least one population. f. High-temp staining (w/ rapid cryopreservation) Nfl'. A method of processing animal sperm cells comprising the steps of: 35 forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; sorting said sperm cells in said staining mixture on the basis of a specified DNA 40 characteristic; 257 obtaining a quantity of sperm cells having a desired DNA characteristic; adding a cryoprotectant to said quantity of sperm cells; 5 cooling said quantity of sperm cells and the cryoprotectant to a holding temperature of about 0-8 0 C; maintaining said sperm cells and said cryoprotectant substantially at the holding 10 temperature for a period of less than 60 minutes; and supercooling said quantity of sperm cells to a temperature of -40*C. Nf2'. The method of claim NfI wherein the step of adding a cryoprotectant comprises 15 adding glycerol. Nf3'. The method of claim Nf1 wherein said specified DNA characteristic is whether a sperm cell contains an X or a Y sex chromosome. 20 Nf4. The method of claii' Nf1 wherein the step of cooling said quantity of sperm cell comprises using a cooling rate that is selected so that said quantity of sperm cells is cooled to about 0-8*C in about 90 minutes. Nf5'. The method of claim Nd4 wherein the cooling rate is a substantially constant 25 cooling rate in the range of about 0.1 -0.3 *C per minute. Nf6'. The method of claim Nfl wherein the step of supercooling said quantity of sperm comprises cooling the sperm cells at a first cooling rate to a temperature that approaches a critical temperature zone at which ice crystal formation and changes in osmotic pressure damage 30 sperm cells and cooling the sperm at a second cooling rate faster than said first cooling rate to a temperature that is less than about -30 *C. 9. Multiple Combinations Ngl'. (high-temperature staining/Multi-channel sorting/ rapid cryopreservation) 35 A method of processing animal sperm cells comprising the steps of: forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40'C; 258 sorting the sperm cells in said staining mixture into different populations of sperm cells on the basis of one or more specified DNA characteristics using a flow cytometry process comprising delivering a sample fluid to a plurality of flow cytometry units each of which is operable to sort the sperm cells on the basis of said one or more DNA characteristics, and 5 operating said units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for 10 delivering fluid containing said sperm cells to said flow cytometry units; obtaining a quantity of sperm cells having a desired DNA characteristic; adding a cryoprotectant to said quantity of sperm cells; 15 cooling said quantity of sperm cells and the cryoprotectant to a holding temperature of about 0-8 0 C; maintaining said sperm cells and said cryoprotectant substantially at the holding 20 temperature for a period of less than 60 minutes; and supercooling said quantity of sperm cells to a temperature of -40*C. Ng2'. (High temperature staining/multi-channel sorting/high purity sort strategy) 25 A method of processing animal sperm cells comprising the steps of: forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; 30 delivering a fluid stream of said staining mixture containing the sperm cells to each of a plurality of flow cytometry units and using the flow cytometry units to break each fluid stream into droplets, said droplets comprising first droplets each containing one or more sperm cells having a desired sex chromosome, second droplets each containing one or more sperm cells having an undesired sex chromosome, and third droplets each containingone or more sperm cells having 35 the desired sex chromosome and one more sperm cells having the undesired sex chromosome; sorting said first droplets from said second and third droplets using a droplet sorting flow cytometry process comprising operating said plurality of flow cytometry units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of 40 sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a 259 common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; 5 collecting said first droplets to provide at least one population of sperm cells having a desired sex chromosome; identifying a quantity of sperm cells having the desired sex chromosome in said at least 10 one population; and varying the rate at which fluid is delivered to one or more of the flow cytometry units as a function of the quantity of sperm cells identified as having the desired sex chromosome In said at least one population relative to the total number of sperm cells having the desired sex 15 chromosome in said first, second, and third and third droplets. Ng3'. (High temperature staining/multi-channel sorting/high recovery sort strategy) A method of processing animal sperm cells comprising the steps of: 20 forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; delivering a fluid stream of said staining mixture containing sperm cells to each of a plurality of flow cytometry units and using the flow cytometry units to break each fluid stream into 25 droplets, said droplets comprising first droplets each containing one or more sperm cells having a desired sex chromosome, second droplets each containing one or more sperm cells having an undesired sex chromosome, and third droplets each containing one or more sperm cells having a desired sex chromosome and one more sperm cells having an undesired sex chromosome; 30 sorting said first droplets and third droplets from said second droplets using a droplet sorting flow cytometry process comprising operating said plurality of flow cytometry units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving 35 and processing information from the units to permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; collecting said first and third droplets to provide at least one population of sperm cells 40 having a desired sex chromosome; 260 identifying a quantity of sperm cells having the undesired sex chromosome in said at least one population; and 5 varying the rate at which fluid is delivered to one or more of the flow cytometry units as a function of the quantity of sperm cells identified as having the undesired sex chromosome in said at least one population. Ng4'. (High temperature staining/multi-channel sorting/sort strategy/ rapid 10 cryopreservation) A method of processing animal sperm cells comprising the steps of: forming a staining mixture containing the sperm cells and a DNA selective fluorescent dye, and subjecting the staining mixture to a temperature of at least about 40*C; 15 delivering a fluid stream of said staining mixture containing sperm cells to each of a plurality of flow cytometry units, using the flow cytometry units to break each fluid stream into droplets, and sorting said droplets according to one or more specified DNA characteristics of the sperm cells contained in the droplets to obtain one or more populations of sperm cells having a 20 desired DNA characteristic by using a droplet sorting flow cytometry process comprising operating said plurality of flow cytometry units while sharing an integrated platform comprising at least one of the following elements: (1) a common supply of sperm cells; (2) a common source of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to 25 permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said sperm cells to said flow cytometry units; varying the rate at which fluid Is delivered to one or more of the flow cytometry units as a function of at least one of the following: (1) the purity of said one or more populations of sperm 30 cells having a desired DNA characteristic; and (2) the quantity of sperm cells having the desired DNA characteristic in said one or more populations of sperm cells relative to the total number of sperm cells having the desired DNA characteristic in said droplets; adding a cryoprotectant to protect a quantity of sperm cells obtained from said one or 35 more populations of sperm cells; cooling said quantity of sperm cells and said cryoprotectant to a holding temperature of about 0-8*C; 261 maintaining said sperm cells and said cryoprotectant substantially at said holding temperature for a period of less than 60 minutes; and supercooling said quantity of sperm cells to a temperature of -40*C. 5 o'. Overall Time Line 01'. A method of processing animal sperm cells comprising the steps of: 10 collecting sperm cells from a male animal; staining the sperm cells with a DNA selective fluorescent dye; illuminating the sperm cells with electromagnetic radiation to cause the DNA selective 15 fluorescent dye to emit fluorescent light; detecting the fluorescent light emitted by the sperm cells; analyzing the fluorescent light emitted by the sperm cells to determine one or more 20 specified DNA characteristics of the sperm cell; sorting the sperm cells into multiple populations of sperm cells on the basis of said one or more specified DNA characteristics; 25 obtaining a quantity of sperm cells having a desired DNA characteristic from one of said multiple populations of sperm cells; and supercooling said quantity of sperm cells; 30 wherein the step of supercooling is completed less than about 12 hours after the sperm cells are collected. 02'. The method of claim 01' wherein the step of supercooling said quantity of sperm cells is completed less than about 8 hours after the sperm cells are collected. 35 03'. The method of claim 01' wherein the step of supercooling said sperm cells is completed less than about 6 hours after the sperm cells are collected. 04'. The method of claim 01' wherein the step of supercooling said quantity of sperm 40 cells is completed less than about 3 hours after the sperm cells are collected.

262 05'. The method of claim 01' wherein the step of supercooling said quantity of sperm cells is completed less than about 2 hours after the sperm cells are collected. 5 06'. The method of claim 01' wherein the step of supercooling said quantity of sperm cells is completed less than about 1 hour after the sperm cells are collected. 07'. The method of claim 01' wherein the sperm cells comprise live sperm cells. 10 08'. The method of claim 07' wherein said one or more DNA characteristics comprises whether the sperm cell contains an X or a Y sex chromosome. 09'. The method of claim 01' further comprising the steps of thawing said quantity of sperm cells after the supercooling step and then fertilizing an egg cell with a sperm cell from said 15 quantity of sperm cells by artificial insemination. 010'. The method of claim 01' further comprising producing a plurality of quantities of sperm cells having a desired characteristic and distributing said plurality of quantities of sperm cells to animal breeders through a commercial distribution system. 20 P'. Sort Speeds P1'. A method of sorting live sperm cells according to chromosome content comprising: 25 (a) adding a DNA selective fluorescent dye to a supply of live sperm cells; (b) causing a sample fluid containing said sperm cells and a sheath fluid to flow through an orienting nozzle that tends to rotate the sperm cells into a desired orientation, said sample 30 fluid and sheath fluid exiting the nozzle as a fluid stream comprising a core stream formed by the sample fluid and sperm cells and a sheath fluid stream surrounding the core stream; (c) applying acoustical energy to the nozzle to cause the fluid stream to break into a stream of droplets at a droplet break-off location downstream from the nozzle; 35 (d) directing a beam of electromagnetic radiation to intersect the fluid stream at an interrogation location upstream from the droplet break-off location to excite the fluorescent dye in the sperm cells, thereby causing fluorescent emissions from the sperm cells; 263 (e) detecting the fluorescent emissions with a photodetector that outputs a time-varying analog signal indicative of the intensity of the detected fluorescent emissions; (f) electronically processing said time-varying analog signal to determine the 5 chromosomal content of a plurality of the sperm cells; (g) selectively applying an electrostatic charge to the fluid stream to selectively apply or not apply an electrical charge to the droplets according to the chromosomal content of sperm cells contained in the droplets; 10 (h) using an electric field to deflect the droplets according to their charge, thereby separating sperm cells contained in droplets having the same charge from sperm cells contained in droplets having a different charge; and 15 (i) collecting at least one population of live sperm cells at a rate of at least 5,000 sperm cells per second. P2'. P1' wherein the at least one population collected in the collecting step has a purity of at least 85%. 20 P3'. P1' wherein said collecting step comprises collecting the at least one population of live sperm cells at a rate of at least 6,000 sperm cells per second. P4'. P1' wherein said collecting step comprises collecting the at least one population of 25 live sperm cells at a rate of at least 7,000 sperm cells per second. P5'. P1' further comprising operating two or more cytometry units in parallel so that each performs steps (b) through (i) while they share an integrated platform, said integrated platform comprising one or more of the following: (1) a common supply of particles; (2) a common source 30 of electromagnetic radiation; (3) a common housing; (4) a common input for controlling operation of the units; (5) a common processor for receiving and processing information from the units to permit evaluation of the operation of one unit relative to another unit; and (6) a common fluid delivery system for delivering fluid containing said particles to said flow cytometry units. 35 P6'. P5' wherein the step of operating said two or more flow cytometry units while they share an integrated platform comprises operating a mode-locked solid state laser to produce a single beam comprising a plurality of electromagnetic pulses, the peak power of each pulse being greater than the average power output of the laser, splitting the single beam into two or more beams, and directing each of said two or more beams to one of the flow cytometry units. 40 264 R'. CSD & slit scanning a. Sperm cells RI'. A method of analyzing chromosomal DNA characteristics of animal sperm cells in a fluid stream having a direction of flow, each sperm cell having a head with a nucleus comprising 5 a localized chromosome region containing at least one chromosome, said nucleus having a length in the direction of stream flow, said method comprising: focusing a beam of electromagnetic radiation on the fluid stream as a generally elliptical spot having a length along a major axis extending generally at right angles to the direction of 10 stream flow and a width along a minor axis extending generally parallel to the direction of stream flow, the width of the beam spot being less than the length of said nucleus, said sperm cells being adapted to pass through said spot resulting in emissions of electromagnetic radiation from the sperm cells, including emissions from said chromosome regions indicative of chromosomal DNA characteristics of the regions; 15 detecting and converting at least some of said emissions from the chromosome regions into time-varying analog electrical signals indicative of said chromosomal DNA characteristics; digitally sampling the time-varying analog signal and providing an output including digital 20 information corresponding to said time-varying analog signal; analyzing the digital information to extract information indicative of a derivative characteristic of the time-varying analog signals; and 25 classifying at least some of the sperm cells as having a particular chromosomal DNA characteristic based at least in part on said extracted information. R2'. The method of claim RI' wherein said chromosomal DNA characteristics are indicative of the sex of the sperm cells. 30 R3'. The method of claim R2' wherein said sperm cells are bovine sperm cells. R4'. The method of claim R3' wherein said chromosome region is localized within an area of the nucleus extending no more than about 20% of the nucleus length on either side of a 35 longitudinal center of the nucleus. R5'. The apparatus of claim R3' wherein said chromosome region is localized within an area of the nucleus extending no more than about 10%-15% of the nucleus length on either side of a longitudinal center of the nucleus. 40 265 R6'. The method of claim RI' wherein the digitally sampling step comprises synchronously sampling the time-varying analog output. R7'. The method of claim RI'wherein said spot width is less than about 3.0 pm. 5 R8'. The method of claim R7' wherein said spot length is greater than about 100 pm. R9'. The method of claim R1'further comprising exerting a force on the sperm cells in the stream tending to bring them into a desired orientation before the stream passes through said 10 beam. RiO'. The method of claim R further comprising droplet sorting droplet said sperm cells according to said chromosomal DNA characteristics. 15 Ri 1'. The method of claim RI' further comprising a photo-damage sorting said sperm cells according to said chromosomal DNA characteristics R12'. The method of claim Ri' further comprising fluid-switching sorting sperm cells according to said chromosomal DNA characteristics. 20 Ref. The method of claim R'wherein said derivative characteristic comprises the slope of the time-varying analog signal at a point of the signal relative to a threshold value. b. Generic Particles 25 R14'. A method of analyzing particles in a fluid stream having a direction of flow, said method comprising: focusing a beam of electromagnetic radiation on the fluid stream as a generally elliptical spot having a length along a major axis extending generally at right angles to the direction of 30 stream flow and a width along a minor axis extending generally parallel to the direction of stream flow, the width of the beam spot being less than the size of saId particles, said particles being adapted to pass through said spot resulting in emissions of electromagnetic radiation from the particles; 35 detecting and converting at least some of said emissions into time-varying analog electrical signals indicative of characteristics of the particles; digitally sampling the time-varying analog signal and providing an output including digital information corresponding to said time-varying analog signal; 40 266 analyzing the digital information to extract information indicative of a derivative characteristic of the time-varying analog signals; and classifying at least some of the particles as having a particular characteristic based at 5 least in part on said extracted information. R15'. The method of claim R14' wherein the digitally sampling step comprises synchronously sampling the time-varying analog output. 10 R16'. The method of claim R14' further comprising droplet sorting droplet said particles according to said classification. R17'. The method of claim R14' further comprising a photo-damage sorting said sperm cells according to said chromosomal DNA characteristics. 15 Ri 8'. The method of claim R1 4'further comprising fluid-switching sorting sperm cells -according to said chromosomal DNA characteristics. R19'. The method of claim R14' wherein derivative characteristic comprises the slope of 20 the time-varying analog signal at a point of the signal relative to a threshold value. S'. Pulsed Laser FCM Aparatus SI'. A flow cytometry apparatus comprising: 25 a flow channel for directing a fluid stream containing sample particles through a particle interrogation location; a laser operable to emit a plurality of electromagnetic radiation (EMR) pulses, each pulse 30 having a peak power that exceeds the average power of the laser, said pulses being directed along a beam path from the laser to the particle interrogation location; a timing circuit operable to produce a timing signal indicative of the of arrival of pulses at the interrogation location; 35 a detector adapted to detect EMR from the interrogation location and operable to output a time-varying analog signal indicative the intensity of the detected EMR; an analog to digital converter adapted to receive the time-varying analog signal as input 40 and to sample the analog signal to produce a digitized output; and 267 an electronic processor operable to analyze the digitized output from the analog to digital converter as a function of the timing signal. S2'. The apparatus of SI' wherein the laser is operable to emit EMR pulses having a 5 width of about 1-100 picoseconds at a pulse frequency of about 50-150 MHz at a power of about 100-500 milliwatts. 83'. The apparatus of S2' wherein the laser is operable to emit EMR pulses having a width of about 5-20 picoseconds at a frequency of about 70-100 MHz. 10 S4'. The apparatus of SI' wherein the timing circuit comprises a sensor adapted to sense light corresponding to the EMR pulses including scattered light generated by interaction of each pulse with the fluid stream or including light of the EMR pulse. 15 S5'. The apparatus of SI' wherein the timing circuit comprises a clock that is operable to trigger the laser to emit a pulse. S6'. The apparatus of S1' wherein the detector is adapted to detect fluorescent emissions stimulated by the excitation energy of the pulses. 20 S'. The apparatus of Si' wherein the laser comprises a mode-locked solid state laser. S8'. The apparatus of Si' wherein the laser comprises a Q-switched laser. 25 39'. The apparatus of S1' wherein the laser comprises a cavity dumping laser. S10'. The apparatus of S1' wherein the detector is a photomultiplier tube. 30 S11'. The apparatus of S9' wherein the photomultiplier tube has a response time of less than about 2 nanoseconds. S12'. The apparatus of 1' wherein the electronic processor is operable to process the digitized output as a pulse waveform. 35 S13'. The apparatus of S12' wherein the electronic processor is operable to extract at least one of the following features from the digitized output: critical slope difference; pulse rise time; pulse peak; and pulse area. 40 268 T'. Pulsed Laser Method Ti'. A method of analyzing particles contained in a fluid stream as they flow through an interrogation location, said method comprising the steps of: 5 emitting a plurality of electromagnetic radiation (EMR) pulses from a laser, wherein the peak power of each pulse exceeds the average power of the laser; intermittently illuminating the fluid stream and the particles contained therein by directing said pulses along a beam path from the laser to the interrogation location; 10 detecting EMR from the interrogation location; generating a time-varying analog signal indicative of the intensity of the detected EMR; 15 generating a timing signal indicative of the arrival of a pulse at the interrogation location; converting the time-varying analog signal into a digital signal; and analyzing the digital signal to determine characteristics of the particles in the fluid 20 stream. T2'. The method of Ti' wherein the step of converting the time-varying analog signal to a digital signal comprises sampling the analog signal at a time that is synchronized to coincide with the illumination of the fluid stream by a pulse. 25 T3'. The method of T1' wherein the step of illuminating the fluid stream results in excitation of a fluorophore associated with said particles and the step of converting the time varying analog signal to a digital signal comprises sampling the analog signal at a predetermined time after illumination of the interrogation and within the fluorescent lifetime decay of said 30 fluorophore. T4'. The method of Ti' wherein each pulse contains sufficient power to saturate said fluorophore. 35 T5'. The method of T1' wherein the step of detecting light from the interrogation location comprises using a photomultiplier tube to detect fluorescent emissions from a fluorophore associated with said particles..

269 T6'. The method of Ti' wherein the step of emitting pulses of electromagnetic radiation comprises the step of emitting between about 50 -150 million pulses per second, wherein each pulse has a width between about 1-100 picoseconds. 5 T7. The method of Ti' wherein the step of generating a timing signal comprises sensing scattered light resulting from interaction of a pulse with the fluid stream. T8'. The method of T1' wherein the step of generating a timing signal comprises generating a clock signal and the step of emitting a plurality of EMR pulses from a laser 10 comprises using the clock signal to trigger the laser to emit a pulse. T9'. The method of TI' wherein the step of analyzing the digital signal comprises analyzing the digital signal as a pulse waveform. 15 T10'. The method of T9' wherein the step of analyzing the digital signal further comprises extracting at least one of the following features from the signal: critical slope difference; pulse rise time; pulse peak; and pulse area. 2 11'. The method of T1' wherein said particles comprise sperm cells. 20 U' - Reservedj V' CV Optimization 25 VI'. A process for evaluating a set of conditions for staining a population of cells for sorting, the population comprising a first type and a second type of cell, the process comprising: (a) staining a fraction of the population of cells with a fluorescent dye under a set of staining conditions; 30 (b) exposing the stained cells to electromagnetic radiation as the stained cells are passed through an interrogation location of a flow cytometer at a rate, R; (c) determining a fluorescence emission characteristic of the exposed cells; 35 (d) using the determined fluorescence characteristic to classify the exposed cells into two or more sub-populations of cells, one of the sub-populations being an enriched sub-population of the first cell type; 270 (e) determining a coefficient of variation for the fluorescence emission characteristic of the cells of the enriched sub-population to provide an indication of sorting efficiency for the staining conditions; and 5 (f) determining whether to modify any staining condition under which cells are to be stained or the rate, R, at which the stained cells are to be passed through the interrogation location of the flow cytometer in order to improve sorting efficiency. V2'. The process of claim V1', wherein said fraction comprises a first fraction and said 10 set of staining conditions comprises a first set of staining conditions, the process further comprising staining a second fraction of said population of cells under a second set of staining conditions different from the first set and performing steps (b) through (e) with said second fraction of the population of cells. 15 V3'. The process of claim V2' wherein the second fraction is stained after the coefficient of variation has been determined for the first fraction. V4'. The process of claim V2' wherein the second set of staining conditions differs from the first set of staining conditions by at least one of the following: (1) concentration of the 20 fluorescent dye; (2) the length of a staining period used to stain the cells; and (3) a temperature of the cells during a staining period used to stain the cells. V5'. The process of claim V2', further comprising staining a third fraction of said population of cells under a third set of staining conditions different from the first and second sets 25 and performing steps (b) through (e) with the third fraction of the population of cells. V6. The process of claim V5', further comprising staining a fourth fraction of said population of cells under a fourth set of staining conditions different from the first, second, and third sets and performing steps (b) through (e) with the fourth fraction of the population of cells. 30 V7'. The process of claim V6, further comprising staining a fifth fraction of said population of cells under a fifth set of staining conditions different from the first, second, third and fourth sets and performing steps (b) through (e) with the fifth fraction of the population of cells. 35 V8'. The process of claim V2', further comprising selectively varying conditions in the first set of staining conditions based upon said determination in order to obtain the second set of staining conditions.

271 V9.' The process of claim V2', wherein a modified staining condition as determined by performing step (f) on the second fraction is applied to the staining of the remainder of the population of cells. 5 V10'. The process of claim V1', wherein multiple fractions Of cells are stained in step (a), each fraction being stained under a unique set of staining conditions, wherein steps (b) through (e) are performed for each fraction, and wherein step (0 comprises using the respective coefficients of variation to determine the set of staining conditions to be used to stain additional cells in said population. 10 VI1'. The process of claim Vi', wherein the cells are sperm cells. VI 2'. The process of claim VI', wherein the first cell type comprises X chromosome bearing sperm cells. 15 . V13'. The process of claim Vi' wherein step (a) comprises staining the cells with Hoechst 33342. V14'. The process of claim V1' wherein said fluorescence emission characteristic 20 comprises a feature of a fluorescence pulse waveform corresponding to movement of a cell through the interrogation location, and wherein said feature is Indicative of at least one of the following: (1) total fluorescence intensity; and (2) peak fluorescence intensity. V1 5'. The process of claim V1' further comprising determining before step (9 whether 25 the coefficient of variation from step (e) is equal to or less than a predetermined coefficient of variation and repeating steps (a) through (e) using a different set of staining conditions to stain a different fraction of the cells each time until the coefficient of variation determined in step (e) is equal to or less than the predetermined coefficient of variation, and wherein step () comprises determining to use the staining conditions to stain additional cells if the coefficient of variation 30 from step (e) for the respective staining conditions is equal to or less than the predetermined coefficient of variation. VI 6' A process for evaluating a set of conditions for staining a population of cells for sorting, the population comprising a first type and a second type of cell, the process comprising: 35 (a) staining a fraction of the population of cells with.a fluorescent dye under a set of staining conditions; (b) exposing the stained cells to electromagnetic radiation as the stained cells are passed through an interrogation location of a flow cytometer at a rate, R; 40ctmtratartR 272 (c) determining a fluorescence emission characteristic of the exposed cells; (d) using the determined fluorescence emission characteristic to classify the 5 exposed cells into two or more sub-populations of cells, one of the sub populations being an enriched sub-population of the first cell type; (e) determining a coefficient of variation for the fluorescence emission characteristic of the cells of the enriched sub-population to provide an indication of sorting 10 efficiency for the staining conditions; (f) determining whether to modify any staining condition under which the fraction of cells are to be stained or the rate, R, at which the stained cells are passed through the interrogation location of the flow cytometer in order to imporve sorting 15 efficiency; and (g) applying the modified staining condition to the remainder of the population of cells. 20 V17'. The process of claim VI 6' further comprising sorting the remainder of the population of cells in a flow cytometer to obtain an enriched sample population of the first cell type. V1 8'. The process of claim VI 6', wherein said fraction comprises a first fraction and said 25 set of staining conditions comprises a first set of staining conditions, the process further comprising staining a second fraction of said population of cells under a second set of staining conditions different from the first set and performing steps (b) through (e) with said second fraction of the population of cells. 30 V19'. The process of claim V18' wherein the second fraction is stained after the coefficient of variation has been determined for the first fraction. V20'. The process of claim VI 8', wherein the second set of staining conditions differs from the first set by at least one of the following: (1) concentration of the fluorescent dye; (2) the 35 length of a staining period used to stain the cells; and (3) the temperature of the cells during a staining period used to stain the cells. V21'. The process of claim V18', further comprising staining a third fraction of said population of cells under a third set of staining conditions different from the first and second sets 40 and performing steps (b) through (f) with the third fraction of the population of cells.

273 V22'. The process of claim V21', further comprising staining a fourth fraction of said population of cells under a fourth set of staining conditions different from the first, second, and third sets and performing steps (b) through (f) with the fourth fraction of the population of cells. 5 V23'. The process of claim V22', further comprising staining a fifth fraction of said population of cells under a fifth set of staining conditions different from the first, second, third and fourth sets and performing steps (b) through (f) with the fifth fraction of the population of cells. 10 V24'. The process of claim V1 8', further comprising prior to step (g), selecting a set of staining conditions for use in step (g) that results in a coefficient of variation level for the fluorescence emission characteristic that Is equal to or less than a predetermined coefficient of variation. 15 V25'. The process of claim V24', wherein the predetermined coefficient of variation is about 1.3% or less. V26'. The process of claim V16', further comprising determining before step (f) whether the coefficient of variation from step (e) is equal to or less than a predetermined coefficient of 20 variation and repeating steps (a) through (e) using a different set of staining conditions to stain a different fraction of the cells each time until the coefficient of variation determined in step (e) is equal to or less than the predetermined coefficient of variation, and wherein step (f) comprises determining to use the staining conditions to stain additional cells if the coefficient of variation from step (e) for the respective staining conditions is equal to or less than the predetermined 25 coefficient of variation. V27'. The process of claim V16', wherein the cells are sperm cells. V28'. The process of claim V27', wherein the first cell type comprises X chromosome 30 bearing sperm cells. V29'. The process of claim V1 6', wherein step (a) comprises staining the cells with Hoechst 33342. 35 V30'. The process of claim V16', wherein said fluorescence emission characteristic comprises a feature of a fluorescence pulse waveform corresponding to movement of a cell through the interrogation location, and wherein said feature is indicative of at least one of the following: (1) total fluorescence intensity; and (2) peak fluorescence intensity.

274 W'. Automated Calibration Usinc Epi-ilfumination Sensors W1'. An apparatus for automatically calibrating a droplet sorting flow cytometer that selectively applies or does not apply one of a set of one or more electrical charges to a plurality of droplets as they break off of a continuous fluid stream at a droplet break-off location and 5 electrostatically sorts the droplets into two or more separate droplet streams, the selection of the electrical charge for each droplet being dependent on the expected contents of the droplet based on a drop delay setting representing an estimate of the time elapsing between the moment a particle contained in the continuous fluid stream is detected at an interrogation location of the flow cytometer and the arrival of that particle at the droplet break-off location, the apparatus 10 comprising: (a) an epi-illumination sensor downstream of the interrogation location for illuminating droplets in one of said separate droplet streams, detecting any fluorescence emissions emitted by particles contained in the droplets, and generating an output signal representative of the 15 detected fluorescence emissions; and (b) a control operable to analyze the output signal and to automatically adjust at least one of: (1) the drop delay setting; and (2) the amplitude of a charge in said set of charges. 20 W2'. The apparatus of W1'wherein the control adjusts the drop delay setting as a function of the difference between the detected fluorescence emissions and the fluorescence emissions that would have been produced by droplets having the expected contents. W3'. The apparatus of W1' wherein the control adjusts the amplitude of a charge in said 25 set of charges as a function of variation in an average peak intensity of fluorescence emissions detected for droplets containing fluorescent particles. W4'. The apparatus of W1' wherein said epi-illumination sensor comprises a light source, a dichroic filter, a lens system, and a photodetector. 30 W5'. The apparatus of W4' wherein the epi-illumination sensor further comprises a fiber optic cable operable to conduct light from the light source to the location at which the sensor illuminates the droplets. 35 W6'. The apparatus of W5'wherein the electrical field is generated by a pair of electrically charged deflector plates, and wherein the epi-illumination sensor is positioned to illuminate said droplets as they pass between said deflector plates. W7'. The apparatus of W6'wherein the epi-illumination sensor Is positioned to illuminate 40 said droplets through a hole in an electrically insulated support holding at least one of the 275 deflector plates as the droplets move through an electric field generated by one or more of the deflector plates. W8'. The apparatus of W4' wherein the light source is operable t6 illuminate particles at 5 the interrogation location. W9'. The apparatus of W1'further comprising an epi-illumination sensor as set forth in paragraph (a) of claim W1'for each of the remainder of said two or more separate droplet streams, said control being operable to analyze the output signals from the epi-illumination 10 sensor for each droplet stream and to automatically adjust at least one of: (1) the drop delay setting as a function of the difference between the detected fluorescence emissions for one or more of the streams and the fluorescence emissions that would have been produced by droplets having the expected contents in the respective droplet stream; and (2) the amplitude of a charge in said set of charges as a function of variation in an average peak intensity of fluorescence 15 emissions detected for droplets containing fluorescent particles at least one of said one or more droplet streams. WIO'. The apparatus of W9' wherein the electrical field is generated by a pair of electrically charged deflector plates, and wherein the epi-illumination sensor is positioned to 20 illuminate said droplets as they pass between said deflector plates. W11'. The apparatus of W1 0' wherein the epi-illumination sensor is positioned to illuminate said droplets through a hole in an electrically insulated support holding at least one of the deflector plates as the droplets move through an electric field generated by one or more of 25 the deflector plates. W12'. The apparatus of W1' wherein the control is operable to automatically maintain the phase of droplet charging within about 36 degrees above or below an optimal phase with respect to droplet formation. 30 W13'. The apparatus of W12' wherein the control is operable to automatically maintain the phase of droplet charging within about 10.8 degrees above or below an optimal phase with respect to droplet formation. 35 X'. Automated Calibration Method X1'. A method of continuously verifying proper sort calibration in a droplet sorting flow cytometer that selectively applies or does not apply one of a set of one or more electrical charges to a plurality of droplets as they form from a continuous fluid stream at a droplet break-off 40 location and electrostatically sorts the droplets into two or more separate droplet streams, the 276 selection of the electrical charge for each droplet being dependent on the expected contents of the droplet based on a drop delay setting representing an estimate of the time elapsing between the moment a particle contained in the continuous fluid stream is detected at an interrogation location of the flow cytometer and the arrival of that particle at the droplet break-off location, the 5 method comprising: (a) illuminating droplets In one of said separate droplet streams by directing an illumination beam along a beam axis in a forward direction through a lens system to cause emission of fluorescent light by any particles contained in the droplets; 10 (b) using said lens system to collect some of said fluorescent light and direct it In a rearward direction along the beam axis; (c) detecting at least some of the collected fluorescent light and generating an output 15 signal representative of the detected light; and (d) analyzing the output signal and, based on the analysis, automatically adjusting at least one of: (1) the drop delay setting; and (2) the amplitude of a charge in said set of charges. 20 X2'. The method of X1' wherein the adjusting step comprises adjusting the drop delay setting as a function of the difference between the detected fluorescence emissions and the fluorescence emissions that would have been produced by droplets having the expected contents. 25 X. The method of Xl'wherein the adjusting step comprises adjusting the amplitude of a charge in said set of charges as a function of variation in an average peak intensity of fluorescence emissions detected for droplets containing fluorescent particles. X4'. The method of Xl'wherein the Illuminating step comprises using a fiber optic cable 30 to guide light from the light source to a position adjacent said sorted droplet streams. X5'. The method of XI wherein the electrical field is generated by a pair of electrically charged deflector plates, and wherein the illuminating step comprises illuminating the droplets as they move between the deflector plates. 35 X6'. The method of X5' wherein at least one of the deflector plates is held by an electrically insulated support, and wherein the illuminating step comprises illuminating the droplets through a hole in the support as the droplets move through the electric field.

277 X7'. The method of Xl'further comprising using the light source to illuminate the particles at the interrogation location. X8'. The method of X1' further comprising performing steps (a)-(c) for each of the 5 remainder of said two or more droplet streams, and wherein step (d) further comprises analyzing each of the respective output signals and adjusting at least one of: (1) the drop delay setting as a function of the difference between the detected fluorescence emissions and the fluorescence emissions that would have been produced by droplets having the expected contents; and (2) the amplitude of a charge in said set of charges as a function of variations in the average peak 10 intensity of fluorescence emissions detected for droplets containing fluorescent particles at least one of said droplet streams. X9'. The method of X8' wherein the electrical field is generated by a pair of electrically charged deflector plates, and wherein the illuminating step comprises illuminating the droplets as 15 they move between the deflector plates. X10'. The method of X9' wherein at least one of the deflector plates is held by an electrically insulated support, and wherein the illuminating step comprises illuminating the droplets through holes in the support as the droplets move through the electric field. 20 Y'. Test Stream Calibration Method Y1'. A method of continuously verifying proper sort calibration in a droplet sorting flow cytometer that selectively applies or does not apply one of a set of one or more electrical charges 25 to a plurality of droplets as they form from a continuous fluid stream at a droplet break-off location and electrostatically sorts the droplets Into two or more separate droplet streams, the selection of the electrical charge for each droplet being dependent on the expected contents of the droplet based on a drop delay setting representing an estimate of the time elapsing between the moment a particle contained in the continuous fluid stream is detected at an interrogation 30 location of the flow cytometer and the arrival of that particle at the droplet break-off location, the method comprising: selecting droplets estimated to have substantially zero probability of containing a particle; 35 applying one charge of said set of charges to the selected droplets in order to form a test stream out of the selected droplets; illuminating the droplets in the test stream; and 40 detecting any light emitted or scattered by any particles in the selected droplets.

278 Y2'. The method of Y1'further comprising adjusting the drop delay setting if light detecting in the detecting step exceeds a threshold level. 5 Y3'. The method of Y2' wherein the adjusting step is performed automatically. Y4'. The method of YI'wherein the charge applied in the charging step is a neutral charge. 10 Y5'. The method of YI' wherein the illuminating and detecting steps are performed using an epi-illumination sensor. Z'. Sort Correction System 15 21'. A sort system correction system for a droplet sorting flow cytometer comprising: a charging element for selectively applying one electrical charge from a set of electrical charges to each droplet in a stream of droplets as the droplets form from a continuous fluid stream at a droplet break-off location; 20 a pair of electrically charged deflector plates downstream from the charging element positioned so the droplets pass between the deflector plates to sort the droplets according to their charge; and a debris removal system comprising at least one of the following elements: (1) a selectively 25 activatable air system for removing debris from the charging element; and (2) a selectively activatable air system for removing debris from the deflector plates. Z2'. The system of Z1' wherein said debris removal system comprises element (1) and element (2). 30 Z3'. The system of ZI' wherein the debris removal system is adapted to be automatically activated by a processor upon determination by the processor that debris from stray droplets is interfering with droplet sorting. 35 Z4'. The system of ZI' wherein the debris removal system comprises element (1), and wherein said selectively activatable air system of element (1) comprises a vacuum passage having an opening adjacent said charging element for vacuuming debris off the charging element.

279 Z5'. The system of Z1 wherein the debris removal system comprises element (2), and wherein said selectively activatable air system of element (2) comprises air passages having openings through which compressed gas is delivered for blowing debris off the deflector plates. Z6.' A method of operating a droplet sorting flow cytometer system, the method comprising: using a charging element to selectively apply one electrical charge from a set of electrical charges to each droplet in a stream of droplets as the droplets form from a continuous fluid stream at a droplet break-off location; passing the droplets between a pair of electrically charged deflector plates downstream from the charging element to sort the droplets according to their charge; using a processor to determine whether debris is interfering with droplet sorting; and removing said debris using a debris removal system under the control of the processor if the processor determines that debris is interfering with droplet sorting, said debris removal system comprising at least one of the following elements: (1) a selectively activatable air system for removing debris from the charging element ; and (2) a selectively activatable air system for removing debris from the deflector plates. With reference to the use of the word(s) "comprise" or "comprises" or "comprising" in the foregoing description and/or in the following claims, unless the context requires otherwise, those words are used on the basis and clear understanding that they are to be interpreted inclusively, rather than exclusively, and that each of those words is to be so interpreted in construing the foregoing description and/or the following claims. Reservation of Rights Applicants expressly reserve all rights with respect to filing amended claims and continuation and/or divisional applications in any designated country to prosecute claims directed to any inventive aspect identified above and any other subject matter described in the specification or shown in the drawings. B W6I 6a

Claims (18)

1. 2. The nozzle as claimed in claim 1, wherein the generally elliptical cross sectional shape of one of the said at least two regions is oriented at about 90 degrees relative to the generally elliptical cross sectional shape of the other of the said at least two regions.
2. 3. The nozzle as claimed in claim 1, wherein the generally elliptical cross sectional shapes having major axises of the first and second regions are oriented in substantially the same direction to define a first torsional zone, and thd generally elliptical cross sectional shape of the third region, constitutes a second torsional zone, which is oriented at about 90 degrees relative to the generally elliptical cross sectional shapes of the first and second regions. 281 /1. The nozzle aq claimed in claim .3, wbwmin (lit first torsional zone has an axial length of 3.0-4.5 mm and the second torsional zone has an axial length of 3.5-5.0 mm.
3. 5. The nozzle as claimed in claim 1, wherein the third axially tapered region tapers at an angle of 42-48 degrees.
4. 6. The nozzle as claimed in claim 1, wherein all of the regions have generally elliptical cross sectional shapes.
5. 7. The nozzle as claimed in any claim 1, wherein the nozzle body has an exterior surface with a non- reflective coating thereon.
6. 8. The nozzle as claimed in claim 1, further comprising a mount for mounting the nozzle in a position pointing upward in its normal attitude of operation to direct the fluid stream along an upward trajectory.
7. 9. The nozzle as claimed in claim 8, wherein the nozzle body is rotatable on the mount on a longitudinal axis of the body.
8. 10. The nozzle as claimed in claim 8 wherein the angle of the taper in the second region is greater than that of the first region but less than that of the third region.
9. 11. The nozzle as claimed claim 1, wherein interior surface of the nozzle includes a fourth non tapered region coaxial with and downstream from the first, second and third axially tapered regions, the fourth tapered region being adjacent to the third axially tapered region,
10. 12. A method of orienting animal sperm cells in a flow cytometry apparatus, the method comprising the steps of: introducing a fluid containing sperm cells into a fluid stream; directing the fluid stream containing the sperm cells under a pressure in the range of 20 to 40 psi through a nozzle body having three or more adjacent axially tapered regions and an nozzle 282 orifice with a diameter in the range of 50-70 microns; accelerating the speed of the fluid stream in a downstream direction toward the nozzle orifice through a first axially tapered region having a first angle of taper, a second axially tapered region having a second angle of taper and a third axially tapered region having a third angle of taper, wherein the second angle of taper is different than the first angle of taper and the third angle of taper; and, applying a torsional force to the fluid stream tending to bring the cells into a desired orientation as they pass through the orifice at a rate in the range of 30,000 to 50,000 sperm cells per second with a generally elliptical cross section shape in at least one of the axially tapered regions.
11. 13. The method as claimed in claim 12, wherein the nozzle has two torsional zones defined by interior surfaces of the nozzle in the three or more axially tapered regions.
12. 14. The method as claimed in claim 12, wherein the nozzle has a flow axis through the nozzle orifice, and wherein at least some of the interior nozzle surfaces have generally elliptical shapes which are rotated relative to one another about the axis.
13. 15. The method as claimed in claim 12, wherein the method further includes directing the stream along an upward non-vertical trajectory.
14. 16. The method as claimed in claim 12, wherein the method further includes rotating the nozzle body on a central longitudinal axis of the body while directing the stream.
15. 17. An apparatus for classifying and sorting sperm cells according to chromosomal DNA characteristics of the cells, comprising: a nozzle system for delivering a fluid stream containing the cells to a first location and for causing the stream to break into droplets at a second location, the nozzle system including a nozzle having an interior surface configured to exert a force on the cells tending to bring them into a desired orientation before reaching the first location, wherein the interior surface of the nozzle comprises: a first axially tapered region having a first angle of taper; a second axially tapered region having a second angle of taper, the second axially tapered region adjacent to and downstream of the first axially tapered region; and a third axially tapered region having a third angle of taper, the third axially tapered region adjacent to and downstream of the second axially tapered 283 region, wherein the taper of the second axially tapered region is different than the taper of the first and third axially tapered regions, and wherein at least two of the regions having generally elliptical cross sectional shapes oriented in different directions for applying torsional forces to the fluid stream passing there through, tending to bring sperm cells in the stream into a desired orientation; an optics system for directing a beam of electromagnetic radiation to intersect the fluid stream at the first location so that cells in the stream pass through the beam resulting in emissions of electromagnetic radiation from the cells; and a photodetector for detecting and converting al: least some of the emissions into electrical signals; and a system for classifying the cells according to the DNA characteristics and for sorting the droplets according to the classification of cells contained in the droplets.
16. 18. The flow cytometer apparatus nozzle of claim 1 substantially as hereinbefore described.
17. 19. The method of claim 12 substantially as hereinbefore described.
18. 20. The apparatus of claim 17 substantially as hereinbefore described. A.871 8B