Number of This Manual: M 60-3-0043 e Gedruckt 06.2012

gedruckt 06.
2012
Number of this manual: M 60-3-0043 e
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Carl Zeiss draws the User's attention to the fact that the information and references
contained in these documents may be subject to technical modifications, in particular
due to the continuous further development of Carl Zeiss's products. The documents
enclosed do not contain any warranty by Carl Zeiss with regard to the technical
processes described in the documentation or to certain reproduced product
characteristics. Furthermore, Carl Zeiss shall not be held liable for any possible printing
errors or other inaccuracies in this documentation, unless proof can be furnished that
any such errors or inaccuracies are already known by Carl Zeiss or that these are not
known to Carl Zeiss due to gross negligence and that furthermore Carl Zeiss has for
these reasons refrained from eliminating these errors or inaccuracies appropriately.
Carl Zeiss hereby explicitly draws the User's attention to the fact that this manual only
contains a general description of the technical processes and information, the
implementation of which in any individual case may not be appropriate in the form
described here. In cases of doubt, we recommend the User to consult Carl Zeiss.
This manual is protected by copyright. Carl Zeiss has reserved all rights to this
documentation. It is prohibited to make copies, partial copies, or to translate this
manual into any other language, except copies for personal use.
Carl Zeiss explicitly draws attention to the fact that the information contained in this
manual will be updated regularly in compliance with the technical modifications and
supplements carried out in the products and furthermore that this manual only reflects
the technical status of Carl Zeiss's products at the time of printing.
Carl Zeiss Microscopy GmbH

Carl-Zeiss-Promenade 10
07740 Jena, Germany
microscopy@zeiss.com
www.zeiss.com/microscopy
Carl Zeiss Microscopy GmbH

Königsallee 9-21
37081 Göttingen, Germany
© Carl Zeiss Microscopy GmbH, 2008

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This Software product ("MTB2011 Configuration") was designed, realized,

verificated, validated and released in a certificated process environment. The
quality management system is certified following the rule of DIN EN ISO 9001.
The fields of application of the Software are common tasks and applications in
microscopy respectively imaging (so called “Off-The-Shelf Software”). Though
the user acknowledges that in any kind of use the end user of the Software is
responsible for the validation of the Software for the end user’s dedicated
intend of use considering all requirements of law and standards (e. g. FDA/21
CFR part 11, IvDD, etc.). If necessary the end user has to establish, to
document, to implement and to maintain a special process to fulfill all the
requirements to be conform with the validate rules of law and standards.
CARL ZEISS DOES NOT WARRANT THAT THIS SOFTWARE IS USABLE FOR
SPECIAL PURPOSES OTHER THAN IN THE FIELDS OF APPLICATION DEFINED
ABOVE.
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Refer to the safety notes and instructions in the manuals of all

necessary devices (e.g. microscope peripherals, cameras,
computers, computer additionals, etc.) before installing and
using the software (see also "Safety Notes AxioVision B 48-
0044 e (SAP 000000-1339-887")).
Table of Contents
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1 Introduction............................................................................................ 1
1.1 General............................................................................................ 1
1.2 Supported microscopes and stereomicroscopes ............................... 2
1.3 Software technology........................................................................ 3
2 Program Overview................................................................................. 4
2.1 Graphic user interface...................................................................... 4
2.2 File menu......................................................................................... 5
New configuration........................................................................ 5
Save configuration........................................................................ 6
Export configuration ..................................................................... 6
Import configuration..................................................................... 7
Delete configuration ..................................................................... 8
Update Configuration................................................................... 8
Update Component Lists ............................................................ 10
Exit ............................................................................................. 12
2.3 Options menu................................................................................ 13
Set active configuration .............................................................. 13
Custom filter set specification ..................................................... 15
Custom Excitation and Emission Filter Specification..................... 16
Custom Camera Emission Splitter Specification........................... 18
Custom ND/Grey Filter Specification ........................................... 19
User-defined VivaTome filter sets................................................ 20
Custom Piezo Focus Specification ............................................... 21
Edit Lasermodul AOTF Data ........................................................ 23
2.4 ? menu .......................................................................................... 24
Help............................................................................................ 24
About ......................................................................................... 24
3 Creating Configurations ...................................................................... 25
3.1 General operating concept ............................................................ 25
3.2 Auto configuration of microscopes with PC connection ................. 29
3.3 Configuring a manual microscope ................................................. 35
3.4 Configuring objectives ................................................................... 38
3.5 Configuring reflector cubes ........................................................... 40
3.6 Configuring eyepieces, camera adapters and cameras ................... 44
Eyepieces .................................................................................... 44
Camera adapters ........................................................................ 44
MTB2011 Configuration / Installation + Reference i

Table of Contents
Cameras ..................................................................................... 45
3.7 Configuring external Components (Colibri, ApoTome, VivaTome,
motorized XY stages, filterwheels and shutters) ............................. 46
Colibri......................................................................................... 46
ApoTome ................................................................................... 49
VivaTome.................................................................................... 51
Motorized XY stages................................................................... 52
Incubation .................................................................................. 55
Temperature Module.......................................................... 57
CO2 Module ...................................................................... 57
O2 Module......................................................................... 58
Air Heater Module.............................................................. 59
Y-Module ........................................................................... 60
Zeiss EMS-1 Control Box ............................................................. 62
Filter wheels and shutters (Ludl and Sutter)................................. 64
Shutters (Uniblitz) ....................................................................... 66
Sutter DG4 resp. DG5................................................................. 68
TILL Photonics Polychrome V....................................................... 70
Piezo focus ................................................................................. 71
3.8 Configuration of illumination components..................................... 71
3.9 Configuration of diaphragm sliders and filter wheels ..................... 73
Diaphragm sliders ....................................................................... 73
Filter wheels in the reflected light and transmitted light beam path74
4 Advanced Programming of the Axio Imager and Axio Observer
Microscopes ............................................................................................... 75
4.1 Saving configurations in the microscope ........................................ 75
4.2 Programming the motorized focus................................................. 76
Parfocality correction .................................................................. 76
Lowering the stage when changing objectives ............................ 77
Focus speed................................................................................ 77
4.3 Setting the key configuration......................................................... 78
4.4 Setting automatic functions ........................................................... 80
Light manager ............................................................................ 81
Contrast manager....................................................................... 82
Dazzle protection........................................................................ 82
Oilstop........................................................................................ 83
Switching stand version .............................................................. 83
5 Generating a Technical Report............................................................ 85
ii M 60-3-0043 e / printed 09.2011

Introduction
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The MTB2011 Configuration software is used to generate and manage

microscope and stereomicroscope configurations.
Information about microscope components (nosepieces, reflector turrets,

shutters etc.) and, if necessary, additional external units (motorized xy stages,
external light sources etc.) is stored in these configurations. Furthermore, the
MTB2011 Configuration program can also be used to enter information about
microscope components, such as objectives, fluorescence filter cubes etc., in a
simple way and to save this information in the microscope (depending on the
type of microscope in question). In this case, the information is saved directly
in the microscope, allowing it to be displayed on the microscope’s TFT screen,
for example.
Various configurations can be created, of which only one is activated at any

time. The active configuration is used by control and imaging software such as
ZEN 2011 from Carl Zeiss to provide graphic control dialogs for the configured
microscope units.
MTB2011 Configuration - Installation+Reference 1

Introduction
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The following microscopes are supported with Version 2.0.0.12 of MTB2011

Configuration.
Axio Observer.Z1 SteREO Lumar.V12

Axio Observer.D1 Stemi 2000C/CS
Axio Examiner Axio Zoom.V16
Axio Imager.Z2 Axiovert 200 M
Axio Imager.M2 Axiovert 200 man
Axio Imager.Z1 Other microscope (manual microscopes of
Axio Imager.M1 undefinded type)
Axio Imager.D1/D2 Axio Scope
Axio Imager.A1/A2 Axiovert 40
Axio Scope mot. LSM Axioplan 2 (only manual components)
SteREO Discovery.V20 Axioskop 2 (only manual components)
SteREO Discovery.V12 Axio Lab.A1
SteREO Discovery.V8
The stereomicroscopes SteREO Discovery.V8, SteREO Discovery.V12, SteREO

Discovery.V20, SteREO Lumar.V12 and Stemi 2000C can be selected in a
largely manual configuration (without EMS control box) or a motorized
configuration (with EMS control box). The components that are possible in
each case are displayed according to the selection made.
2 M 60-3-0043 e / printed 09.2011

Introduction
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MTB2011 Configuration is the graphic user interface for configuring the

MicroToolBox 2011 (MTB2011). MTB2011 is a server application which, in
the background, enables communication between the control software for
the microscope (e.g. ZEN 2011) and the microscope itself.
MTB2011 Configuration is the graphic user interface for configuring the

server application.
MTB2011 Configuration can be installed on the following operating systems:
• Microsoft® Windows 7 64bit

• Microsoft® Windows 7 32 bit (nur ZEN 2011 LE

Program Overview
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Start MTB2011 Configuration by double-clicking on the corresponding icon

on the Microsoft Windows desktop.
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The start screen is divided into different areas:
Selection bar
Menu bar
Information area
Configuration area
4 M 60-3-0043 e / printed 09.2011

Program Overview
Menu bar
The menu bar contains a list of tasks and functions.
Configuration area
In this area, all the available configurations are listed and managed.
Selection area
In the selection area, a series of selection options for configuring your
microscope are listed. Here, for example, the type of microscope being used
and the objectives, filter cubes, xy stage etc. are displayed.
Information area
This is where additional information about selected microscope units and
equipment is displayed. Additional buttons and selection options may also be
displayed in this area.
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With this function, a new microscope configuration is created and displayed

as a new entry in the configuration area. The default name is New
Configuration1, and the number will increase consecutively each time a new
configuration is created. The name of the configuration has a purely
descriptive character and can be changed at any time. To do this, select the
configuration by clicking on the appropriate entry in the configuration tree
and change the name in the right-hand information area. It makes sense to
allocate "meaningful names", e.g. the product name of the microscope being
used.

Program Overview
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Using this function, you can save the newly created configurations and make
them available for imaging software, e.g. ZEN 2011.
Changes will be adopted by clicking on .
Changes will be adopted and the MTB2011 Configuration will be closed by

clicking on .
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Using this function, you can export configurations as files. This function is
useful, for example, for generating back-up copies of the configurations that
have been created. The configurations are saved as files with the extension
"mtb" on a data carrier such as a hard drive, floppy disk or memory stick.
6 M 60-3-0043 e / printed 09.2011

Program Overview
Click on the configuration entry that you wish to export. The corresponding
configuration is shown with a blue background.
Select the Export Configuration function in the File menu.
Use the standard Microsoft Windows dialog for saving files to save the
configuration file.
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Using this function, you can read in configurations from an “mtb” file (see
also Export Configuration section). The file containing the configurations
can also be read in from a data carrier such as a hard drive, floppy disk or
memory stick.
Select the Import Configuration function in the File menu.

Program Overview
Use the standard Microsoft Windows dialog for opening files to load the
configuration file.
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Click on the configuration entry that you wish to remove. The corresponding
configuration is shown with a blue background.
¾ Select the Delete Configuration function in the File menu.
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Use this function to update a configuration. For updating, proceed as follows:
¾ In the configuration tree, click on the microscope name or on a

subordinate branch (as, for example, Nosepiece or Reflector Changer).
¾ In the File menu, select the Update Configuration function.
8 M 60-3-0043 e / printed 09.2011

Program Overview
After the start of this function, the MTB2011 Software identifies the
microscope or the microscope components selected, as well as any further
peripheral equipment, and adds them to the configuration, thus updating it.
The software only updates those microscope components that are arranged
below the selected branch of the configuration tree. If, e.g., you select the
branch "6x Motorized Reflector Changer" for updating, the software only
reads and updates the fluorescence filters contained in the reflector changer
of the respective microscope.
If there are components that cannot be detected automatically (manual/non-

coded components) under these microscope components, these are queried
automatically during the update and can be added manually (see "Creating
Configurations" - "Auto configuration").
Note:
• The File menu functions described can also be called up directly via a
context menu. To do this, click the right mouse button in the configuration
area. This will open a context menu.
In the context menu, select an entry to have the respective command

executed. In addition, the context menu allows you to save changes of
configurations of the microscope stand. This function is described in chapter
5.1.

Program Overview
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This function allows you to update the list of all available objectives or filter
sets that are being used in MTB2011. If necessary, updated component lists
are made available to download from the internet at
www.zeiss.de/micro
under the Support/Download Overview section.
To carry out an update, proceed as follows:
¾ Save the file made available on the internet to your computer.
¾ Select the Update Component Lists function from the File menu.
¾ In the following dialog you can select and load the saved file containing
the up-to-date component lists.
10 M 60-3-0043 e / printed 09.2011

Program Overview
¾ The version of the selected file is checked automatically. If the selected file
is older than the component list currently installed, you are asked whether
you nevertheless want to install this file. If the selected file is more recent
than the component list currently installed, it is installed immediately.
The objective and reflector lists that have been updated in this way can then
also be written to the microscope (Axio Observer and Axio Imager only) so
that the up-to-date lists are also available on the TFT. To do this, select, in a
configuration, the microscope for which you want to update the component
list and click in the information area on:
The up-to-date component list is written to the microscope and is then

available for all configurations on the TFT.

Program Overview
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Use this function to exit the MTB2011 Configuration software.
If changes have been made to the configurations or configurations have been

added or deleted, you will be asked whether you want the changes to be
stored (Yes button) or rejected (No button).
Click on the Cancel button to continue using MTB2011 Configuration.
12 M 60-3-0043 e / printed 09.2011

Program Overview
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On the Options menu you can activate configurations that have already been
created, define your own filter sets and set the AOTF data of a laser module.
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In the configuration area you have the option of creating and managing
several configurations.
To ensure that imaging and microscope control software such as ZEN 2011 is
able to detect the configuration that should be used, the configuration needs
to be activated.
Select a configuration by clicking on the name of the configuration you wish
to use – the name of the configuration will then be shown with a blue
background.
Now select the Set Active Configuration function in the Options menu.

Program Overview
The configuration is shown to be active by means of a green icon. All other

configurations are displayed as being inactive (gray).
Note:
• The function described from the Options menu can also be called up
directly via a shortcut menu. Right-click in the configuration area – this
will open a shortcut menu.
Select Set Active Configuration in the shortcut menu to execute the

corresponding function.
14 M 60-3-0043 e / printed 09.2011

Program Overview
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This function is used to define the dialog for generating user-defined filter sets
for fluorescence microscopy. If you wish to use special filter sets or individual
combinations of excitation filters, beam splitters and emission filters on your
microscope, you can define descriptive and technical data in this dialog. This
information will be displayed in the ZEN 2011 imaging and microscope control
software in accordance with the entries you have made and will be saved
together with acquired image data.
¾ Click on the New button to create a new filter set. The default name is
NewReflector.
¾ The name can be changed directly in the Name list box. Select a name
that is as meaningful as possible. You can enter additional descriptive
names (with a maximum of 6 characters) in the ShortName1 and
ShortName2 list boxes.
¾ ShortName1 and ShortName2 are used to label the buttons for

controlling the reflector turret on the TFT display of the Axio Imager.Z1
and the Axio Imager.M1. ShortName1 is displayed on the top line of the
button and ShortName2 on the bottom line.

Program Overview
¾ The technical data concerning the fluorescence wavelengths of the filters

used is entered in the table in the lower area. A wavelength range is
given for both excitation and emission, while the beam splitter is defined
by means of a wavelength limit.
User-defined filter sets can be removed by selecting the name of the entry and
clicking on the button.
Click on the button to reject any changes and exit the dialog.
Click on the button to save the changes and finish the

procedure.
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Using this function you can specify excitation and emission filters for different
devices.
¾ First select the type of filter you want to define (i.e. general excitation
filter, colibri excitation filter, emission filter, Yokogawa CSU emission
filter).
16 M 60-3-0043 e / printed 09.2011

Program Overview
¾ Click on the New button to create a new filter set.
¾ The default name is New Filter. Select a name that is as meaningful as

possible.

given for both excitation and emission, while the beam splitter is defined
by means of a wavelength limit.
¾ Click on the button to reject any changes and exit the

dialog.
¾ Click on the button to save the changes and finish the

procedure.

Program Overview
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Using this function you can specify the beam splitter and emission filters for a
dual camera setup.
¾ Click on the New button to create a new filter set. The default name is
NewSplitter. Select a name that is as meaningful as possible.

given for both excitation and emission.

dialog.

procedure.
18 M 60-3-0043 e / printed 09.2011

Program Overview
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Using this function you can specify the user-specific neutral density (ND) or
Grey filters.
¾ Click on the New button to create a new filter. The default name is
NewGreyFilter. Select a name that is as meaningful as possible.
¾ The technical data concerning the transmission of the filters used is

entered in the table in the lower area.

dialog.

procedure.

Program Overview
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Using this function you can specify the user-specific excitation and emission
filters to be used in VivaTome.
¾ Click on the button to create a new filter set.
¾ The default name is NewVivaTomeFilterunit. The name can be changed

directly in the Filter Unit Name edit field. Select a name that is as
meaningful as possible.
20 M 60-3-0043 e / printed 09.2011

Program Overview
¾ Enter the relevant data for the three positions in the list boxes for
Excitation, Beamsplitter and Emission.
Note:
• As a rule Beamsplitter is always the same. Area 1 – 4 is only used for
multi-bandpass filters.

dialog.

procedure.
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Using this function you can specify your own Piezo focusing unit.
¾ Click on the button to create a new focusing unit. The

default name is NewPiezoFocus. Select a name that is as meaningful as
possible.

Program Overview
¾ Type: choose either Stage or Objective.
¾ Travel range: the available travel range of the device.
¾ Voltage: the maximal analog voltage allowed to drive the device
¾ Settle Time: the delay time that is allowed to let the device settle after a
move.
¾ Travel Speed: either default (manufacturers’ firmware default) or custom

values.
User-defined focusing units can be removed by selecting the name of the

entry and clicking on the button.

dialog.

procedure.
22 M 60-3-0043 e / printed 09.2011

Program Overview
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The laser modules from Carl Zeiss for Laser TIRF 3, CSU spinning disc systems
and FRAP have so-called "acousto-optical tunable filters (AOTF)" for the
selection of wavelengths and for setting the wavelength energy. This function
allows you to edit the AOTF data. Each AOTF has its own individual data for
controlling the wavelength and the intensity. These data are normally entered
during system integration here and should only be changed by authorized
personnel or the Carl Zeiss service team.
The optimal Frequency and Power must be entered here for each
Wavelength in order to achieve the maximum brightness possible.
Note:
• To adopt these data into a pre-existing configuration, the MTB 2011
configuration program must be restarted and the configuration then
saved once again.
Click on the button to reject any changes and exit the dialog.

Program Overview
Click on the button to save the changes and finish the

procedure.
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Here you can call up the online help for MTB2011 Configuration.
Note:
• The online help can be called up at any time by pressing the F1 key.
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In the About MTB2011 Configuration dialog you will find legal information
as well as details on the program version being used.
Clicking on the Show Details button displays additional information on the

version numbers of individual program and configuration files. These details
may be important in the event that a service is required.
24 M 60-3-0043 e / printed 09.2011

Creating Configurations
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For microscopes that are entirely manual and are not connected to the PC, the
configuration must be created manually, for motorized or coded devices an
auto configuration can also be used.
Note:
• For motorized or coded microscopes, please ensure that the devices are
connected to the PC and are switched on. Further information on the
devices can be found in the relevant manual.
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When you start the MTB2011 Configuration program for the first time, there
are not yet any microscope or stereomicroscope configurations. To familiarize
yourself with the software, create a new configuration manually as a practice
exercise:
¾ Select the NewConfiguration function in the File menu. This action will
create a new microscope configuration in a tree view in the left-hand area
of the user interface (configuration area). Different microscope
components, such as the nosepiece, reflector turret, tube etc., are
displayed as entries in this tree view.

¾ The default name of this configuration is NewConfiguration1. The

name can be changed by entering a different name in the Name field (in
the right-hand area of the user interface). Change the name of the
configuration, e.g. to "Inverse microscope". Instead of
NewConfiguration1, the configuration name Inverse microscope will
now be displayed in the configuration area.
¾ The first entry in the tree view below Inverse Microscope describes the
type of microscope used. In this case, Other Stand is displayed. Click on
the Other Stand entry to select it; the entry will then be shown with a
blue background:
¾ On the right-hand side in the selection area of the software, a list of Carl
Zeiss microscopes will now be displayed for you to choose from.
26 M 60-3-0043 e / printed 09.2011

¾ Now click on Axio Observer.Z1, for example. The Axio Observer.Z1

entry will then be shown with a blue background. If you click on the
button, this selection will then be assigned to the configuration on
the left-hand side. Alternatively you can assign the entry by double-
clicking on the Axio Observer.Z1 entry or using the mouse to drag &
drop. The result of this is that the Axio Observer.Z1 entry can now be
seen next to the microscope icon in the tree view and possible
components and add-on components for the Axio Observer.Z1 are
displayed in the configuration tree.
¾ Following the assignment of the entry, additional information and setting

options are displayed in the information area of the user interface.

¾ In the example shown, the serial port to which the microscope is

connected is being set. Select the appropriate port and check the
connection by clicking on the button. If the
microscope is found at this port, the connection will be shown by means
of a green symbol next to the button.
If the microscope is not found, a red symbol will be displayed.
By activating the check box, you also have the option

of simulating the microscope and therefore of operating it virtually in the
ZEN 2011 microscope control and imaging software. This function can be
very helpful if you are using a manual microscope (for more information
read section 4.3). In this case, the setting options for connecting the
microscope to the PC are deactivated.
Note:
• The principle described above for selecting an entry in the tree view of the
user interface, assigning an entry by selecting one on the right-hand side
and displaying additional information and setting options is a feature of
all the configuration steps in MTB2011 Configuration and is applied in
the same or a very similar way for every other configuration step.
Note:
• Should it be necessary to transfer a new objective and reflector list into
the firmware of the selected microscope, this can be initiated by clicking
on the button. This function is not

available for all microscopes.
Tip:
• The procedure for manual configuration has been described above.
Microscope configuration can be performed automatically to a large
extent by using the Auto Configuration function, as described in the
next section.
28 M 60-3-0043 e / printed 09.2011

Now delete the configuration you have created if you do not use an Axio
Observer.Z1.
¾ Click on the configuration name Inverse Microscope, this selects the

entry, which is then shown with a blue background.
¾ Select the Delete Configuration function in the File menu.
¾ Click on to adopt the changes and close MTB2011

Configuration. closes MTB2011 Configurationwithout
adopting the changes. applies the changes in the
configuration without closing MTB2011 Configuration.
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If the microscope has a PC connection, Auto Configuration is the quickest

and easiest option for creating a microscope configuration. Please refer to the
appropriate manual for information on the microscope in question.
Make sure that the microscope is connected to the PC and switched on.
Follow the procedure set out below for auto configuration:
¾ Start MTB2011 Configuration.

¾ Select Auto Configuration at the top of the configuration area.
¾ If you also want non-detectable components (e.g. objectives or reflector

cubes without ACR, manual components) to be queried systematically
during configuration, activate the Show Selection Dialog for non-
detectable Components check box in the information area.
¾ Click on the button.
When you start auto configuration, all the options for connecting a
microscope to the PC will be searched through automatically one after the
other. These are usually the serial ports (COM1 to COM8), the USB ports and
the network port (Ethernet).
If MTB2011 Configuration detects a microscope or another device (e.g.

incubation components or the ApoTome) at one of the ports named,
information on all the device’s components will be read out. In this way, all
the motorized and coded components of the microscope will be identified
and listed.
30 M 60-3-0043 e / printed 09.2011

If you have deactivated the selection dialogs for non-detectable components,

all non-motorized and non-coded components of the microscope will be set
as manual or not available and may then have to be configured manually (see
below).
If you have activated the selection dialogs for non-detectable components, a

dialog window is displayed for each component that could not be detected,
but for which manual or non-identifiable variants exist, in which you can
make a selection from all non-identifiable variants or define that this
component is not available. If no reflector turret is identified, for example, the
various manual reflector turrets are offered for selection.

All components that are dependent on this component are also then queried
automatically. In this case this relates to the reflector cubes installed.
Once your system has been fully configured, you can avoid queries being
displayed for further components by activating the Don't ask again! check
box.
32 M 60-3-0043 e / printed 09.2011

The following information is generally read out automatically:
• Type of microscope
• Nosepiece
• Reflector turret
• Focus
• Tube lens turret
• Reflected-light beam path
• Transmitted-light beam path
• Tube
• Sideport
• Objectives installed
• Equipment installed in reflector turret
• Incubation components
• ApoTome
• EMS-1 control box
• Certain motorized stages
Additional information is also read out on:
• How the keys are configured

• Automatic functions
Note:
• Auto Configuration finds components that belong directly to the
microscope or are directly connected to the microscope via a CAN bus
connection, as well as external components that are connected to the
computer via a CAN bus, serial port or USB connection. Nevertheless,
certain external components, such as motorized XY stages, external
shutters or external filter wheels, are not necessarily detected
automatically and may have to be configured manually. You will find
further information on this in the section “Configuring external
components”.

The configuration tree is structured hierarchically. Components such as

nosepieces or reflector turrets have additional sub-components. Information
on these sub-components can be displayed by opening the component tree at
the corresponding point. Every component that has additional sub-
components is indicated in the tree by means of a small +:
¾ Click on the plus sign to open up the tree at the corresponding point.
¾ The sub-components are now displayed. A more common application

scenario is the changing of the objective and reflector cube combinations
on the microscope. These changes can be performed quickly and easily in
MTB2011 Configuration (see section 4.4 and 4.5).

Configuration. closes MTB2011 Configuration without
34 M 60-3-0043 e / printed 09.2011

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Even if you are using a manual microscope that is not connected to a PC, it
may be useful to configure it in combination with the Carl Zeiss ZEN 2011
software. In this case, you are shown the configured control elements in ZEN
2011 and, using these virtual control elements, you can adjust the status of
the microscope in the software. As, in ZEN 2011, the microscope settings are
saved together with the image information, you can check what the
acquisition conditions were on the microscope in a particular case at any time.
There are two application scenarios that are particularly well-suited to this
kind of virtual operation of the microscope:
1. Magnification
Configure all the microscope units which affect the microscope’s

magnification (objectives, Optovar, tube lenses, camera adapter). If you adjust
these units virtually in ZEN 2011, you can determine the scaling (scale of
magnification) in the acquired image at any time. This will allow you to insert
scale bars into the image, for example. Furthermore, the correct allocation of
the magnification scale is the prerequisite for being able to perform
quantitative measurements in the image.
Consult the ZEN 2011 manual for information on the Scaling, Annotations
and Measure functions.
2. Fluorescence
Configure the reflector turret if you wish to acquire fluorescence images using
the microscope. If you adjust the setting of the reflector turret virtually in ZEN
2011, a record of the fluorescence filter set you have used will be saved with
every image acquired. Furthermore, in this case, you can generate semi-
automatic multichannel images in which different fluorescence channels (e.g.
DAPI and FITC) are acquired sequentially and stored in one image file. You can
allocate pseudo colors to the individual channels and overlay them in order to
display the fluorescence channels in combination.
Consult the ZEN 2011 manual for information on the Microscope Control,
Multichannel Acquisition, Settings and Settings Editor functions.

In principle, there are two options for configuring a manual microscope:
• Either use auto configuration and activate the selection dialogs for non-
detectable components, as described above. This means that all
components are queried one after the other, enabling you to create a full
configuration, “under guidance”, even for a manual microscope.
• If, on the other hand, you only wish to configure a small number of
components, it may be quicker to carry out configuration manually.
To perform manual configuration, proceed as follows:
¾ Start MTB2011 Configuration.
¾ Select the New Configuration function in the File menu. A new

configuration will be created with the name NewConfiguration1.
Note:
• Only an "empty" configuration has been created in which there are no
microscope components.
¾ Click on NewConfiguration1 and enter a name that is as meaningful as

possible for the configuration in the Name entry field (e.g. the product
name of the microscope, such as Axioskop 40). This entry will change
the configuration name accordingly.
36 M 60-3-0043 e / printed 09.2011

¾ Click on No Nosepiece in the configuration tree and select a suitable

manual nosepiece on the right-hand side in the selection area.
Then allocate the objective being used to each position on the nosepiece,
as described in section 4.4.
¾ Click on No Reflector Changer in the configuration tree and select a

suitable manual reflector turret on the right-hand side in the selection
area.
Then allocate the reflector cube being used to each position of the
reflector turret, as described in section 4.5.


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In the configuration tree on the left-hand side of the user interface, click on
the objective position that you wish to change. All the Carl Zeiss objectives
will now be listed in the selection area on the right-hand side with additional
information such as magnification, numerical aperture and order number. The
list is sorted by default in ascending order according to the magnification of
the objective.
Notes:
• You will also find the order numbers printed on each Carl Zeiss objective.
These numbers can be helpful in ensuring that you select the correct
objective in the list.
• If you wish to configure a new objective that is not displayed in the list,
you have the option of downloading an up-to-date version of the list of
available objectives from the internet and updating it on the File menu
under Update Component Lists (see 3.2 " Update Component Lists").
¾ Select the objective by clicking on the corresponding name. The objective

name will then be shown with a blue background.
38 M 60-3-0043 e / printed 09.2011

¾ The selected objective can now be assigned to the chosen position on the
nosepiece by clicking on the button or by double-clicking.
Tip:
• You can assign the objectives very quickly and simply by means of drag &
drop, i.e. by holding down the left-hand button on the mouse and
moving the objectives to the appropriate positions on the nosepiece.
Notes:
• After you have assigned an objective to a position on the nosepiece,
additional information relating to the objective, such as possible contrast
procedures, immersion, working distance etc., is displayed in the
information area of MTB2011 Configuration.
• In addition, for certain objectives that can be used with various immersion
media (e.g. LCI Plan-Neofluar 63x/1.3 Imm Corr) it is possible to define
the immersion medium actually being used. This means, for example, that
when you switch between objectives with different immersion media a
corresponding warning can be displayed on the TFT.
• In the case of DIC-compatible objectives, where appropriate, you can

also define the type of contrast: HR (high resolution) or HC (high
contrast).

In a similar way, for objectives that can be used with high-resolution or high-
contrast DIC sliders (e.g. Plan-APOCHROMAT 63x/1.4) it is also possible to
configure the DIC slider actually being used and thereby ensure, for example,
that it is correctly synchronized with settings on the condenser.
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In the configuration tree on the left-hand side of the user interface, click on
the reflector position that you wish to change. In the selection area on the
right-hand side, a list containing contrast methods, fluorescence filters and
fluorescent dyes will now be displayed.
40 M 60-3-0043 e / printed 09.2011

Note:
• If you wish to configure a new reflector cube that is not displayed in the
list, you have the option of downloading an up-to-date version of the list
of available reflector cubes from the internet and updating it on the File
menu under Update Component Lists (see 3.2 " Update Component
Lists").
¾ Select an entry that you would like to assign to the selected reflector
position. The selection will then be shown with a blue background.

¾ The selected entry can now be assigned to the chosen position on the
reflector turret by clicking on the button or by double-clicking.
Tip:
• You can allocate the entries very quickly and simply by means of drag &
drop, i.e. by holding down the left-hand button on the mouse and
moving the list entries to the appropriate positions on the reflector turret.
Note:
• After you have assigned a fluorescence filter, for example, to a position
on the reflector turret, additional information relating to the filter, such as
the properties of the excitation and emission filter and of the beam
splitter used, is displayed in the information area of MTB2011
Configuration.
42 M 60-3-0043 e / printed 09.2011

Notes:
• For the Axio Imager 2 and Axio Observer, it is possible, if you are using
Colibri and/or a motorized switching mirror, to define an allocation to the
light source for each reflector position. If the contrast manager is
switched on, Colibri, for example, would then switch on the LEDs
allocated to a reflector position (namely to the filter set configured there).
The lamp mirror would switch to the allocated lamp accordingly.
• By clicking on the Read Parameters button, you can read out the
allocation that is currently defined. Clicking on Save Parameters allows
you to pass on changes to the microscope accordingly.


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Some microscope components, such as eyepieces and camera adapters,

cannot be read out automatically. This information can be useful for
microscope control and imaging software such as ZEN 2011 from Carl Zeiss,
e.g. to enable the total magnification to be displayed.
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Eyepieces with different magnifications and field of view numbers can be used
on any tube of a microscope. The type of eyepiece is defined in the
configuration tree under tubes.
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Different camera adapters can be attached to any camera port of a

microscope. You can define the camera adapters in the configuration tree
under Tube, Sideport and Baseport.
44 M 60-3-0043 e / printed 09.2011

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If a camera adapter is configured, you can define different types of camera at

this camera port. A range of AxioCam camera models from Carl Zeiss are
available.
Note:
• If you configure the camera adapters and cameras correctly, a geometric
scaling will be allocated automatically (in the ZEN 2011 microscope
control and imaging software) to every image acquired, if you are
working with a motorized or coded microscope stand. For further
information on Scalings, Annotations and Measure please read also
the ZEN 2011 Manual and the ZEN 2011 Online help.

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External components are not completely recognized automatically by the

AutoConfiguration function; some of the components need subsequently to
be configured manually.
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The Colibri illuminating system is an LED-based light source for fluorescence

microscopy. Each of the 11 LEDs available emits a different wavelength range.
Up to four LED modules for different fluorescence excitations can be used in
Colibri at a time. LED modules and beam combiners (see below) can be easily
exchanged at any time to suit the application. Colibri can be operated either
as a stand-alone product without software, computer or motorized
microscope stand, or fully linked with the ZEN 2011 microscope and imaging
software.
Colibri is recognized through autoconfiguration. Each LED module features

ACR (automatic component recognition) and is therefore recognized and
configured automatically.
The user only needs to enter manually the beam combiners (BC) used in the
Colibri lighting module. The beam combiners combine the wavelengths
emitted by the different LEDs and direct them into the microscope’s epi-
illumination path. All beam combiners are designed as high-pass filters; i.e.,
they transmit wavelengths longer while reflecting wavelengths shorter, than
the respective module’s rated wavelength threshold.
Alternatively, the LED modules can be equipped with excitation filters of the
fluorescence filter sets. This further restricts the wavelength range, which can
be useful with certain LED combinations to prevent crosstalk between the
channels. Whether an excitation filter, and which, is to be used before an LED
module can also be manually configured in the MTB.
Note:
• If you wish to use a self-defined excitation filter, e.g. to achieve other
bandwidths, it is possible to define this on the Options menu under
46 M 60-3-0043 e / printed 09.2011

Custom Colibri Filter Specification (see 3.3 "Custom Colibri Filter

Specification").
For further information, see the Colibri and ZEN 2011 manuals.
¾ Make sure that the Colibri Controller is connected to the PC either

immediately via USB, or via the Can bus of the microscope stand, and
that the Controller is switched on.
¾ Open the configuration tree at Reflected Light.
¾ Click on the Empty Lamp Port entry. This highlights the entry in blue.
¾ To select Colibri, click on Colibri in the selection area on the right side of
the user interface, and assign Colibri.
¾ Now you can select the type of connection (USB or CAN bus) in the
information area.

¾ Check the connection by clicking on the button.

If Colibri is found at the port selected, a green pilot light appears next to
the button .
Note:
• By activating the check box , you can virtually simulate
the operation of Colibri, e.g. in the ZEN 2011 Microscope Control and
Imaging Software (simulation mode).
¾ In the configuration area, assign to each position of Colibri (4 at

maximum) the respective LED with which the unit has been equipped. If
Colibri was added by autoconfiguration, the LEDs present were
recognized automatically, as each LED module is coded. Optionally you
can use an excitation filter together with each LED; this filter has to be
added to the configuration manually.
¾ It is further necessary that you specify the beamsplitter used for each LED
position. This must be done manually in any case. To do so, click on the
FT entry under each occupied LED position in the configuration area, and
assign to it the respective beamsplitter in the selection area.
48 M 60-3-0043 e / printed 09.2011

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The ApoTome can be selected for the Axio Imager.Z1, Axio Imager.D1, Axio
Observer.Z1, Axio Observer.D1 and Axiovert 200 microscopes in MTB2011
Configuration. The ApoTome can only be used in connection with the ZEN
2011 microscope and imaging software.
Please refer to the ApoTome and ZEN 2011 manuals for further information.
The ApoTome is recognized by Auto Configuration. If manual configuration

is nevertheless required, please proceed as follows:
¾ Make sure that the ApoTome control box is connected to the PC and is
switched on.
¾ Open the configuration tree under Reflected Light Path
¾ Click on the No ApoTome entry. The entry will be shown with a blue
background.
¾ Select the ApoTome by clicking on ApoTome in the selection area on the

right-hand side of the user interface and assign it.

¾ In the information area, you can now select the connection type (RS232
or CAN bus) and the COM port being used (port 1 to 5).
Check the connection by clicking on the Check Connection button. If the

ApoTome is found at the specified port, a green symbol is displayed next to
the button .
Note:
• If you activate the check box, for example, the
function of the ApoTome can be adjusted virtually in the ZEN 2011
microscope control and imaging software (simulation mode).
50 M 60-3-0043 e / printed 09.2011

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The VivaTome can be configured at any camera port. First select the camera
port that is to be used and the corresponding camera adapter.
Then select the combination of filter sets that is to be used.

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If MTB2011 Configuration is installed from the ZEN 2011 product DVD, a

range of motorized XY stages are available. These may differ depending on
the choice of microscope.
Axio Observer
• Motorized stage (internal control)
• Motorized stage (MCU28)
• Motorized stage (Palm II)
• Motorized stage (Palm IIa/c))
• Motorized stage (Palm IIb)
• Motorized Maerzhaeuser stage (MAC5000 control box)
• Motorized stage (generic - MAC5000 control box)
• Motorized stage from ASI (MS-2000 control box)
Axio Imager
• Coded stage 75x50
• Motorized stage 225x85 (Wienecke&Sienske controller)
Axio Examiner
• Coded stage SCD5
• Coded stage 75x50
52 M 60-3-0043 e / printed 09.2011

Axiovert 200
• Motorized stage (Palm II)
• Motorized stage (Palm IIa/c))
• Motorized stage (Palm IIb)
• Motorized stage from ASI (MS-2000 control box)
SteREO
• Motorized stage 75x50
Please refer to the relevant manuals for the stages for further information.
¾ Make sure that the control boxes for the motorized XY stages are
connected to the PC and are switched on or that the stages are
connected directly to the microscope.
¾ Click on the Manual Stage / No Stage entry in the configuration tree.

¾ Select the required XY stage by clicking on a stage name in the selection

area on the right-hand side of the user interface and assign it.
¾ Depending on the stage you have selected, further setting options will be
available to you in the information area. You can use these to set the
connection of the stage to the PC as well as the orientation of the axes.
Note:
• If you activate the check box, for example, the
function of the motorized stages can be adjusted virtually in the ZEN
2011 microscope control and imaging software (simulation mode).
54 M 60-3-0043 e / printed 09.2011

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You can configure several Zeiss incubation components. The incubation

components are found by autoconfiguration. Optionally you can select or set
extended control parameters. The following modules are available:
1. Temperature module
2. CO2 module
3. O2 module
4. Air Heater module
5. Y module
These components can only be controlled in conjunction with the ZEN 2011
Microscope and Imaging Software, or directly on the TFT display of the Axio
Observer.
For further information, see the manuals for the respective incubation
component and for ZEN 2011.
¾ Make sure that the components used are connected to the PC and
switched to power.
¾ In the configuration area, click under Zeiss Incubation Components on

the No Atmosphere Control entry. This will highlight the entry in blue.
¾ To select the incubation components, click on Atmosphere Control in

the selection area on the right side of the user interface, and assign the
components.

¾ In the information area you can now select the type of connection (USB
or CAN bus).
In case of controlling additional thermostats:
In the configuration area click on Flow Control. The entry will be shown with
a blue background.
¾ In the information area you can now select the connection type (USB or
CAN bus).
¾ Check the connection by clicking on the button.

If the Components are found, a green pilot light appears next to the
button .
You can now set a number of parameters for each component. To do this,
click on the respective incubation component in the configuration area, and
set the desired parameters in the information area.
56 M 60-3-0043 e / printed 09.2011

Note:
• By activating the check box , you can virtually simulate
equipment operation, e.g. in the ZEN 2011 Microscope Control and
Imaging Software (simulation mode).
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The temperatures of maximally four devices can be controlled. Typically, the

following devices are used:
1. Heating insert P S1 (alternatively: Heater inserts M06 through M96)
2. Incubator PM S1 (alternatively: Heating unit S1)
3. Objective heater S1 (various models)
4. Air humidity heater S1
Note:
• A suitable parameter-set is automatically set for each temperature
channel or device, respectively. Under rarely ever prevailing environmental
conditions, such as, e.g., a lab room temperature below 10°C, a special
parameter-set is required to ensure proper operation of the device.
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In the Device drop-down list you can choose between two entries:
1. CO2 Small V (= CO2 Small Volume)

This setting is required if you use either Incubator PM S1 or CO2 Cover PM
S1.
2. CO2 Med. V (= CO2 Medium Volume)

This setting is required if you use Incubator S TIRF S1.
Note:
• A suitable parameter-set is automatically set. Under rarely ever prevailing
environmental conditions, a special parameter-set is required to ensure
proper operation of the device.
In the state as supplied, the Fan Speed and Pump Level are set to 5. Here
again it may be necessary in special cases to adapt the settings manually.

To transfer the changes made to the devices, you need to click on the
button.
CO2 control can be recalibrated. To do this, click on the

button. This will open a pop-up window with
a green, a yellow and a red area.
Use the control on the rear of the CO2 module to get the indication into the
green area.
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In the Device drop-down list you can choose between two entries:
1. O2 Small V (= O2 Small Volume)

This setting is required if you use either Incubator PM S1 or CO2 Cover PM
S1.
2. O2 Med. V (= O2 Medium Volume)

This setting is required if special incubators will be used.
58 M 60-3-0043 e / printed 09.2011

Note:
button.
O2 control can be recalibrated. To do this, click on the
button. This will open a pop-up window.
Complete the operation and click on .
The calibration is finished after approx. 30 seconds. Then click .
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This module is only needed if the Incubator S for TIRF is used.
Note:

In the state as supplied, the Fan Speed is set to 5. It may be necessary in

special cases to adapt the settings manually.
button.
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The Y-Module is required in case of software based temperature control via

thermostats. You can maximally connect two thermostats. With the present
release 4.6, only Julabo thermostats are supported.
The internal sensor of the thermostat or the sensor of the temperable insert P
(external) can be used. In this case, connect the sensor of the temperable
insert directly to the Y-Module.
Note: The control sensor in the cell cultivation dish can not be used.
¾ In the configuration area under the entry Zeiss Incubation Components

click on Flow Control and then on Y-Module. This will highlight the
entry in blue.
At the beginning the thermostats has to be initialized (provided that

the thermostat is adjusted and the display is shown OFF).
60 M 60-3-0043 e / printed 09.2011

¾ In the information area click in the left field on Initialize Circulator.
¾ In the Pop-up click on Initialize.
¾ Wait until the sand glass disappears.

¾ Press the Menu key at the thermostat twice (the Control menu will be
displayed).
¾ Press the Enter key at the thermostat to open the Control menu.
¾ Select an external or an internal sensor. To do so, use the arrow keys up
and down.
¾ Press the Enter key at the thermostat to confirm the entries.
¾ Press the Escape key at the thermostat to leave the Control menu.
¾ Press the Menu key at the thermostat to display the Configuration
menu.

¾ Press the Enter key at the thermostat to open the Configuration menu.
¾ Select the configuration serial at the thermostat. To do so, use the arrow
keys up and down.
¾ Press the Enter key at the thermostat to confirm the entries.
¾ Press the Escape key at the thermostat to leave the Configuration
menu.
Repeat this procedure if you want to use a second thermostat.
The connection between thermostat and Y-Module can enabled or disabled

under RS232 Connection.
In the state as supplied, the Pump Level is set to 4. It may be necessary in

special cases to adapt the settings manually.
Note:
• To transfer the changes made to the devices, you need to click on the
button.
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The Zeiss EMS-1 controller can be used for controlling the KL 2500 LCD cold-
light sources. You can connect up to 2 cold light lamps to the control box.
For further information, see the manuals on the cold light sources and on ZEN
2011.
62 M 60-3-0043 e / printed 09.2011

¾ Make sure that the EMS-1 control box is connected to the PC and
switched to power.
¾ Open the configuration tree.
¾ Click on the No Control Box EMS-1 entry. This highlights the entry in
blue.
¾ Select the control box by clicking on EMS-1 control box in the selection
area on the right side of the user interface, and assign the control box.
¾ Now you can select the type of connection (USB or CAN bus) in the
information area.
¾ Check the connection by clicking on the Check Connection button. If

the EMS-1 is found at the port specified, a green pilot light appears next
to the button .

Note:
• By activating the check box Simulate Hardware, you can virtually
simulate the operation of the ApoTome, e.g. in the ZEN 2011 Microscope
Control and Imaging Software (simulation mode).
¾ Finally, in the configuration area below the Controller name entry,

assign the cold-light source to the transmitted-light (TL) or reflected-light
position (RL). It is also possible to control two lamps for transmitted and
reflected light.
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range of filter wheels and shutters are available to you.
• Filter wheels and shutters (MAC5000)

• Filter wheels and shutters (Lambda 10-2)
• Filter wheels and shutters (Lambda 10-3)
• Filter wheels and shutters (Sutter generic)
Please refer to the relevant manuals for the filter wheels and shutters for
further information.
¾ Make sure that the appropriate control boxes are connected to the PC
and are switched on.
¾ Click on the No Filter Wheels and Shutter entry in the configuration

tree.
64 M 60-3-0043 e / printed 09.2011

¾ Select the required filter wheels and shutters by clicking on an entry in the
selection area on the right-hand side of the user interface and assign
them.
In the information area, additional setting options are available to you for
connecting devices to the PC.
Note:
• If you activate the Simulate Hardware check box, for example, the
function of the filter wheels and shutters can be adjusted virtually in the
ZEN 2011 microscope control and imaging software (simulation mode).
Depending on the filter wheels and shutters that you select, additional
configuration options may appear in the configuration tree.

Click on the individual sub-branches to perform additional configurations

relating to the position of the components concerned (reflected light,
transmitted light, observation) and the filters with which the filter wheels are
equipped.
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range of shutters with various control boxes are available to you.
• Shutter (VMM-D1)
• Shutter (VCM-D1)
• Shutter (Uniblitz generic)
Please refer to the relevant manuals for the shutters for further information.
¾ Click on the No Shutter entry in the configuration tree.
66 M 60-3-0043 e / printed 09.2011

¾ Select the required combination of shutter and control box by clicking on

an entry in the selection area on the right-hand side of the user interface
and assign it.
In the information area, additional setting options are available to you for
Note:
• If you activate the Simulate Hardware check box, the function of the
shutters can be adjusted virtually in the ZEN 2011 microscope control and
imaging software (simulation mode).
Once you have selected the shutter, additional configuration options will
appear in the configuration tree.
¾ Click on the individual sub-branches to perform additional configurations

relating to the position of the components concerned (reflected light,
transmitted light, observation).

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If MTB2011 Configuration is installed from the ZEN 2011 product DVD, the
option of configuring the Sutter DG4 or DG5 is available to you, in
combination with the Axiovert 200 microscope.
Please refer to the relevant manuals for the device in question for further
information.
¾ Open the configuration tree at the Reflected Light Path branch and
click on the Empty Lamp Port entry.
¾ Select the Sutter DG4 or DG5 by clicking on an entry in the selection

68 M 60-3-0043 e / printed 09.2011

¾ In the information area, additional setting options are available to you for
Note:
• Sutter DG4 and DG-5 have a slider for light attenuation in front of the
optical fiber. The degree of attenuation can be specified in the
Attenuator Filter field in the information area.
Click on the individual sub-branches in order to perform additional

configurations for the filters being used. You can add additional filters by
clicking on the Custom Sutter-DG4 Filter Specifications function in the
Options menu and defining a new filter.

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option of configuring the TILL Photonics Polychrome 5 is available to you,
in combination with the Axiovert 200 microscope.
Please refer to the relevant manuals for the device for further information.
¾ Make sure that the Polychrome 5 is connected to the PC and is switched

on.
¾ Open the configuration tree at the Reflected Light Path branch and
click on No Polychrome 5.
¾ Select the TILL Polychrome 5 by clicking on the entry in the selection

Note:
70 M 60-3-0043 e / printed 09.2011

máÉòç=ÑçÅìë=
option of configuring a piezo focusing device is available to you (this applies
when you select Axiovert, Axio Observer or Other Microscope).
Please refer to the relevant manuals for the devices for further information.
¾ Make sure that the necessary components for piezo focusing are
connected to the PC and are switched on.
¾ Click on the No Piezo Focus entry in the configuration tree.
¾ Select the piezo unit being used by clicking on the appropriate entry in
the selection area on the right-hand side of the user interface and assign
it.
Note:
PKU `çåÑáÖìê~íáçå=çÑ=áääìãáå~íáçå=ÅçãéçåÉåíë=
For the motorized microscopes Axio Imager 2, Axio Observer and Axio
Examiner at least, the correct configuration of the illumination sources in
reflected and transmitted light is important for correct functioning.

To ensure the configuration is correct, first select the illumination source at

the lamp connection for the reflected and transmitted light beam path. If a
switching mirror is used for two lamps (manual or motorized), please select
this from the list accordingly.
You can then make a selection from the list once again for each of the two
lamp connections.
Notes:
• Bear in mind that only one switching mirror can be configured per
microscope. This can be used in either the reflected or transmitted light
beam path.
• Make sure that the lamps are described correctly (internal or external/Hal
100 or LED). This influences the functioning of the microscope. Please
refer to the relevant operating instructions for further details.
72 M 60-3-0043 e / printed 09.2011

PKV `çåÑáÖìê~íáçå=çÑ=Çá~éÜê~Öã=ëäáÇÉêë=~åÇ=ÑáäíÉê=
ïÜÉÉäë=
aá~éÜê~Öã=ëäáÇÉêë=
To ensure that the light manager and contrast manager can function fully in
reflected light and transmitted light, the diaphragm sliders and filter wheels
being used must be configured. For the Axio Imager 2 this takes place in
MTB2011 Configuration and not by means of the TFT.
If you perform the configuration manually or need to add a component to an

existing configuration, first look in the component tree for the component
that is to be configured:
Then highlight the desired entry and, in the second step, select the
corresponding option from the list.
Proceed in the same way for the components in the transmitted light beam
path.

cáäíÉê=ïÜÉÉäë=áå=íÜÉ=êÉÑäÉÅíÉÇ=äáÖÜí=~åÇ=íê~åëãáííÉÇ=
äáÖÜí=ÄÉ~ã=é~íÜ==
With the Axio Imager 2 you can select different filter sets for the motorized
filter wheels. These are also incorporated into the Smart Mode of the light
manager.
Users can also define their own filter set.
If this is selected, however, it is not possible to work in the Smart Mode of the
light manager, but only in the Classic Mode (see Axio Imager 2 operating
instructions).
74 M 60-3-0043 e / printed 09.2011

Advanced Programming of the Axio Imager and Axio Observer Microscopes
Q ^Çî~åÅÉÇ=mêçÖê~ããáåÖ=çÑ=íÜÉ=^ñáç=fã~ÖÉê=
~åÇ=^ñáç=lÄëÉêîÉê=jáÅêçëÅçéÉë=
Using the functions described below, a range of settings can be carried out
easily on the Axio Imager and programmed directly into the microscope.
Note:
• The Axiovert 200 cannot be programmed via MTB2011 Configuration.
For this purpose use the Axioset program, which can be found on the
same installation DVD as MTB2011 Configuration?
QKN p~îáåÖ=ÅçåÑáÖìê~íáçåë=áå=íÜÉ=ãáÅêçëÅçéÉ=
Once you have made changes in MTB2011 Configuration, you have the
option of saving them in the microscope. It makes sense to save these
changes after changing the objectives installed or after equipping the reflector
turret with other modules, for example.
¾ In the configuration tree, click on the configuration that has been
changed and that you wish to save in the microscope.
¾ To save the changes in the microscope, click on the Write Configuration

in Hardware button in the information area in the bottom right-hand
area of the user interface.

Advanced Programming of the Axio Imager and Axio Observer Microscope
QKO mêçÖê~ããáåÖ=íÜÉ=ãçíçêáòÉÇ=ÑçÅìë=
You can carry out a range of settings for a motorized focus.
¾ Click on the Motorized Focus entry in the configuration tree. You can
carry out the settings described below in the information area at the
bottom of the right-hand side of the user interface.
m~êÑçÅ~äáíó=ÅçêêÉÅíáçå=
Parfocality correction balances out the various focus positions of the objectives
used.
Note:
• The correction values are determined by means of a software wizard on
the microscope’s TFT display. You can call up this wizard by selecting
Settings on the TFT display, followed by the Focus property page. Press
the Adjust button to start the wizard.
Please refer to the microscope manual for further information on

parfocality correction.
• Activating the Parfocal Correction check box in MTB2011 Configuration

switches on parfocality correction.
76 M 60-3-0043 e / printed 09.2011

içïÉêáåÖ=íÜÉ=ëí~ÖÉ=ïÜÉå=ÅÜ~åÖáåÖ=çÄàÉÅíáîÉë=
Using this option, the stage can be lowered automatically when the objective
is changed. It makes sense to lower the stage to prevent damage to the
specimen, as a result of the rotation of the nosepiece for example.
¾ Activating the Quickdrop on Objective Changed check box switches on

this function.
¾ You can determine the distance that the stage is lowered in mm using the
radio buttons.
cçÅìë=ëéÉÉÇ=
If you are using a motorized focus, the focus speed can be set individually for
each objective. This function allows you to set an optimum focus speed in
each case for objectives with low, medium and high magnification.
If you click on Motorized Focus in the configuration tree, the focus speeds
that are currently set are displayed in the information area.

¾ Use the sliders to set the focus speed for each objective. Allocate
objectives with low magnifications (e.g. 5x) relatively high focus speeds
and objectives with high magnifications (e.g. 63x) relatively low focus
speeds.
¾ Clicking on the Save Parameters button saves the changed values in the
microscope. If you click on the Read Parameters button the focus
speeds are read in again from the microscope.
QKP pÉííáåÖ=íÜÉ=âÉó=ÅçåÑáÖìê~íáçå=
In the default state, the keys on the Axio Imager 1 and Axio Observer have a
defined function assigned to them. Click on the Button settings entry in the
configuration tree.
In the information area you will see that the keys are in the standard
configuration (= default state). The functions of the individual keys and 2-key
combinations are displayed graphically for the keys on the left and right-hand
side of the microscope. It is not possible to change the key configuration in
78 M 60-3-0043 e / printed 09.2011

the Standard mode. This is why the list boxes next to the keys are inactive
(gray).
Administrator Priviledges (password-protected) are required in MTB2011

Configuration in order to change the key configuration. To change the key
configuration, follow the procedure below:
¾ Activate the Administrator Priviledges check box.
¾ Enter the password in the Password dialog box and confirm the entry by
clicking the Log in button.
Note:
• In the microscope’s default state, the password is 12345. The password
can be changed on the microscope’s TFT display under Settings – User.
Please contact the person in charge of the microscope if you wish to
switch between BioMed and MAT and you do not know the password.
¾ In the Button Settings field, you can now switch over to Personal
Settings. This action activates the check boxes in the graphic
representation of the keys and the function of the individual keys or 2-key
combinations can be changed.

¾ The changes become effective if you click on the Save Parameter

button. You can display the current setting on the microscope by clicking
on the Read Parameter button.
Once you have changed the functions assigned to the keys on the microscope
it is possible to switch between the Default and Personal Settings modes.
Note:
• The user administration for the Axio Imager was revised. The keyboard
shortcuts can be managed by the user. Therefore the keyboard shortcuts
for the M- and Z-stands are only available via the TFT display.
QKQ pÉííáåÖ=~ìíçã~íáÅ=ÑìåÅíáçåë=
With the Axio Imager 1 and Axio Observer a number of functions are available
that allow convenient operation of the microscope. In the case of the Axio
Imager 2, automatic functions are not configured via MTB 2011
Configuration. This is only possible by means of the TFT display or via ZEN
2011.
80 M 60-3-0043 e / printed 09.2011

iáÖÜí=ã~å~ÖÉê=
Using the light manager you can control the brightness of the transmitted
light illumination (halogen or LED illumination) when changing the objective.
The following settings are available to you:
1. Off
When you change the objective, the set lamp voltage is retained.
2. Smart
When you change the objective, the lamp voltage is automatically adjusted to
keep the brightness as constant as possible when you look into the
microscope. The microscope calculates the necessary adjustments from the
objective’s technical values. The system always tries to adjust the brightness by
switching a gray filter wheel in order to keep the illumination temperature as
constant as possible.
3. Classic
In this mode a certain combination of lamp voltage and gray filter wheel
position is allocated to each objective by the user and automatically restored
when the objective is changed.
Please refer to the relevant manual for the microscope for further information.
¾ The changes become effective if you click on Save Parameter.

You can display the current setting on the microscope by clicking on the
Read Parameter button.
`çåíê~ëí=ã~å~ÖÉê=
If the Contrast Manager check box is activated, the contrast procedure

being used on the microscope (e.g. phase contrast, DIC etc.) is retained as far
as possible when the objective is changed.
The changes become effective if you click on the Save Parameter button.
You can display the current setting on the microscope by clicking on the Read
Parameter button.
a~òòäÉ=éêçíÉÅíáçå=
If the Dazzle Protection check box is activated, the light path to the
eyepieces is interrupted using shutters or by lowering the light voltage if you
change the positions of the nosepiece or reflector turret, in order to prevent
the user being dazzled .
82 M 60-3-0043 e / printed 09.2011

¾ The changes become effective if you click on the Save Parameter

button.
You can display the current setting on the microscope by clicking on the
Read Parameter button.
láäëíçé=
If the Oilstop check box is activated, when the objective position is changed,
the system checks whether the objective in question is a dry or immersion
objective. If, for example, you wish to change from an air objective to an oil-
immersion objective, the stage lowers itself automatically to allow the
immersion oil to be dropped onto the sample. In this case, a corresponding
message and input options are displayed on the TFT display.
Conversely, the stage is also lowered if you wish to change from an objective
position with immersion to a dry objective so that you can remove the
immersion medium. In this case too, additional information and input options
are displayed on the TFT display.
Parameter button.
pïáíÅÜáåÖ=ëí~åÇ=îÉêëáçå=
In principle, the Axio Imager microscope can be supplied and operated in two
stand variants (BioMed or MAT). These differ slightly from each other with
regard to the automatic functions. To change the mode of operation, follow
the procedure below:
¾ Activate the Administrator Priviledges check box.

¾ As you will need administrator rights for the microscope in order to

change the mode of operation, enter the password for the administrator
rights in the pop-up window.
Note:
• In the microscope’s default state, the password is 12345. The password
can be changed on the TFT display under Settings – User. Please contact
the person in charge of the microscope if you wish to switch between
BioMed and MAT and you do not know the password.
¾ Once you have entered the password, it will be possible to switch

between the BioMed and MAT modes of operation.
Parameter button.
84 M 60-3-0043 e / printed 09.2011

Generating a Technical Report
R dÉåÉê~íáåÖ=~=qÉÅÜåáÅ~ä=oÉéçêí=
If your microscope does not work as expected, it may be helpful, in cases

where support or service are required, to have detailed information about
your microscope’s hardware and firmware to hand. A technical report can be
created in MTB2011 Configuration for this purpose.
¾ Click on the configuration in the configuration tree for which you want a
technical report to be produced.
¾ Click on the Create technical report button in the information area in

the bottom right-hand area of the user interface.
Following this action, the technical report for the selected configuration will
be generated automatically and displayed in Microsoft Editor (default name of
the report: MTB2011TechReport.txt). The report can be saved as a file and
printed out so that it can be forwarded to the appropriate service center, for
example.

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Carl Zeiss Microscopy GmbH

Carl Zeiss Microscopy GmbH

© Carl Zeiss Microscopy GmbH, 2008

This Software product ("MTB2011 Configuration") was designed, realized,

Refer to the safety notes and instructions in the manuals of all

MTB2011 Configuration / Installation + Reference i

ii M 60-3-0043 e / printed 09.2011

The MTB2011 Configuration software is used to generate and manage

Information about microscope components (nosepieces, reflector turrets,

Various configurations can be created, of which only one is activated at any

MTB2011 Configuration - Installation+Reference 1

The following microscopes are supported with Version 2.0.0.12 of MTB2011

Axio Observer.Z1 SteREO Lumar.V12

The stereomicroscopes SteREO Discovery.V8, SteREO Discovery.V12, SteREO

2 M 60-3-0043 e / printed 09.2011

MTB2011 Configuration is the graphic user interface for configuring the

MTB2011 Configuration is the graphic user interface for configuring the

MTB2011 Configuration can be installed on the following operating systems:

• Microsoft® Windows 7 64bit

MTB2011 Configuration - Installation+Reference 3

Start MTB2011 Configuration by double-clicking on the corresponding icon

The start screen is divided into different areas:

4 M 60-3-0043 e / printed 09.2011

With this function, a new microscope configuration is created and displayed

MTB2011 Configuration - Installation+Reference 5

Changes will be adopted by clicking on .

Changes will be adopted and the MTB2011 Configuration will be closed by

6 M 60-3-0043 e / printed 09.2011

Select the Export Configuration function in the File menu.

Select the Import Configuration function in the File menu.

MTB2011 Configuration - Installation+Reference 7

¾ Select the Delete Configuration function in the File menu.

Use this function to update a configuration. For updating, proceed as follows:

¾ In the configuration tree, click on the microscope name or on a

¾ In the File menu, select the Update Configuration function.

8 M 60-3-0043 e / printed 09.2011

If there are components that cannot be detected automatically (manual/non-

In the context menu, select an entry to have the respective command

MTB2011 Configuration - Installation+Reference 9

To carry out an update, proceed as follows:

¾ Save the file made available on the internet to your computer.

10 M 60-3-0043 e / printed 09.2011

The up-to-date component list is written to the microscope and is then

MTB2011 Configuration - Installation+Reference 11

Use this function to exit the MTB2011 Configuration software.

If changes have been made to the configurations or configurations have been

Click on the Cancel button to continue using MTB2011 Configuration.

12 M 60-3-0043 e / printed 09.2011

MTB2011 Configuration - Installation+Reference 13

The configuration is shown to be active by means of a green icon. All other

Select Set Active Configuration in the shortcut menu to execute the

14 M 60-3-0043 e / printed 09.2011

¾ ShortName1 and ShortName2 are used to label the buttons for

MTB2011 Configuration - Installation+Reference 15

¾ The technical data concerning the fluorescence wavelengths of the filters

Click on the button to save the changes and finish the

16 M 60-3-0043 e / printed 09.2011

¾ Click on the New button to create a new filter set.