Abstract
We present a novel system for storing and manipulating microscopic images from sections through the brain and higher-level data extracted from such images. The system is designed and built on a three-tier paradigm and provides the research community with a web-based interface for facile use in neuroscience research. The Oracle relational database management system provides the ability to store a variety of objects relevant to the images and provides the framework for complex querying of data stored in the system. Further, the suite of applications intimately tied into the infrastructure in the application layer provide the user the ability not only to query and visualize the data, but also to perform analysis operations based on the tools embedded into the system. The presentation layer uses extant protocols of the modern web browser and this provides ease of use of the system. The present release, named Functional Anatomy of the Cerebro-Cerebellar System (FACCS), available through The Rodent Brain Workbench (http://rbwb.org/), is targeted at the functional anatomy of the cerebro-cerebellar system in rats, and holds axonal tracing data from these projections. The system is extensible to other circuits and projections and to other categories of image data and provides a unique environment for analysis of rodent brain maps in the context of anatomical data. The FACCS application assumes standard animal brain atlas models and can be extended to future models. The system is available both for interactive use from a remote web-browser client as well as for download to a local server machine.
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Amari, S. I., Beltrame, F., Bjaalie, J. G., et al. (2002) Neuroinformatics: The integration of shared databases and tools towards integrative neuroscience. J. Int. Neuroscience 1:117–128.
Arnold, K., Gosling, J., and Holmes, D. (2000) The Java Programming Language 3rd ed., Addison-Wesley Professional, Boston.
Bjaalie, J. G. (2002) Localization in the brain: new solutions emerging. Nature Neurosci. Rev. 3:322–325.
Bjaalie, J. G. and Leergaard, T. B. (2005) Three-dimensional visualization and analysis of wiring patterns in the brain: experiments, tools, models, and databases. In: Koslow, S. H. and Subramaniam, S. (eds.) Databasing the brain: From data to knowledge, John Wiley & Sons, Inc., pp. 349–368.
Bjaalie, J. G. and Leergaard, T. B. (2006) Threedimensional computerized reconstruction from serial sections: cell populations, regions, and whole brain. In: Zaborszky, L., Wouterlood, F. G., and Lanciego, J. L. (eds.) Neuroanatomical tract tracing: Molecules, neurons and systems, 3rd ed., Springer/Kluwer/Plenum, pp. 530–565.
Bjaalie, J. G., Diggle, P. J., Nikundiwe, A., Karagülle, T., and Brodal, P. (1991) Spatial segregation between populations of ponto-cerebellar neurons. Statistical analysis of multivariate spatial interactions. Anat. Rec. 231:510–523.
Bjaalie, J. G., Leergaard, T. B., Lillehaug, S., et al. (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience 136:681–695.
Bjaalie, J. G., Leergaard, T. B., and Pettersen, C. (2006) Micro3D: Computer program for three-dimensional reconstruction, visualization, and analysis of neuronal populations and brain regions. Int. J. Neurosci. 116:515–540.
Bloom, F. R. and Young, W. G. (2005) Database needs of neuroscience: schema and design. In: Koslow, S. H. and Subramaniam, S. (eds.) Databasing the Brain: From data to knowledge, John Wiley & Sons, Inc., pp. 3–25.
Bota, M., Dong, H. W., and Swanson, L. W. (2003) From gene networks to brain networks. Nature Neurosci. 6:795–799.
Bota, M., Dong, H. W., and Swanson, L. W. (2005) Brain architecture management system. Neuroinformatics 3:15–48.
Brevik, A., Leergaard, T. B., Svanevik, M., and Bjaalie, J. G. (2001) Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualization, and comparison of spatial distribution data. Anat. Embryol. 204:319–332.
Brodal, P. and Bjaalie, J. G. (1992) Organization of the pontine nuclei. Neuroscience Res. 13:83–118.
Bug, W. and Nissanov, J. (2003) Aguide to building image-centric databases. Neuroinformatics 1:359–377.
Eckersley, P., Egan, G. F., Amari, S., et al. (2003) Neuroscience data and tool sharing: a legal and policy framework for neuroinformatics. Neuroinformatics 1:149–165.
Gardner, D., Abato, M., Knuth, K. H., and Robert, A. (2005) Neuroinformatics for Neurophysiology: The Role, Design, and Use of Databases. In: Koslow, S. H. and Subramaniam, S. (eds.) Databasing the Brain: From data to knowledge, John Wiley & Sons, Inc., pp. 47–67.
Hopson, K. C. and Ingram, S. E. (1996) Developing professional Java applets, Sams Book and Web Edition, Indiana.
Kötter, R. (2004) Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database. Neuroinformatics 2:127–144.
Leergaard, T. B., Alloway, K. D., Mutic, J. J., and Bjaalie, J. G. (2000a) Three-dimensional topography of corticopontine projections from rat barrel cortex: correlations with corticostriatal organization. J. Neurosci. 20:8474–8484.
Leergaard, T., Lyngstad, K. A., Thompson, J. H., et al. (2000b) Rat somatosensory cerebro-pontocerebellar pathways: spatial relationships in the SI somatotopic map are preserved in a threedimensional clustered pontine map. J. Comp. Neurol. 422:246–266.
Leergaard, T. B., Alloway, K. D., Pham, T. A., et al. (2004) Three-dimensional topography of corticopontine projections from rat sensorimotor cortex: Comparisons with corticostriatal projections reveal diverse integrative organization. J. Comp. Neurol. 478:306–322.
Leergaard, T. B., Bjaalie, J. G., Devor, A., Wald, L. L., and Dale, A. M. (2003) In vivo tracing of major rat brain pathways using manganese enhanced magnetic resonance imaging and three-dimensional digital atlasing. NeuroImage 20:1591–1600.
Leergaard, T. B., Lillehaug, S., De Schutter, E., Bower, J. M., and Bjaalie, J. G. (2006) Topographical organization of pathways from somatosensory cortex through the pontine nuclei to tactile regions of the rat cerebellar hemispheres. Eur. J. Neurosci. 24:2801–2812.
Li, J., Ning, Y., Hedley, W., et al. (2002) The Molecule Pages database. Nature 420:716–717.
Lillehaug, S., Øyan, D., Leergaard, T. B., and Bjaalie, J. G. (2002) Comparison of semi-automatic and automatic data acquisition methods for studying three-dimensional distributions of large neuronal populations and axonal plexuses. Network 13:343–356.
MacKenzie-Graham, A., Jones, E. S., Shattuck, D. W., Dinov, I. D., Bota, M., and Toga, A. W. (2003) The informatics of a C57BL/6J mouse brain atlas. Neuroinformatics 1:397–410.
Maer, A., Saunders, B., Unwin, R., and Subramaniam, S. (2005) Biology Workbenches. In: Koslow, S. H. and Subramaniam, S. (eds.) Databasing the Brain: From data to knowledge, John Wiley & Sons, Inc., pp. 153–165.
Martone, M. E., Gupta, A., and Ellisman, M. H. (2004) E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nature Neurosci. 7:467–472.
Murray, G. and Johnson, M. (2002) Designing enterprise applications with the J2EE Platform, 2nd ed., Sun Microsystems, Inc., California.
Odeh, F., Ackerley, R., Bjaalie, J. G., and Apps, R. (2005) Pontine maps linking somatosensory and cerebellar cortices are in register with climbing fiber somatotopy. J. Neurosci. 25:5680–5690.
Paxinos, G. and Watson, C. (1998) The Rat Brain in Stereotaxic Coordinates. Academic Press, San Diego.
Rosen, G. D., La Porte, N. T., Diechtiareff, B., et al. (2003) Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics 1:327–342.
Stephan, K. E., Kamper, L., Bozkurt, A., Burns, G. A., Young, M. P., and Kotter, R. (2001) Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac). Philos. Trans. R. Soc. Lond. B. Biol. Sci. 356:1159–1186.
Subramaniam, S. (1998) The Biology Workbench — a seamless database and analysis environment for the biologist. Proteins 32:1–2.
Swanson, L. W. (1999) Brain Maps: Structure of the Rat Brain. Elsevier Academic Press, San Diego.
Swanson, L. W. (2000) A history of neuroanatomical mapping. In: Toga, A. W. and Mazziotta, J. C. (eds.) Brain Mapping. The Systems, Academic Press, San Diego, pp. 77–109.
Toga, A. W. (2002) Neuroimage databases: the good, the bad and the ugly. Nature Rev. Neurosci. 3:302–309.
Toga, A. W. and Thompson, P. (1999) An introduction to brain warping. In: Toga, A.W. (ed.) Brain Warping. Academic Press, San Diego, pp. 1–26.
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Moene, I.A., Subramaniam, S., Darin, D. et al. Toward a workbench for rodent brain image data systems architecture and design. Neuroinform 5, 35–57 (2007). https://doi.org/10.1385/NI:5:1:35
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DOI: https://doi.org/10.1385/NI:5:1:35