, Volume 1, Issue 4, pp 397–410 | Cite as

The informatics of a C57BL/6J mouse brain atlas

  • Allan MacKenzie-Graham
  • Eagle S. Jones
  • David W. Shattuck
  • Ivo D. Dinov
  • Mihail Bota
  • Arthur W. TogaEmail author
Original Article


The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulation by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers’ computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at

Index Entries

Anatomy atlas brain C57BL/6 gene expression mouse MRM 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bard, J. L., Kaufman, M. H., Dubreuil, C., et al. (1998) An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev. 74, 111–120.CrossRefGoogle Scholar
  2. Bota, M. and Arbib M. A. (2002) The Neurohomology database: An online-KMS for handling and evaluation of neurobiological information, in A Practical Guide to Neuroscience Databases and Associated Tools. (Kotter, R., ed.) Kluwer Academic Publishers, Boston, MA. pp. 203–220.Google Scholar
  3. Bota, M., Dong, H. W., and Swanson, L. (2003) From gene networks to brain networks. Nat. Neurosci. 6, 795–799.CrossRefGoogle Scholar
  4. Bowden, D. M. and Martin, R. F. (1995) NeuroNames Brain Hierarchy. Neuroimage 2, 63–83.CrossRefGoogle Scholar
  5. Carson, J. P., Thaller, C., and Eichele, G. (2002) A transcriptome atlas of the mouse brain at cellular resolution. Curr. Opin. Neurobiol. 12, 562–565.CrossRefGoogle Scholar
  6. Franklin, K. B. J. and Paxinos, G. (1997) The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego.Google Scholar
  7. Gallyas, F. (1979) Silver staining of myelin by means of physical development. Neurol. Res. 1, 203–209.Google Scholar
  8. Ghosh, P., O’Dell, M., Narasimhan, P. T., Fraser, S. E. and Jacobs, R. E. (1994) Mouse lemur microscopic MRI brain atlas. Neuroimage 1, 345–349.CrossRefGoogle Scholar
  9. Hof, P. R. and Young, W. G. (2000) Comparative Cytoarchitectonic Atlas of the C57BL 6 and 129 Sv Mouse Brains, Elsevier, Amsterdam.Google Scholar
  10. Kahn, M. A., Kumar, S., Liebl, D., Chang, R., Parada, L. F., and De Vellis, J. (1999) Mice lacking NT-3, and its receptor TrkC, exhibit profound deficiencies in CNS glial cells. Glia 26, 153–165.CrossRefGoogle Scholar
  11. Nicolelis, M. A., Tinone, G., Sameshima, K., Timo-Iaria, C., Yu, C. H., and Van de Bilt, M. T. (1990) Connection, a microcomputer program for storing and analyzing structural properties of neural circuits. Comput. Biomed. Res. 23, 64–81.CrossRefGoogle Scholar
  12. Ourselin, S., Roche, A., Subsol, G., Pennec, X., and Ayache, N. (2001) Reconstructing a 3D Structure from Serial Histological Sections. Image Vision Comput. 19, 25–31.CrossRefGoogle Scholar
  13. Paxinos, G. and Watson, C. (1998) The Rat Brain in Stereotaxic Coordinates, 4th ed., Academic Press, San Diego.Google Scholar
  14. Paxinos, G. and Franklin, K. B. J. (2001) The Mouse Brain in Stereotaxic Coordinates, 2nd ed., Academic Press, San Diego.Google Scholar
  15. Rex, D. E., Ma, J. Q., and Toga, A. W. (2003) The LONI Pipeline Processing Environment. Neuroimage 19, 1033–1048.CrossRefGoogle Scholar
  16. Ringwald, M., Baldock, R., Bard, J., et al. (1994) A database for mouse development. Science 265, 2033–2034.CrossRefGoogle Scholar
  17. Rosen, G. D., Williams, A. G., Capra, J. A., et al. (2000) The Mouse Brain Library Scholar
  18. Shattuck, D. W. and Leahy, R. M. (2002) BrainSuite: an automated cortical surface identification tool. Med. Image Anal. 6, 129–142.CrossRefGoogle Scholar
  19. Simmons, D. M. and Swanson, L. W. (1993) The Nissl Stain, in Neuroscience Protocols, Wouterlood, F. G., ed., Elsevier, Amsterdam, pp. 93-050-12-1–93-050-12-7.Google Scholar
  20. Smith, B. R., Johnson, G. A., Groman, E. V. and Linney, E. (1994) Magnetic Resonance Microscopy of Mouse Embryos. Proc. Natl. Acad. Sci. U S A 91, 3530–3533.CrossRefGoogle Scholar
  21. Stephan, K. E., Zilles, K., and Kotter R. (2000) Coordinate-independent mapping of structural and functional data by objective relational transformation (ORT). Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355, 37–54.CrossRefGoogle Scholar
  22. 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.CrossRefGoogle Scholar
  23. Swanson, L. W. (1998) Brain Maps: Structure of the Rat Brain, 2nd ed., Elsevier, Amsterdam.Google Scholar
  24. Toga, A. W. and Thompson, P. M. (1998) Multimodal Brain Atlases, in Medical Image Databases. Kluwer Academic Press, Dordrecht, The Netherlands, pp. 53–88.Google Scholar
  25. Toga, A. W., Santori, E. M., Hazani, R., and Ambach, K. (1995) A 3D digital map of rat brain. Brain Res. Bull. 38, 77–85.CrossRefGoogle Scholar
  26. Woods, R. P., Grafton, S. T., Holmes, C. J., Cherry, S. R., and Mazziotta, J. C. (1998a) Automated image registration: I. General methods and intrasubject, intramodality validation. J. Comput. Assist. Tomogr. 22, 139–152.CrossRefGoogle Scholar
  27. Woods, R. P., Grafton, S. T., Watson, J. D. G., Sicotte, N. L., and Mazziotta, J. C. (1998b) Automated image registration: II. Intersubject validation of linear and nonlinear models. J. Comput. Assist. Tomogr. 22, 153–165.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc 2003

Authors and Affiliations

  • Allan MacKenzie-Graham
    • 1
  • Eagle S. Jones
    • 1
  • David W. Shattuck
    • 1
  • Ivo D. Dinov
    • 1
  • Mihail Bota
    • 2
  • Arthur W. Toga
    • 1
    Email author
  1. 1.Laboratory of Neuro Imaging, Department of NeurologyUniversity of CaliforniaLos AngelesUSA
  2. 2.NIBS—Neuroscience ProgramUniversity of Southern CaliforniaLos AngelesUSA

Personalised recommendations