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A multimodal, multidimensional atlas of the C57BL/6J mouse brain

MacKenzie-Graham, Allan and Lee, Erh-Fang and Dinov, Ivo D. and Bota, Mihail and Shattuck, David W. and Ruffins, Seth and Yuan, Heng and Konstantinidis, Fotios and Pitiot, Alain and Ding, Yi and Hu, Guogang and Jacobs, Russell E. and Toga, Arthur W. (2004) A multimodal, multidimensional atlas of the C57BL/6J mouse brain. Journal of Anatomy, 204 (2). pp. 93-102. ISSN 0021-8782.

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Strains of mice, through breeding or the disruption of normal genetic pathways, are widely used to model human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison. We have developed a digital atlas of the adult C57BL/6J mouse brain as a comprehensive framework for storing and accessing the myriad types of information about the mouse brain. Our implementation was constructed using several different imaging techniques: magnetic resonance microscopy, blockface imaging, classical histology and immunohistochemistry. Along with raw and annotated images, it contains database management systems and a set of tools for comparing information from different techniques. The framework allows facile correlation of results from different animals, investigators or laboratories by establishing a canonical representation of the mouse brain and providing the tools for the insertion of independent data into the same space as the atlas. This tool will aid in managing the increasingly complex and voluminous amounts of information about the mammalian brain. It provides a framework that encompasses genetic information in the context of anatomical imaging and holds tremendous promise for producing new insights into the relationship between genotype and phenotype. We describe a suite of tools that enables the independent entry of other types of data, facile retrieval of information and straightforward display of images. Thus, the atlas becomes a framework for managing complex genetic and epigenetic information about the mouse brain. The atlas and associated tools may be accessed at

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Jacobs, Russell E.0000-0002-1382-8486
Additional Information:© 2004 Anatomical Society of Great Britain and Ireland. Accepted for publication 21 November 2003. Article first published online: 20 Jan 2004. This work was generously supported by research grants from the National Institute of Mental Health (5 RO1 MH61223) and the National Institutes of Health/National Center for Research Resources (P41 RR13642). We also wish to thank the members of the Laboratory of Neuro Imaging.
Funding AgencyGrant Number
National Institute of Mental Health (NIMH)5 RO1 MH61223
National Center for Research Resources (NCRR)P41 RR13642
Subject Keywords:brain atlas; HRI; infomatics; mouse database; C57BL/6J map
Issue or Number:2
Record Number:CaltechAUTHORS:20160229-145252856
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Official Citation:MacKenzie-Graham, A., Lee, E.-F., Dinov, I. D., Bota, M., Shattuck, D. W., Ruffins, S., Yuan, H., Konstantinidis, F., Pitiot, A., Ding, Y., Hu, G., Jacobs, R. E. and Toga, A. W. (2004), A multimodal, multidimensional atlas of the C57BL/6J mouse brain. Journal of Anatomy, 204: 93–102. doi: 10.1111/j.1469-7580.2004.00264.x
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:64863
Deposited By: Ruth Sustaita
Deposited On:29 Feb 2016 23:08
Last Modified:03 Oct 2019 09:41

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