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Three-Dimensional Digital Mouse Atlas Using High-Resolution MRI

Dhenain, Marc and Ruffins, Seth W. and Jacobs, Russell E. (2001) Three-Dimensional Digital Mouse Atlas Using High-Resolution MRI. Developmental Biology, 232 (2). pp. 458-470. ISSN 0012-1606. doi:10.1006/dbio.2001.0189.

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We present an archetypal digital atlas of the mouse embryo based on microscopic magnetic resonance imaging. The atlas is composed of three modules: (1) images of fixed embryos 6 to 15.5 days postconception (dpc) [Theiler Stages (TS) 8 to 24]; (2) an annotated atlas of the anterior portion of a 13.5 dpc (TS 22) mouse with anatomical structures delineated and linked to explanatory files; and (3) three-dimensional renderings of the entire 13.5 dpc embryo and specific organ systems. The explanatory files include brief descriptions of the structure at each volume element in the image and links to 3D reconstructions, allowing visualization of the shape of the isolated structures. These files can also contain or be linked to other types of information and data including detailed anatomical and physiological information about structures with pointers to online references, relationships between structures, temporal characteristics (cell lineage patterns, size, and shape changes), and gene expression patterns (both spatial and temporal). As an example, we have “painted” in the expression pattern of Dlx5/Dlx6 genes. This digital atlas provides a means to put specific data within the context of normal specimen anatomy, to analyze the information in 3D, and to examine relationships between different types of information.

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Jacobs, Russell E.0000-0002-1382-8486
Additional Information:© 2001 by Academic Press. Received for publication September 19, 2000; Revised January 4, 2001; Accepted January 4, 2001; Published online March 13, 2001. This work was funded in part by the Human Brain Project (DA08944) with contributions from the National Institute on Drug Abuse and the National Institute of Mental Health, the NCRR (RR13625), and MH61223. M.D. was supported by the Bettencourt-Schueller foundation. S.R. was also supported by NRSA NS 11008-02. Anne Dhenain rendered able assistance in annotation work. We thank T. Stühmer and J. L. R. Rubenstein for their generous contribution of histological slices displaying Dlx5/Dlx6 expression patterns.
Funding AgencyGrant Number
Human Brain ProjectDA08944
National Institute on Drug AbuseUNSPECIFIED
National Center for Research Resources (NCRR)RR13625
National Institute of Mental Health (NIMH)MH61223
Bettencourt-Schueller FoundationUNSPECIFIED
National Research Service Award (NRSA)NS 11008-02
Subject Keywords:anatomy; brain; embryo; development; Dlx5/Dlx6; gene expression pattern; imaging; microscopy; mouse; MRI
Issue or Number:2
Record Number:CaltechAUTHORS:20160106-145904725
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Official Citation:Marc Dhenain, Seth W. Ruffins, Russell E. Jacobs, Three-Dimensional Digital Mouse Atlas Using High-Resolution MRI, Developmental Biology, Volume 232, Issue 2, 15 April 2001, Pages 458-470, ISSN 0012-1606, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63440
Deposited By: Tony Diaz
Deposited On:07 Jan 2016 00:58
Last Modified:10 Nov 2021 23:16

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