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Standard atlas space for C57BL/6J neonatal mouse brain

Lee, Erh-Fang and Jacobs, Russell E. and Dinov, Ivo and Leow, Alex and Toga, Arthur W. (2005) Standard atlas space for C57BL/6J neonatal mouse brain. Anatomy and Embryology, 210 (4). pp. 245-263. ISSN 0340-2061.

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A standard atlas space with stereotaxic co-ordinates for the postnatal day 0 (P0) C57BL/6J mouse brain was constructed from the average of eight individual co-registered MR image volumes. Accuracy of registration and morphometric variations in structures between subjects were analyzed statistically. We also applied this atlas coordinate system to data acquired using different imaging protocols as well as to a high-resolution histological atlas obtained from separate animals. Mapping accuracy in the atlas space was examined to determine the applicability of this atlas framework. The results show that the atlas space defined here provides a stable framework for image registration for P0 normal mouse brains. With an appropriate feature-based co-registration strategy, the probability atlas can also provide an accurate anatomical map for images acquired using invasive imaging methods. The atlas templates and the probability map of the anatomical labels are available at http://​www.​loni.​ucla.​edu/​MAP/​.

Item Type:Article
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Jacobs, Russell E.0000-0002-1382-8486
Additional Information:© 2005 Springer-Verlag. Accepted: 9 August 2005; Published online: 14 October 2005. This work was supported by the NIBIB research grant R01 EB002172, the NCRR BIRN grant U24 RR021760, and the Beckman Institute at Caltech. Additional support was provided by the NCRR resource grant P41 RR013642 and the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 RR021813 entitled Center for Computational Biology (CCB). Information on the National Centers for Biomedical Computing can be obtained from <>.
Funding AgencyGrant Number
National Institute of Biomedical Imaging and Bioengineering (NIBIB)R01 EB002172
National Center for Research Resources (NCRR)U24 RR021760
Caltech Beckman InstituteUNSPECIFIED
National Center for Research Resources (NCRR)P41 RR013642
NIHU54 RR021813
Subject Keywords:Mouse atlas – Stereotaxic co-ordinate – Feature-based registration – Anatomical morphometry – MR imaging – Gene expression mapping – Developing brain
Issue or Number:4
Record Number:CaltechAUTHORS:20160212-104125399
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:64472
Deposited By: Tony Diaz
Deposited On:19 Feb 2016 20:23
Last Modified:03 Oct 2019 09:38

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