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Waxholm Space: An image based reference for coordinating research in the mouse brain

G. Allan Johnson, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Song Liu, Jonathan Nissanov. Neuroimage 53 (2) 365-372, 2010. PMCID: PMC2930145

We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 microns (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing.

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  • All MR imaging was performed at the Duke Center for In Vivo Microscopy, an NCRR/NCI National Resource (P41 RR05959/ 5 U24 CA 092656). Additional support was supplied by the Mouse Bioinformatics Research Network (U24 RR021760) and the International Neuroinformatics Coordinating Facility ( We are grateful to Sally Gewalt, MS for technical assistance and Sally Zimney, MEd for editorial assistance.