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

• Published in: NeuroImage (Orlando, Fla.) Vol. 53; no. 2; pp. 365 - 372
• Main Authors: Johnson, G. Allan, Badea, Alexandra, Brandenburg, Jeffrey, Cofer, Gary, Fubara, Boma, Liu, Song, Nissanov, Jonathan
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2010; Elsevier Limited
• Subjects: Acquisitions & mergers; Animals; Atlases as Topic; Brain; Brain - anatomy & histology; Databases, Factual; Digital imaging; Gene expression; Histology; Image Processing, Computer-Assisted - standards; Imaging, Three-Dimensional - methods; Magnetic Resonance Imaging; Male; Medical imaging; Mice - anatomy & histology; Mice, Inbred C57BL; Microscopy; Reference Standards; Rodents; Software; Staining and Labeling; Thalamus - anatomy & histology; Tomography
• ISSN: 1053-8119; 1095-9572
• DOI: 10.1016/j.neuroimage.2010.06.067

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 μm (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. All the data is available for download via the web. ► Atlas of C57BL/6 mouse brain using 3 different MR protocols and conventional Nissl histology. ► Fourteen specimens actively stained to enhance tissue contrast. ► Spatial resolution of 21.5 μm (isotropic). ► Nissl performed on limited set of same specimens and registered to the MR data. ► Includes probabilistic and average atlases for 37 structures. ► Provides options for registration of other atlases to same coordinate system, to facilitate data-sharing. ► All data available for web download.