A symmetrical Waxholm canonical mouse brain for NeuroMaps

J Neurosci Methods. 2011 Feb 15;195(2):170-5. doi: 10.1016/j.jneumeth.2010.11.028. Epub 2010 Dec 14.


NeuroMaps (2010) is a Web-based application that enables investigators to map data from macaque studies to a canonical atlas of the macaque brain. It currently serves as an image processor enabling them to create figures suitable for publication, presentation and archival purposes. Eventually it will enable investigators studying any of several species to analyze the overlap between their data and multimodality data mapped by others. The purpose of the current project was to incorporate the Waxholm canonical mouse brain (Harwylycz, 2009) into NeuroMaps. An enhanced gradient echo (T2*) magnetic resonance image (MRI) of the Waxholm canonical brain (Johnson et al., 2010) was warped to bring the irregular biological midplane of the MRI into line with the mathematically flat midsagittal plane of the Waxholm space. The left hemisphere was deleted and the right hemisphere reflected to produce a symmetrical 3D MR image. The symmetrical T2* image was imported into NeuroMaps. The map executing this warp was applied to four other voxellated volumes based on the same canonical specimen and maintained at the Center for In-Vitro Microscopy (CIVM): a T2-weighted MRI, a T1-weighted MRI, a segmented image and an image reconstructed from Nissl-stained histological sections of the specimen. Symmetric versions of those images were returned to the CIVM repository where they are made available to other laboratories. Utility of the symmetric atlas was demonstrated by mapping and comparing a number of cortical areas as illustrated in three conventional mouse brain atlases. The symmetric Waxholm mouse brain atlas is now accessible in NeuroMaps where investigators can map image data to standard templates over the Web and process them for publication, presentation and archival purposes: http://braininfo.rprc.washington.edu/MapViewData.aspx.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology*
  • Brain Mapping*
  • Functional Laterality
  • Image Processing, Computer-Assisted / methods*
  • Magnetic Resonance Imaging / methods
  • Mice
  • Mice, Inbred C57BL
  • Models, Neurological