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Variational Mouse Brain Atlas

A fundamental question when studying mice is “Is this mouse an outlier?” This question is easily answered when measuring one-dimensional parameters like heart rate or red blood cell count. The measurement obtained in the subject mouse is simply compared to the population mean and standard deviation. The situation is not quite as easy when dealing with large and complicated image datasets. We have developed image registration tools to “morph” together nine age- and sex-matched 129SV/S1 mouse brains.

The average brain as well as some 40 labelled substructures are available through a 3D viewer developed by the Pittsburgh Supercomputing Centre:

Mac OS X Users: download the vb.dmg file; when you open this file, it will contain the vb (Volume Browser) application, which you can run directly from the DMG or, if you want to use it more than once, drag it to a location such as /Applications.

Windows Users: download the vb_win.zip file; this file contains the vb.exe program as well as the glut32.dll which implements some graphics features; these two files must be installed in a directory on your system from which you will run the vb (Volume Browser) application.

Navigation suggestions: Load up the Dataset “Toronto Mouse Brain”:
Toronto Mouse Brain anatomical atlas
Toronto Mouse Brain labeled atlas
Mapping between labeling and structures
The left window is the slice viewer and the right window is the 3D viewer. The ‘l’ key toggles between the normal MRI greyscale image and the superimposed labels. Moving the mouse button over the image in the left window will bring up the names and the coordinates at the bottom of the screen. In the right window, selecting a label in Surfaces will render that surface in 3D.


Below: Two views comparing an individual 129SV/S1 mouse brain (left) to an average of nine different brains. (Adapted from (1)).



Kovacevic, N., Henderson, J.T., Chan, E. Lifshitz, N., Bishop, J. Evans, A.C., Henkelman, R.M. & Chen, X.J. 3D Atlas of average and variability for an inbred mouse brain. Cer. Cortex. (In press).

Other Links

Pittsburgh Supercomputing Centre http://www.psc.edu
Laboratory of Neuro Imaging Mouse Atlas Project, UCLA http://www.loni.ucla.edu/MAP/index.html

The Hospital for Sick Children
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