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The Allen Mouse Brain Common Coordinate Framework (CCF) is a 3D reference atlas for the mouse brain which can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. The spatial template is constructed as a population average of 1,675 young adult mouse brains imaged using serial two photon tomography.
The average template brain were parcellated and annotated in 3D space, with the assistance of multimodal reference datasets deformably registered to the average template brain. Reference data included histology stains, immunohistochemistry, transgene expression, in situ hybridization (ISH), and anterograde tracer connectivity experiments. CCFv3 is parcellated into 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures (per hemisphere).
STPT images were acquired at high resolution (x, y = 0.35 μm/pixel) every 100 μm through the anterior-posterior axis of the brain, then downsampled to 50, 25, and 10 μm in x-y axes. Slight offsets in the position where imaging starts for each brain provide sufficient coverage to allow interpolation along the z axis to obtain isotropic voxel resolution to 10 μm. Assuming uniform sampling along the z axis, each 10 μm is spanned by data from 335 hemispheres.
