The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/). [Display omitted] •Created a 3D average template brain from 1,675 mice at 10-μm voxel resolution•Delineated 43 isocortical areas from multiple surface views using curved coordinates•Delineated 329 subcortical areas, 8 ventricle structures, and 81 fiber tracts in 3D•The Allen CCF is open access and available with related tools at https://atlas.brain-map.org/ The Allen Mouse Brain CCF is an openly accessible, cellular level resolution 3D reference atlas for analysis, visualization, and integration of multimodal and multiscale datasets.