The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.
IF: 66.850
Cited by: 212


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 (


3D brain atlas
average mouse brain
brain anatomy
brain parcellation
common coordinate framework
fiber tracts
mouse cortex
reference atlas
transgenic mice

MeSH terms

Atlases as Topic
Brain Mapping
Image Processing, Computer-Assisted
Imaging, Three-Dimensional
Mice, Inbred C57BL


Wang, Quanxin
Ding, Song-Lin
Li, Yang
Royall, Josh
Feng, David
Lesnar, Phil
Graddis, Nile
Naeemi, Maitham
Facer, Benjamin
Ho, Anh
Dolbeare, Tim
Blanchard, Brandon
Dee, Nick
Wakeman, Wayne
Hirokawa, Karla E
Szafer, Aaron
Sunkin, Susan M
Oh, Seung Wook
Bernard, Amy
Phillips, John W
Hawrylycz, Michael
Koch, Christof
Zeng, Hongkui
Harris, Julie A
Ng, Lydia

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