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

Cell 2020 1,399 cites
2020:792021:1302022:1842023:2252024:2512025:2642026:266
2020 2026
1,399

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

Abstract

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/).

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