PMID- 32386544 OWN - NLM STAT- MEDLINE VI - 181 IP - 4 TI - The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. PG - 936-953.e20 CI - Copyright © 2020 Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 IS - 1097-4172 (Electronic) LID - S0092-8674(20)30402-5 [pii] LID - 10.1016/j.cell.2020.04.007 [doi] FAU - Wang, Quanxin AU - Wang Q AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Ding, Song-Lin AU - Ding SL AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Li, Yang AU - Li Y AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Royall, Josh AU - Royall J AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Feng, David AU - Feng D AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Lesnar, Phil AU - Lesnar P AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Graddis, Nile AU - Graddis N AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Naeemi, Maitham AU - Naeemi M AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Facer, Benjamin AU - Facer B AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Ho, Anh AU - Ho A AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Dolbeare, Tim AU - Dolbeare T AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Blanchard, Brandon AU - Blanchard B AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Dee, Nick AU - Dee N AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Wakeman, Wayne AU - Wakeman W AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Hirokawa, Karla E AU - Hirokawa KE AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Szafer, Aaron AU - Szafer A AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Sunkin, Susan M AU - Sunkin SM AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Oh, Seung Wook AU - Oh SW AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Bernard, Amy AU - Bernard A AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Phillips, John W AU - Phillips JW AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Hawrylycz, Michael AU - Hawrylycz M AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Koch, Christof AU - Koch C AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Zeng, Hongkui AU - Zeng H AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. FAU - Harris, Julie A AU - Harris JA AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. Electronic address: julieha@alleninstitute.org. FAU - Ng, Lydia AU - Ng L AD - Allen Institute for Brain Science, Seattle, WA 98109, USA. Electronic address: lydian@alleninstitute.org. IS - 0092-8674 (Linking) SB - IM MH - Animals MH - Atlases as Topic MH - Brain/*anatomy & histology/*metabolism/*physiology MH - Brain Mapping/methods MH - Image Processing, Computer-Assisted/methods MH - Imaging, Three-Dimensional/methods MH - Male MH - Mice MH - Mice, Inbred C57BL OTO - NOTNLM OT - 3D brain atlas OT - CCFv3 OT - average mouse brain OT - brain anatomy OT - brain parcellation OT - common coordinate framework OT - fiber tracts OT - mouse cortex OT - reference atlas OT - transgenic mice PMC - PMC8152789 DCOM- 20210104 LR - 20230601 DP - 20200514 DEP - 20200507 AB - 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/).