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

被引：797

作者：

Wang, Quanxin ^{[1
]}

Ding, Song-Lin ^{[1
]}

Li, Yang ^{[1
]}

Royall, Josh ^{[1
]}

Feng, David ^{[1
,2
]}

Lesnar, Phil ^{[1
]}

Graddis, Nile ^{[1
]}

Naeemi, Maitham ^{[1
]}

Facer, Benjamin ^{[1
]}

Ho, Anh ^{[1
]}

Dolbeare, Tim ^{[1
]}

Blanchard, Brandon ^{[1
,3
]}

Dee, Nick ^{[1
]}

Wakeman, Wayne ^{[1
]}

Hirokawa, Karla E. ^{[1
]}

Szafer, Aaron ^{[1
,4
]}

Sunkin, Susan M. ^{[1
]}

Oh, Seung Wook ^{[1
,5
]}

Bernard, Amy ^{[1
]}

Phillips, John W. ^{[1
]}

Hawrylycz, Michael ^{[1
]}

Koch, Christof ^{[1
]}

Zeng, Hongkui ^{[1
]}

Harris, Julie A. ^{[1
]}

Ng, Lydia ^{[1
]}

机构：

[1] Allen Inst Brain Sci, Seattle, WA 98109 USA

[2] Tableau Software, Seattle, WA 98103 USA

[3] 343 Ind, Redmond, WA 98052 USA

[4] Microsoft Corp, Redmond, WA 98052 USA

[5] MDimune, Seoul 04790, South Korea

来源：

CELL | 2020年 / 181卷 / 04期

关键词：

AUTOMATED SEGMENTATION; IMAGE REGISTRATION; GENE-EXPRESSION; CRE-RECOMBINASE; MRI ATLAS; ORGANIZATION; MAPS; CONNECTIONS; REVEALS; AVERAGE;

D O I：

10.1016/j.cell.2020.04.007

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 vim voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 mu m 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/).

引用

页码：936 / +

页数：38

共 90 条

[1] Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain [J].