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

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2020 May 11

PMID 32386544

Citations 517

Authors

Quanxin Wang

Song-Lin Ding

Yang Li

Josh Royall

David Feng

Phil Lesnar

Nile Graddis

Maitham Naeemi

Benjamin Facer

Anh Ho

Tim Dolbeare

Brandon Blanchard

Nick Dee

Wayne Wakeman

Karla E Hirokawa

Aaron Szafer

Susan M Sunkin

Seung Wook Oh

Amy Bernard

John W Phillips

Michael Hawrylycz

Christof Koch

Hongkui Zeng

Julie A Harris

Lydia Ng

Affiliations

Soon will be listed here.

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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