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Related Experiment Video

Updated: Apr 9, 2026

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Published on: July 26, 2014

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

Quanxin Wang¹, Song-Lin Ding¹, Yang Li¹

¹Allen Institute for Brain Science, Seattle, WA 98109, USA.

|May 11, 2020

Summary

This summary is machine-generated.

Researchers created the Allen Mouse Brain Common Coordinate Framework (CCFv3), a 3D reference atlas. This standardized framework integrates large-scale mouse brain data, enabling comprehensive analysis and visualization across various scales and modalities.

Keywords:

3D brain atlas CCFv3 average mouse brain brain anatomy brain parcellation common coordinate framework fiber tracts mouse cortex reference atlas transgenic mice

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Last Updated: Apr 9, 2026

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Published on: August 1, 2022

Area of Science:

Neuroscience
Computational Biology
Brain Mapping

Background:

Large-scale mouse brain research collaborations generate vast, multi-modal datasets.
Integrating these diverse datasets necessitates a standardized 3D reference atlas.

Purpose of the Study:

To introduce the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3) as a standardized 3D reference atlas.
To facilitate the integration and analysis of large-scale mouse brain data.

Main Methods:

Constructed an average template brain at 10 μm voxel resolution using serial two-photon tomography from 1,675 mice.
Parcellated the entire brain in 3D using multimodal reference data, labeling each voxel with a specific brain structure.

Main Results:

The CCFv3 provides detailed 3D parcellation of the mouse brain, including 43 isocortical areas, 329 subcortical structures, 81 fiber tracts, and 8 ventricular structures.
The atlas achieves 10 μm voxel resolution, enabling fine-grained spatial analysis.

Conclusions:

The Allen Mouse Brain CCFv3 serves as a crucial resource for analyzing, visualizing, and integrating multimodal and multiscale mouse brain datasets.
The CCFv3 is openly accessible, promoting collaborative research in neuroscience.