Mouse Brain Atlas

3D anatomical and multimodal information about the mouse brain at different spatial and temporal scales, facilitating a broad range of neuroscience research.

Explore the Allen Mouse Brain Common Coordinate Framework in the interactive atlas viewer.
Find and access data shared through EBRAINS and registered to the Allen Mouse Brain Atlas.
Use EBRAINS tools to register your data to the Allen Mouse Brain Common Coordinate Framework and to perform automated spatially-linked image analysis.

The Allen mouse brain atlas is a comprehensive digital resource that provides detailed information on the structure and function of the mouse brain. A wide range of structural and functional experimental data mapped to the Allen mouse brain atlas are shared via the EBRAINS research infrastructure.

Explore the Allen Mouse Brain Common Coordinate Framework in the EBRAINS Interactive Atlas Viewer

EBRAINS utilises the Allen Mouse Brain Common Coordinate Framework (CCFv3) to compare, analyse and showcase neuroscience data from the mouse brain. The CCFv3 is defined in a population-averaged image volume, acquired from 1,675 male C57BL/6J mice using serial two-photon tomography (STPT).

The most recent version of the CCFv3 (CCFv3-2017) contains more than 600 brain regions delineated in 3D based on this template.

Atlas files and the technical information needed to download and use the Allen Mouse Brain Common Coordinate Framework are available from the Allen Brain Map Portal.

Allen Mouse Brain Common Coordinate Framework in the EBRAINS interactive atlas viewer

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Allen Mouse Brain Atlas CCFv3 original publication

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Allen Mouse Brain Atlas CCFv3 technical white paper

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Related tools

The Allen Mouse Brain Common Coordinate Framework is the backbone of spatially-focused workflows and tools that support spatial registration of new data to the atlas framework, semi-automatic analyses using the brain region hierarchy and delineations, and visualisation of extracted data in 3D.

The atlas is incorporated in the QuickNII tool for spatial registration of serial 2D images, and employed in the QUINT workflow for extracting and quantifying labelled objects from images registered to the atlas.

Learn more about the QuickNII tool Learn more about the QUINT workflow

Related software

All software

siibra-explorer

siibra-explorer is an frontend module wrapping around nehuba for visualizing volumetric brain volumes at possible high resolutions, and connecting to siibra-api for offering access to brain atlases of different species, including to navigate their brain region hierarchies, maps in different coordinate spaces, and linked regional data features. It provides metadata integration with the EBRAINS knowledge graph, different forms of data visualisation, and a structured plugin system for implementing custom extensions.

Data analysis and visualisationBrain atlases

siibra-api

siibra-api is an HTTP API for querying and retrieving contents of EBRAINS atlases. Originally built as a backend service for the interactive atlas viewer siibra-explorer, the API has been documented for connecting the brain atlases to other applications and web services.

Brain atlases