Mouse Brain Atlas
Explore open access 3D anatomical atlas for the mouse brain
Mice have taken a prominent role as experimental animals in neuroscience over the last two decades. The most widely used and openly shared atlas for the mouse brain is the Allen Mouse Brain Atlas. EBRAINS is using the Allen Mouse Brain Common Coordinate Framework (CCFv3) as a basis for combining and comparing data from mouse brains. The atlas is embedded in our interactive atlas viewer, as well as in spatially-focused workflows and several other EBRAINS tools for analysing data from the mouse brain.
- Explore the Allen Mouse Brain Common Coordinate Framework in an intuitive web-based 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
- Use the atlas embedded in other EBRAINS tools, allowing data integration and automated spatially-linked image analysis
Tools
Interactive Atlas Viewer
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.
Related EBRAINS 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.