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The Allen Brain Explorer (beta) is a browser-based 3D visualization tool to browse multimodal datasets in an annotated 3D spatial framework. The is beta release allows users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space.

Launch the browser

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Browser Support

The following web browsers have been tested for support:

  • Edge
  • Firefox
  • Chrome
  • Safari


Navigation Controls

All interaction with the tool is via the mouse:


The Web Viewer displays anatomical structures defined as part of the Allen Mouse Common Coordinate Framework.  Briefly, this space is a population average of 1675 P56 mouse brains with 662 structures drawn in 3D. See the technical whitepaper for more details.  

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Anatomical Structure Ontology


Once you have one or more projection data sets loaded, you can view primary images from the Connectivity Atlas by clicking either on injection site or projection site voxel objects and opening the "Source Image" panel.

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