Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.



The Allen Brain Explorer (beta) is an application that allows users to browse multimodal datasets in an annotated 3D spatial framework.  The most recent release of this application is an integrated web-based navigator, allowing users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space.

The Brain Explorer 2 software is a desktop application for viewing the Allen Mouse Brain Connectivity Atlas projection data and the Allen Mouse Brain Atlas gene expression data in the framework of the Allen Reference Atlas (ARA). This downloadable software will be discontinued in 2019, as improved functionality and new features will be available via an integrated web-based platform. Ongoing updates to this software will be discontinued after that time. 


Using the Brain Explorer 2 software, you can:

  • View a fully interactive version of the ARA in 3-D.
  • View projection and gene expression data in 3-D at 200 μm3 resolution.
  • View projection and expression data from multiple image series superimposed on each other in 3-D.
  • Navigate the high-resolution 2-D projection and ISH images using the 3-D model.
  • Link to associated projection and gene metadata in the Allen Mouse Brain Atlas web application.

Atlas-specific User Guides