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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  Updates to this software will be discontinued after that time. 

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Using the Brain Explorer 2 software, you users can:

  • View a fully interactive version of the ARA in 3-D3D.
  • View projection and gene expression data in 3-D 3D at 200 μm3 resolution.
  • View projection and expression data from multiple image series superimposed on each other in 3-D3D.
  • Navigate the high-resolution 2-D 2D projection and ISH images using the 3-D 3D model.
  • Link to associated projection specimen and gene experimental metadata in the Allen Mouse Brain Atlas and Connectivity web applicationapplications.

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Detailed User Guides