Allen Brain Explorer: How to

Notice - June 2020

Dear community members,

Due to technical considerations and competing priorities, the Allen Institute plans to retire the desktop Allen Brain Explorer application by mid 2021, roughly 12 months from now.

Much of the functionality that this application offers is available in the browser in the Allen Brain Explorer beta. More functionality will be added in the browser over the next 12 months.

If your work would be impeded without this tool, please reach out via this thread on our community forum. We would like to hear from what your needs are, so that we can find a sustainable way to help you moving forward. We hope the advanced nature of this notice ensures that no community member is left in a challenging position that jeopardizes their work.

Thank you for your understanding and, again, please reach out on this thread if the Allen Brain Explorer desktop application is critical to your work.


The Allen Brain Explorer (beta) is an application that allows users to browse multimodal datasets in an annotated 3D spatial framework. This new 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 the integrated web-based platform. Updates to this software will be discontinued after that time.


Using the Brain Explorer 2 software, users can:

  • View a fully interactive version of the ARA in 3D.
  • View projection and gene expression data in 3D at 200 ╬╝m3 resolution.
  • View projection and expression data from multiple image series superimposed on each other in 3D.
  • Navigate the high-resolution 2D projection and ISH images using the 3D model.
  • Link to associated specimen and experimental metadata in the Allen Mouse Brain Atlas and Connectivity web applications.

Detailed User Guides