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This site is a community space for sharing ideas and information about educational applications of the Allen Institute's public resources, including the Allen Mouse Brain Atlas, Allen Spinal Cord Atlas and the Allen Developing Mouse Brain Atlas.  These and other resources created by the Allen Institute for Brain Science are publicly available for free online at

You are invited to post a comment and share your experiences.  If you are willing, please include your name and affiliation.

Examples of how instructors have used the Allen Mouse Brian Atlas include:

  • Use the built-in neuroanatomical reference atlas, histology data and gene expression data to teach neuroanatomy
  • Use the interactive Brain Explorer 3D interactive visualization tools to better illustrate structural neuroanatomy and explore the molecular organization of the brain
    • Build a brain, take it apart piece by piece -- virtually, in 3D
    • See gene expression patterns of interesting structural or neuropharmacological markers in 3D
  • Use the comprehensive anatomic and genome-wide gene expression data to create investigative "laboratory" exercises, immersing students in real data, in conjunction with or in place of wet lab curricula

Getting Started with Brain Explorer 3D visualization tools from the Allen Mouse Brain Atlas

The self-guided tour posted here comprises three exercises, which together provide an introduction to what the Brain Explorer tools can do and how to use them.  Through this tutorial, users also learn how to access Allen Mouse Brain Atlas primary data through the Brain Explorer tool and use some of the basic Allen Mouse Brain Atlas features.

Acknowledgement:  The tour is based on the self-guided PowerPoint tutorial developed by Bruce G. Jenks at the Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen.

Publications & Presentations

Below is a list of publications and presentations about using Allen Institute resources in education.  Scientific publications by the Allen Institute for Brain Science are listed [here].

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