Educational Resources

This page is for those interested in using the Allen Brain Atlas as a neuroanatomy teaching tool. Follow the stepwise instructions on this page and take advantage of the Included video tutorials, explainer videos and powerpoint presentations that facilitate being able to master the tools and data available from

This page was created to complement an article in the Journal of Undergraduate Neuroscience Education. Link to article here.


Lesson Plan summary

Download the above powerpoint to begin to plan a neuroanatomy lesson using the Allen Brain Atlas resources. Follow these steps using the tools below.

1.     Familiarize yourself with the resource.

2.     Pose a question.

3.     Train on the basic and advanced search and navigation features available with that resource.

4.     Practice on the resource so you have the skills to troubleshoot issues that arise from conducting research with real data.

familiarize yourself with the resources at

Since 2004, the Allen Institute for Brain Science has been releasing data to the public designed to allow students of the brain to better understand the structure and the function of the brain across development and across species. Familiarize yourself with the vast and multi-modal data here.

These tools are ideal to study neuroanatomy at the cellular and structural level in mice, the non-human primate (rhesus macaque) and humans. The gene expression patterns can also be defined over development across these three species. These tools are also well suited to understand structural connectivity in the mouse brain. The latest projects underway at the Allen Institute for Brain Science lend themselves quite well to teaching neuroinformatics and using real data to learn how to work with big data.

Dopa decarboxylase gene expression in the adult mouse brain.

Dopa decarboxylase gene expression in the adult mouse brain.

pose a question

The next step is to pose a question. Questions range from the very simple and straight-forward, “Where is dopa decarboxylase (or other gene of interest) expressed in the adult mouse brain?” to very complex, “Are axon guidance molecules expressed during early chick P1 development conserved in mammals?”

Train on the basic and advanced search and navigation features

Once you have picked a question and determined the best resource to use to explore that question, spend time learning and exploring the search and navigation features of that resource.


Please feel free to use this gallery of videos and links to help you with navigating the resources at the Allen Brain Atlas.

links to more training materials