Allen Brain Explorer functionality: Loading 3D Brain Reference Map Models into MatLab/Python/R

We have been asked the following questions from the community:

Q: Is there a way to save an image from the Allen Brain Explorer beta? Is it possible to open the 3D image of structures and projections of choice in Matlab or Python?

A: Currently there is no way to export 3D models from the Allen Brain Explorer to Python/Matlab, however the AllenSDK does provide everything necessary to do so.

The Allen SDK provides examples and use cases for software extensible solutions, including one that will be useful for this purpose: get_structure_mesh function will give access to the 3D volume meshes from the Mouse Brain Reference Atlas. Additionally meshes have been used for Matlab in this github issue.

Q: With the old Allen Brain Explorer (downloadable desktop version), it was possible to isolate the projection to one target structure, I can´t find a way of doing this using the web viewer, is it possible to do it?

A: This is not currently supported, but it’s a great idea and we will add it to our list of feature requests for the future. Thanks!

  • Brandon

If you’re an R user, we’ve made the cocoframer package, which makes retrieving and plotting 3D CCF meshes very straightforward with the help of the rgl framework.

See for details.

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