Access connectivity streamline data

The new and beautiful web-based Brain Explorer shows streamlines when selecting a mouse connectivity experiment. The raw microscopic sections have been available for quite some time, but I can’t get my hands on the processed streamline data. It would be very useful for establishing termination patterns. Is it publicly available? I have searched documentation, but this data seems to have been recently generated, it isn’t mentioned anywhere.

Hi @erpuntbakker,

Welcome to the forum!

There is unfortunately not a nice way to download the streamlines for a given experiment. The closest is the python script on this page, which I don’t think is updated for the latest version of our reference and connectivity data. It seems like an up-to-date version of this functionality might be a cool thing to have, so I’ve made an issue on AllenSDK, our open-source Python package for data access and analysis tools, to track it.

Depending on the specifics of your work, you might be able to instead use our voxelized projection data (from which the streamlines were generated using a fast-marching algorithm). You can learn more about how to access these data from the AllenSDK’s notebook of mouse connectivity example code.

Thanks for writing,


Thanks a lot for the helpful answer.
I am able to access the streamline data from the developer tools in Chrome, while using the web-version of Brain Explorer. For now I use that as a work-around.

1 Like