We received a question from a researcher who wanted to know if it is possible to get calcium imaging data from the Allen Brain Observatory quantifiably mapped at the pixel level into the mouse common coordinate framework, or CCF (the description of the CCF can be downloaded here). The goal would be to view something analogous to the “projection intensity” which is available in 3D via the Allen Brain Explorer for the Allen Mouse Brain Connectivity Atlas, viewable at 10, 25, 50, or 100 um voxel-level registration.
This is a great idea and we hope to work on this functionality in the future. Currently the open API and AllenSDK provide some tools to do data analysis, but this level of integration is complex and such functionality is not currently supported by the data model.
If anyone wants to take on this challenge using the tools available above, let us know! We’d love to work with you on this.