I’ve recently started using the code from this repository for some analysis of connectivity data (https://github.com/AllenInstitute/mouse_connectivity_models).
What I am trying to do is to look at connectivity between region in higher resolution compared to regional averages.
For instance I may want to look at projection strength from all voxels in brain region A to all voxels in brain region B to look at the spatial organisation of inputs and outputs.
I can use the package to get the voxel data for the source and target region and look at the resulting matrix of projection strengths, but I get stuck when I try to extract any spatial information from this data.
To do that, I would need to know the CCF coordinates of each voxel, but I haven’t found a way to extract this information yet.
Is anyone familiar with this code or is there anyone that can suggest how to get the coordinates for each voxel in the connectivity models?