Do you know how to find out which voxels in the 3D adult mouse brain correspond to a specific region (e.g. the dorsal raphe nucleus) and how to then extract expression information for all genes in each one of those specific voxels
There are a couple of good posts about quantification of ISH data and extracting gene expression values for each gene. Instructions for mapping voxels to brain regions in the adult mouse brain atlas is available through the API, 3D-reference models.