I am trying to build a pipeline in which it would be possible to extract the list of genes expressed in a specific set of x,y,z coordinates.
However, I am new to work with the Allen Brain API and have a bit of trouble to see how I can do such a query and on which dataset.
Thanks in advance for the answer.
One approach to doing this is the download expression grid for each ISH dataset. Since these grids are all aligned to a common reference, you can then look across all genes for your location / voxel of interest.
Take a look at
API - Allen Mouse Brain Atlas (brain-map.org)
Downloading 3-D Expression Grid Data - Allen Brain Atlas API (brain-map.org)