X,Y,Z query for gene expression

Technical
1

Hi everyone,

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.

Cheers,
C

2

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)