Hey technical team!
My understanding is that some but not all of the ISH data has quantification by brain area, or at least some sort of grid with intensity values, right? I was trying to see if this was available for the schizophrenia and autism human ISH studies, but it seems like there isn’t any quantification for these studies. Could someone confirm that I’m not missing something, and possibly suggest an open access package (ideally Python) to do such a rough ISH quantification? Perhaps we should simply use ImageJ? 
Thanks in advance.
Hello,
I see that some time has passed since your post without a response. I have the same question… I am wondering if you found any solution to your question? Thanks for any advice!
Sorry we missed this question @ajuavinett and @sharastough! I hope I am understanding your question right, but you can access image-level (e.g., cell by cell) quantification of gene expression levels from the gene view (e.g., NDNF here) but not from the specimen view (e.g., here). If you are on the specimen view and want to get to the gene view, click on the “Gene” name name in the Section information on the left:
It is also worth noting that there is some additional ISH for Autism and Schizophrenia as part of the BrainSpan Atlas of the Developing Human Brain.
I don’t know of any Python tools, but maybe someone else on the forum can help with that.