How do I download a list of all genes with ISH data?

The API is the tool to access information about the data at the Allen Institute.
General help information about the API is here:

Something that may help the novice user are these example queries for experiment metadata:

Examples are included for download of a list of ISH experiments (genes) for Developing Human Brain, Mouse Brain (adult), Developing Mouse Brain, and Human Brain ISH Autism Study.

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