Find ISH data related to specific atlas plate

I’m trying to download ISH section for a specific region of the brain. Is there a function in the allenSDK to find the image of an ISH experiment that is closest a specific location in the atlas?

I found the image_to_atlas function, but what I would need is the opposite.


Hi Michael,

Do neither of these API functions get close to what you need?

Best regards,

Hi Wayne,

Yes, the second one is exactly what I need. My next question is, once I found a a section in the atlas I’m interested in, where do find the x,y,z coordinates of the seed location (in my case I just want to find the center of the section) within the reference space.


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Copying the offline response here…

To get reference coords, download CCF and use tools (python, ITK-SNAP, …) that will give you and x,y,z read out

For example, the spatial search target tool in connectivity can provide a read out

Pick the image-series you are interested in and use the API

<Response success="true" start_row="0" num_rows="0" total_rows="0">

Use the coordinates to find your ISH data

  • Note there is a left-right flip when we deal with ISH data.

This API example documents the function

Image Synchronization (

Note: this service was primarily designed to support image sync viewing where the user can do the last step to refine the matching. Don’t expect it to have greater accuracy