Find ISH data related to specific atlas plate

Technical
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1

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.

Thanks,
Michael

2

Hi Michael,

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

http://help.brain-map.org/display/api/Image-to-Image+Synchronization#Image-to-ImageSynchronization-Structure-To-Image

http://help.brain-map.org/display/api/Image-to-Image+Synchronization#Image-to-ImageSynchronization-Reference-To-Image

Best regards,
Wayne

3

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.

Thanks,
Michael

1 Like
4

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
image

Pick the image-series you are interested in and use the API
http://api.brain-map.org/api/v2/reference_to_image/10.xml?x=7100&y=2550&z=4550&section_data_set_ids=77280584

<Response success="true" start_row="0" num_rows="0" total_rows="0">
<image-sync-helper-image-syncs>
<images-sync-helper-images-syncs>
<section-data-set-id>77280584</section-data-set-id>
<section-image-id>77317100</section-image-id>
<section-number>262</section-number>
<x>6409.195296434186</x>
<y>2821.873804416311</y>
</images-sync-helper-images-syncs>
</image-sync-helper-image-syncs>
</Response>

Use the coordinates to find your ISH data

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

http://mouse.brain-map.org/experiment/siv?id=77280584&imageId=77317100&initImage=ish&coordSystem=pixel&x=6409.195296434186&y=2821.873804416311&z=6

This API example documents the function

Image Synchronization (brain-map.org)

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