# Find ISH data related to specific atlas plate

**URL:** <https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078>\
**Category:** Technical\
**Tags:** atlas-mouse-brain-adult, software, anatomy, atlas-reference-maps, allensdk\
**Created:** [May 14, 2021, 8:47pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078 "2021-05-14T20:47:19Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mkunst23](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/mkunst23/32/320_2.png) [@mkunst23](https://community.brain-map.org/u/mkunst23)\
**Post date:** [May 14, 2021, 8:47pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078/1 "2021-05-14T20:47:19Z")

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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

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<div class="post-metadata">

**Author:** ![wayne](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/wayne/32/16_2.png) [@wayne](https://community.brain-map.org/u/wayne)\
**Post date:** [May 19, 2021, 3:02pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078/2 "2021-05-19T15:02:07Z")

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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-Structure-To-Image)

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

Best regards,  
Wayne

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<div class="post-metadata">

**Author:** ![mkunst23](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/mkunst23/32/320_2.png) [@mkunst23](https://community.brain-map.org/u/mkunst23)\
**Post date:** [May 19, 2021, 4:53pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078/3 "2021-05-19T16:53:38Z")

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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

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<div class="post-metadata">

**Author:** ![wayne](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/wayne/32/16_2.png) [@wayne](https://community.brain-map.org/u/wayne)\
**Post date:** [May 28, 2021, 8:28pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078/4 "2021-05-28T20:28:03Z")

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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  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/64da03be0a3947c1703171c417d6b10d3439a34b.jpeg)

**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](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](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmouse.brain-map.org%2Fexperiment%2Fsiv%3Fid%3D77280584%26imageId%3D77317100%26initImage%3Dish%26coordSystem%3Dpixel%26x%3D6409.195296434186%26y%3D2821.873804416311%26z%3D6&data=04%7C01%7C%7C79121cacad5c4d3e3a8408d91c75f7fa%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C637572115281916272%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IH8fw2H4fB6GQ1oY6G8%2BWI6WAN9IDcF032I2fhb7hM8%3D&reserved=0)

**This API example documents the function**

[Image Synchronization (brain-map.org)](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fapi.brain-map.org%2Fexamples%2Fimagesync%2Findex.html&data=04%7C01%7C%7C79121cacad5c4d3e3a8408d91c75f7fa%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C637572115281916272%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iX82YiOigi60WdGLJbK21qbTEsVZ0I%2Bv3XNtv628t5E%3D&reserved=0)

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