# Color duplicates in reference atlas images

**URL:** <https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720>\
**Category:** General\
**Tags:** anatomy, atlas-reference-maps\
**Created:** [October 12, 2025, 6:37am UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720 "2025-10-12T06:37:50Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![julianrode](https://avatars.discourse-cdn.com/v4/letter/j/ea5d25/32.png) [@julianrode](https://community.brain-map.org/u/julianrode)\
**Post date:** [October 12, 2025, 6:37am UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720/1 "2025-10-12T06:37:50Z")

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Hi everyone!

I am working on implementing atlas registration in ImageJ, and have used the color of the brain regions together with the color\_hex\_triplet from the structure ontology .csv file:

> [http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Structure,rma::criteria,[ontology\_id$eq1],rma::options[order$eq’structures.graph\_order’][num\_rows$eqall]](http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Structure,rma::criteria,%5Bontology_id$eq1%5D,rma::options%5Border$eq'structures.graph_order'%5D%5Bnum_rows$eqall%5D)

But specific, deep-level brain-regions (like CA1, CA1sp, CA2, CA2sp etc.) all use the same color (#FF5974).

The implementation of the ABA from the Scalable Brain Atlas ([https://scalablebrainatlas.incf.org/mouse/ABA\_v3](https://scalablebrainatlas.incf.org/mouse/ABA_v3)) has a specific color for each subregion. Is there any way to obtain the same level of detail directly from the source?

All the best!

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**Author:** ![yelgreb\_nelg](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/yelgreb_nelg/32/807_2.png) [@yelgreb\_nelg](https://community.brain-map.org/u/yelgreb_nelg)\
**Post date:** [October 26, 2025, 10:29pm UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720/2 "2025-10-26T22:29:03Z")

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Hi Julian,

As far as I can tell, those SVG hex codes are unique to the website - I could be wrong, though.

I have found the SVG hex codes pretty useful for websites. But if you’re in ImageJ, can you just use the TIFF greyscale values instead? (‘id’ column).

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**Author:** ![julianrode](https://avatars.discourse-cdn.com/v4/letter/j/ea5d25/32.png) [@julianrode](https://community.brain-map.org/u/julianrode)\
**Post date:** [October 28, 2025, 5:13pm UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720/3 "2025-10-28T17:13:19Z")

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Hi Yelgreb,

Huge thanks, I will give the greyscale values a try.

And I just found your forum post on this, so I guess you tackled this a while ago.

Best

Julian

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<div class="post-metadata">

**Author:** ![julianrode](https://avatars.discourse-cdn.com/v4/letter/j/ea5d25/32.png) [@julianrode](https://community.brain-map.org/u/julianrode)\
**Post date:** [December 1, 2025, 10:16pm UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720/4 "2025-12-01T22:16:06Z")

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One more question: I am currently pulling the files using the API ( [Downloading and Displaying SVG](https://community.brain-map.org/t/downloading-and-displaying-svg/2868) ). Those are, as far as I can tell, colorized. Where did you obtain the greyscale tiff files? Thanks a ton!

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<div class="post-metadata">

**Author:** ![yelgreb\_nelg](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/yelgreb_nelg/32/807_2.png) [@yelgreb\_nelg](https://community.brain-map.org/u/yelgreb_nelg)\
**Post date:** [December 1, 2025, 10:36pm UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720/5 "2025-12-01T22:36:27Z")

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I had forgotten about that post! Thanks for the trip down memory lane. To get the greyscale values, you can download the annotation file in NRRD format in various resolutions from: [Directory Tree](https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/)