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]
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) 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!
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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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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One more question: I am currently pulling the files using the API ( Downloading and Displaying SVG ). Those are, as far as I can tell, colorized. Where did you obtain the greyscale tiff files? Thanks a ton!
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