New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Anyone tried using the ABA Mouse CCF v3 as Atlas and Annotation files? #26
Comments
Apparently, it is not going to work because the new CCF has a different annotation structure thn the annotation file provided by Renier et al. ClearMap functions expect a specific format...now...anyone has an idea on how to read/modify the annotation files or, conversely, modify the code? |
Can you give examples of differences? They are both .nrrd files, correct? |
Hi Vytas, Yes, they are both .nrrd files. The differences are in the way they have been annotated. From what I can gather, CCF v3 (the one from 2017, with more structures and finer divisions) used a different structure tree: As an example, lets compare what the region Cerebrum shows in each annotation file: So clearly the structure of the annotation files have changed and Clearmap is not prepared to understand it, I guess thats why I dont get any cell at all in the heatmaps using the provided test files (saline, haloperidol) while it works perfectly using the provided annotation. Of course, the idea of being able to use other annotation files in Clearmap (apart from the fact of gaining precision with the newer, more refined atlases) would open the possibility use it for other animal models. |
Thanks for the summary. I'm just speculating at this point, as without trying it's hard to say how involved it would be, but I think in principle you should be able to modify Label.py to use the structure of the new atlas. The fact that the new version has finer "resolution" should not matter. |
Thanks for the input. |
Just for clarity - yes that's what I meant by "resolution" (hence the quotation marks), so I don't think it should matter and the collapse function should still work with more regions. |
I had a look at the Label.py and the ARA2_annotation files provided in the Data folder of Clearmap. |
It can be found here in format .nrrd:
http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/
So far the resampling and aligning works well, but the heatmaps are empty...
The text was updated successfully, but these errors were encountered: