JRC2018Unisex Fly Brain Atlas - #808
Conversation
for more information, see https://pre-commit.ci
|
Hey Amirreza, I just ran this and it seems just to be downloading the atlas files not generating them so ive converted it to draft for the moment. Let me know when its ready for review :) |
|
| return json.loads(term_info) | ||
|
|
||
|
|
||
| def _load_nrrd_array(nrrd_path): |
There was a problem hiding this comment.
Hey, I adressed all of the comments.
There was a problem hiding this comment.
Hey I think this comment hasnt been addressed
There was a problem hiding this comment.
Yes I missed that. Addressed!
for more information, see https://pre-commit.ci
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
|
0.5189161um how is this derived? Given that 0.0000001um is the width of a virus I am sceptical of this level of precision |
|
lets keep it rounded to 3 decimal places |
The original 0.5189161 µm value came directly from the VFB NRRD header, but you are right that this level of precision is unnecessary and basically meaningless here. I have rounded the packaged resolution to 0.519 µm and updated the atlas name accordingly, while keeping the exact source spacing internally for coordinate conversion. |
for more information, see https://pre-commit.ci
|
3 participants
Description
What is this PR?
Why is this PR needed?
This PR adds script for packaging the VFB ROI annotation on the JRC2018Unisex fly adult brain template into BrainGlobe format.
What does this PR do?
This PR adds
atlas_scripts/jrc2018u_neuropils_fly.py.References
Relates to #471 .
Main atlas/template source:
Main citation:
Bogovic JA, Otsuna H, Heinrich L, Ito M, Jeter J, et al. (2020) An unbiased template of the Drosophila brain and ventral nerve cord. PLOS ONE 15(12): e0236495. https://doi.org/10.1371/journal.pone.0236495
How has this PR been tested?
Is this a breaking change?
No. This PR only adds a new atlas generation script and should not change existing atlas behavior.
Does this PR require an update to the documentation?
No documentation update has been added in this PR.
Checklist
Link to the .tar file
https://drive.google.com/file/d/1T0DniDHTzqChrmHZJbStn-zz2R03QRyu/view?usp=sharing
Some images of the atlas in napari