Fix AZBA #305
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Fix AZBA #305
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The packaged atlas looks fine, and passes the validation script. It just looks weird in brainrender-napari. The problem seems to be specific to the root mesh though: |
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Yes, there's already a draft PR for standardisation: #296 |
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From AF: the RGB triplet for the root mesh may be black, should update it to white. |
alessandrofelder
approved these changes
May 22, 2024
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RGB issue fixed, atlas passes validation script and works well in brainrender, brainrender-napari & brainreg. |
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Fixes the adult zebrafish atlas. The meshes were scaled correctly, so it just needed the parameter passing to the wrap up function. I also made some small changes, such as downloading the data with pooch. i removed the options for parallel processing, because it always seems to crash (as seen with other scripts).
There's still a lot that can be done to tidy up and standardise things, but I thought I'd raise this PR now as it seems to fix the issue (need to run the script through fully first to be sure though). I guess it's worth going through and standardising all the atlas scripts in one go @alessandrofelder, @viktorpm?
@alessandrofelder one thing that I don't understand - the meshes look fine in brainrender, but in brainrender-napari, they are basically invisible. The easiest way to know they are there is because they make the underlying arrays look darker. I haven't seen this before, do you have any idea?
We're going through all the atlases to fix any problems, but #213 specifically mentions the human atlas and this one. Following #290, I guess this PR closes #213.