Add cavefish atlas 🐟 #277
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Add cavefish atlas 🐟 #277
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VascoSch92
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May 3, 2024
adamltyson
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May 21, 2024
brainglobe_atlasapi/atlas_generation/atlas_scripts/cavefish_atlas.py
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tweaks: * renamed some variables * use pooch to unzip * make root mesh white * add additional reference * downsample both references to match annotation (with slight fudge) * use new URL * remove broken parallelisation part * make additional reference uint16 * make annotations uint8 * resolution now isotropic 2x2x2 micron
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| reference_volume = zoom( | ||
| reference_volume, (1, 1.0 / 3.995, 1.0 / 3.995), order=0 | ||
| ) # 1/3.995 is a fudge to match annotation dimensions |
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I'd like to get this clarified so if we're going to fudge something, we know exactly why.
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Description
What is this PR
Why is this PR needed?
We'd like to support @Robkozol 's cavefish atlas.
What does this PR do?
Adds a packaging script for the cavefish atlas.
Some notes:
For now, I've ever so slightly fudged the downsampling factors to make them both match the (isotropic) annotation image dimensions exactly.
This is what it looks like currently in grid view (row-wise from top left: root mesh, Pons mesh, Prepontine mesh; annotations, main (terk) reference, additional (cartpt) reference)
It passes our general internal validation for atlases.
References
Closes #259
How has this PR been tested?
Visual inspection and running atlas validation locally.
Is this a breaking change?
No
Does this PR require an update to the documentation?
We should add the cavefish atlas to the list of available atlases on the website (brainglobe/brainglobe.github.io#192)
Checklist: