Standardise the axial resolution of the allen spinal cord atlas

brainglobe / brainglobe-atlasapi

A lightweight python module to interact with atlases for systems neuroscience

https://brainglobe.info/documentation/brainglobe-atlasapi/index.html

BSD 3-Clause "New" or "Revised" License

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Standardise the axial resolution of the allen spinal cord atlas #289

Open adamltyson opened 1 month ago

adamltyson commented 1 month ago

Currently the atlas has resolution (20.0, 10.0, 10.0). However, multiple axial planes repeat, so although there are voxels every 20um, the image isn't really sampled every 20um. We should either:

Make it isotropic (i.e. resample to (10,10,10)
Make it properly anisotropic, where each axial plane is unique

N.B. We've "inherited" this from the original source, but doesn't mean we shouldn't fix it.

imagesc-bot commented 1 month ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/spinal-cord-atlas-appears-squashed-in-abba-python/96242/12