search

brainglobe / brainglobe-heatmap

Rendering anatomical heatmaps with brainrender and matplotlib
https://brainglobe.info
MIT License
34 stars 10 forks source link

Allen cord example results in a squashed image #52

Closed adamltyson closed 3 months ago

adamltyson commented 3 months ago

See https://forum.image.sc/t/allen-spinal-cord-atlas-appears-disfigured-in-python/99256/5 for context

imagesc-bot commented 3 months ago

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

https://forum.image.sc/t/allen-spinal-cord-atlas-appears-disfigured-in-python/99256/6

adamltyson commented 3 months ago

I think the issue is to do with https://github.com/brainglobe/brainglobe-atlasapi/issues/231. The meshes need to be regenerated I think.

adamltyson commented 3 months ago

When regenerated, the meshes seem ok, but brainrender-napari still produces weird results. Need to dig into this when the newest version of the atlas is released.

adamltyson commented 3 months ago

This is now fixed with the latest version of the cord atlas. Although the example script is not wrong, it is a bit strange to have it sagittally sliced so #53 was raised fixes this.