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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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[BUG] Hemisphere map not correctly set for mpin_zfish_1um_v1.0 #268

Open PolarBean opened 2 months ago

PolarBean commented 2 months ago

Describe the bug My understanding is that the hemisphere map should be a binary image in the same shape as the template with a 0 or 1 labeling each hemisphere as either left or right hemisphere respectively. However the provided hemispheres.tiff file appears only to have labeled the left hemisphere for voxels where y==0 (ie, only one row). Everything else is labeled as 1.

To Reproduce open both hemispheres.tiff and reference.tiff in itksnap. set the hemispheres colourmap to Jet and it will become apparant.

Expected behaviour All voxels in the left hemisphere should be labeled 0.

Screenshots image

adamltyson commented 2 months ago

Thanks @PolarBean, this does seem to be a long undiscovered error.

@alessandrofelder, @viktorpm does the validation script check the hemisphere files?

alessandrofelder commented 2 months ago

@alessandrofelder, @viktorpm does the validation script check the hemisphere files?

Not yet, but that's a good idea!