[Usage question] - Discrepancy between ibl brain atlas and allen ccfv3 #407
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I am trying to remap channel_locations (output from IBL ephys GUI) to another brain atlas, kim_mouse_25um through brainglobe api. I found the result is quite different because of the annotations so I tried to remap to allen_mouse_25um through brainglobe first to check the conversion part. I converted IBL coordination to Allen CCF coordination using brain_atlas.xyz2ccf, and I reorganized the sequence from mlapdv to apdvml to be able to plot correctly in Allen CCFv3. Surprisingly, the result is still a little bit different (first picture from IBL gui, second one after conversion). It seems the probe is a little bit shift after conversion. I also attached a demo code to show the coordination conversion. If the IBL ephys GUI is using Allen CCFv3 and the origin is same as documented ( "bregma": [5739,5400,332]), then the brain region of each channel should be exactly same. I don't know why I am seeing this difference. Please advise! Thank you so much!
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IBL ephys GUI/brain atlas in IBL
https://github.com/int-brain-lab/iblapps
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Demo showing coordination from xyz to ccf
Convert coordination from xyz to ccf (mlapdv), then change to ccf (apdvml)
