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VirtualBrainLab / Pinpoint

Multi-probe trajectory planning in an intuitive 3D environment
https://data.virtualbrainlab.org/Pinpoint/
GNU General Public License v3.0
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Coordinates nonzero at Bregma #635

Open Virginia9733 opened 5 months ago

Virginia9733 commented 5 months ago

Describe the bug We updated the latest version of Pinpoint but found that the coordinates look a bit peculiar. The bregma was not set to zero and it's a bit less intuitive to match the probes to the position that was described in the atlas coordinates.

Also, the brain regions look a bit different between PinPoint and SpikeGLX. In PinPoint, all recording channels evenly distributed on the bottom of four shanks were all in dorsal CA1, while in SpileGLX, the depth of recording regions was a bit higher, and some of the recording channels were not in CA1.

PinPoint-coordinates PinPoint-coordinates-1 Free-moving-OF-PinPoint

dbirman commented 5 months ago

Hey @Virginia9733 thanks for reporting these issues, some of these may already be fixed. Can you confirm which version of Pinpoint you are on? The mis-aligned channels bug shouldn't be a problem anymore in version 1.1.1.

The Bregma coordinate not getting set to the default value is a bug, I'll go see what's going on there.

Virginia9733 commented 5 months ago

@dbirman Thank you for your reply. I confirm that the version we tested today is 1.1.1

dbirman commented 5 months ago

Thanks, I'm investigating... will try to get this patched soon.

dbirman commented 4 months ago

Bregma coordinate default fix on 1.1.2 a515adf6e5a1bffd3433ad9e253b711d9b190ae5

dbirman commented 4 months ago
dbirman commented 4 months ago

Atlas fix on 1.1.3 9db92faa29aef565712778a6bd8050de73c6a5fd