Arjun ccf qc update#1
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arjunsridhar12345 wants to merge 14 commits into
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Thanks a lot! I'll check it out and try to run on all sessions. Regarding the raw data for surface channel recordings, I thought I had fixed that here, released in v0.0.277: |
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ah I think what happened was I was uv synced but not updated. I think the lock file has v0.0.276 I'll try and updating and see! |
- Add surface_timeseries parameter to _plot_ephys_noise for concurrent surface/probe data plotting - Extract timestamp/data extraction logic into get_ts_data helper function - New _plot_structure_areas_ccb function for CCF area coloring on plot background - Update _plot_structure_areas signature to accept ccfAreas parameter - Handle surface channels in _plot_ephys_noise_with_unit_density_areas when available
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This PR attempts to update the ccf qc, by adding the LFP correlation plot and scale factor between anchors. I tried to add some comments in the code and clean up some stuff. This seems to do something for recordings without surface findings. The default scaling of 1.06 at the end seemed to be confirmed in a teams message from Corbett: "since the CCF is actually LARGER than in vivo brains, by a factor of... drumroll... 1.06!"
I had claude help do some stuff and tried to review it, so hopefully there's nothing super embarassing. Claude said the qc plot looked good and is "quite information rich". It also said this: "The alignment looks reasonable here — the MOp/CP boundary at ~300µm on the histology lines up with the transition in the correlation matrix block structure, and the unit density has a visible change around that boundary too."
The LFP correlation is currently using the epochs from the session object, and then looking at the onset of the
DynamicRouting1task, and then using the first 300 seconds of the task. Also just doing a basic cmr. The LFP data is currently fetched from the session object by using thissession._raw_lfp.For recordings with surface finding, when trying to get the raw_lfp data with the session object, there was an error saying no sync file was present. I think it tries to align the timestamps when getting the lfp data, so this makes sense since the surface findings only have the ephys data uploaded. Not sure how hard it would be to modify the session object to handle this
Adding the logic for concatenating the correlation matrix from the surface with the main still needs to be added once the above gets resolved.
I think that's it, let me know if I missed something!