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LorenFrankLab / spyglass

Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF
https://lorenfranklab.github.io/spyglass/
MIT License
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SpikeSortingRecording whitens data or not. #1038

Open shijiegu opened 1 month ago

shijiegu commented 1 month ago

Describe the bug

  1. Please clarify whether SpikeSortingRecording stores whitened data here in issue 143 [https://github.com/LorenFrankLab/spyglass/issues/143] and in doc string of the preprocessing parameter table and SpikeSortingRecording. The preprocessing parameters do have an entry related to whitening. If it is redundant, a comment would be helpful so as not to cause confusion.
  2. Tutorial Notebook 10_Spike_SortingV0.ipynb has chosen to set whitening = False for mountainsort. If SpikeSortingRecording does not whiten data, this would be a bug.

  3. Similar problems in v1 may apply.

edeno commented 1 month ago

From the code, it looks like the data is always whitened as long as it isn't the clusterless thresholder. There is a bit of confusing code that prevents the whitening happening in the spike interface run_sorter command.

shijiegu commented 1 month ago

Loren says the waveforms do not look liked the Recording is whitened.