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Kilosort Post-Processing

Clean up Kilosort outputs by removing putative double-counted spikes.

Kilosort occasionally fits a spike template to the residual of another spike. See this discussion for more information.

This module aims to correct for this by removing spikes from the same unit or neighboring units that occur within 5 samples (0.16 ms) of one another. This is not ideal, since it can potentially remove legitimate spike times, but on the whole it seems worth it to avoid having spurious zero-time-lag correlation between units.

We are not currently taking into account spike amplitude when removing spikes; the module just deletes one spike from an overlapping pair that occurs later in time.

SpikeInterface implementation

Putative double-counted spikes can be deleted using the remove_duplicated_spikes method in the curation module:

from spikeinterface.curation import remove_duplicated_spikes

# returns a new sorting object with putative double-counted spikes removed
cleaned_sorting = remove_duplicated_spikes(sorting=sorting, 
                                           censored_period=0.3, # in ms
                                           method='keep_first') # determines which spike to remove

More information can be found in the documentation for remove_duplicated_spikes.

Running

python -m ecephys_spike_sorting.modules.kilosort_postprocessing --input_json <path to input json> --output_json <path to output json>

Two arguments must be included:

  1. The location of an existing file in JSON format containing a list of paths and parameters.
  2. The location to write a file in JSON format containing information generated by the module while it was run.

See the _schemas.py file for detailed information about the contents of the input JSON.

Input data

  • Kilosort output files : .npy files containing spike times, cluster labels, templates, etc.

Output data

  • Updated Kilosort output files : overwrites .npy files for spike times, cluster labels, amplitudes, and PC features. The original outputs can be extracted from the rez.mat file if necessary.