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AllenInstitute / ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes
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waveform variance #10

Closed NileGraddis closed 5 years ago

NileGraddis commented 6 years ago

@jsiegle @jiaxx @wbwakeman

In the past we've discussed providing some measure of waveform variance (such as a stdev array) along with the mean waveforms. Is this still planned? I think this means an additional file tracked in LIMS as well as produced by this set of modules.

jiaxx commented 6 years ago

the std of waveform is calculated in the mean time as mean. It is nice to save that information. I'm not sure whether that will result in additional file.

jsiegle commented 6 years ago

The current extract_waveforms module calculates the mean and std waveform for an arbitrary number of epochs, which will allow us to check whether or not the waveform changes over time due to probe drift. However, it is currently only writing the mean waveform for the entire recording, so it's consistent with the output format we've used in the past. Do we want to update the format to include the standard deviation and/or waveforms from multiple time points? The current mean_waveforms.npy files are about 30 MB in size.

jsiegle commented 5 years ago

Going to close this one...if we want to change the output to include waveform variance, it will be straightforward.