Recommended_preprocessing

Neuropixels probes have 384 channels with very closely matched impedances and gains. For this reason, noise sources (both those from the brain and those from interference/referencing) tend to appear identically on all channels. In those cases, common average referencing, in which the median of all channels is subtracted from each channel at each time point, effectively removes most noise and can be done as a default first processing step.

Note that Phase3A probes produce data that is offset from zero (even in the high-pass filtered AP band), so subtracting the median across time of each channel from itself should be done first.

The function "applyCARtoDat" in the "spikes" repository performs both of these operations in matlab. Note that it will produce a whole new file of equal size to the original, and will take a while to run.

nChansTotal = 385; % for spikeglx, Neuropixels phase3a. Needs to be the number of rows in the data file.
applyCARtoDat(filename, nChansTotal, outputDir);