Cross-channel cleanning of noise in spike rejection.

[NxNiki]

There are two steps, in the first step, spikeCodes are calculated in which fractionConcurrent and fractionConcurrentPrecise are created and saved in *spikeCodes.mat. In the second step, calculate the probability the spike is real based on fractionConcurrent and channelsConcurrentPrecise (not fractionConcurrentPrecise). So far, I do not see channelsConcurrentPrecise created or saved, and neither fractionConcurrentPrecise is used in spike rejection.

As shown here:

nwbPipeline/src/spikeSort/getSpikeCodes.m

Lines 118 to 126 in 968f332

	[binEdges, binEdgesPrecise] = createBinEdge(duration, param.sr);
	bin = discretize(spikeTimestamps, binEdges);
	fractionConcurrent = percentConcurrentSpikes(bin);
	spikeCodes = [spikeCodes, table(fractionConcurrent(:), 'VariableNames', {'fractionConcurrent'})];
	binPrecise = discretize(spikeTimestamps, binEdgesPrecise);
	fractionConcurrentPrecise = percentConcurrentSpikesPrecise(binPrecise);
	spikeCodes = [spikeCodes, table(fractionConcurrentPrecise(:), 'VariableNames', {'fractionConcurrentPrecise'})];

nwbPipeline/src/spikeSort/getSpikesToReject.m

Lines 74 to 75 in 968f332

	probabilityParams.fractionConcurrentLR = [0.2 0.5];
	probabilityParams.channelsConcurrentPreciseLR = [3 6];

nwbPipeline/src/spikeSort/createBinEdge.m

Lines 5 to 6 in 968f332

	binEdges = 0:3:1000*(duration)+3;
	binEdgesPrecise = 0:2000/samplingRate:1000*(duration)+1;

Spike rejection uses the 3ms time window to reject spikes across all the channels. It will be rejected if more than 50% of channels have spikes within the time window. For the precise time window (2000/SR), if there are more than 6 channels that have spikes, it will be rejected.

In addition, these values are converted to a probability that is multiplied by the probability derived from other features. The threshold for spike rejection is determined by the turning point of the curve of probabilities for all channels.

It seems the precise time window fractionConcurrentPrecise is not applied in rejecting spikes. Spike rejection checks if channelsConcurrentPrecise exists in the spike code, if not it will not be considered. fractionConcurrentPrecise is also calculated based on all channels across all bundles.

[NxNiki]

fractionConcurrentPrecise is created in getSpikeCodes.m, but getSpikesToReject.m checks channelsConcurrentPrecise. Is this a typo?