List of all quality metrics and parameters

List of all the quality metrics, and associated parameters

Quality metrics and associated parameters

• Noise quality metrics

Brief description	Quality metric field	Calculated	Associated parameter	Associated classification parameter
Number of waveform peaks	nPeaks	Always	N/A	param.maxNPeaks
Number of waveform troughs	nTroughs	Always	N/A	param.maxNTroughs
Waveform peak-to-trough duration	waveformDuration_peakTrough	Always	Yes (see below)	param.minWvDuration,param.maxWvDuration
Waveform spatial decay slope	spatialDecaySlope	Always	Yes (see below)	param.minSpatialDecaySlope
Waveform baseline flatness	waveformBaselineFlatness	Always	Yes (see below)	param.maxWvBaselineFraction
'Repolarization peak'-to-trough ratio	scndPeakToTroughRatio	Always	N/A	param.maxScndPeakToTroughRatio_noise

• Non-somatic quality metrics:

Brief description	Quality metric field	Calculated	Associated parameter	Associated classification parameter
'First peak'-to-'repolarization (second) peak' ratio	peak1ToPeak2Ratio	Yes (see below)	N/A	param.maxPeak1ToPeak2Ratio_nonSomatic
'Main peak'-to-trough ratio	mainTroughToPeak2Ratio	Always	N/A	param.maxMainPeakToTroughRatio_nonSomatic

• Multi-unit quality metrics:

Brief description	Quality metric field	Calculated	Associated parameter	Associated classification parameter
Number of spikes	nSpikes	Always	N/A	param.minNumSpikes
Percentage of spikes below detection threshold	percentageSpikesMissing _gaussian	Always	N/A	param. maxPercSpikesMissing
Fraction of refractory period violations	fractionRPVs_estimatedTauR	Always	Yes (see below)	param. maxRPVviolations
Drift estimate	maxDriftEstimate	Always	N/A	param.maxDrift
Presence ratio	presenceRatio	Always	Yes (see below)	param. minPresenceRatio
Mean raw waveform amplitude	rawAmplitude	if param.extractRaw	Yes (see below)	param.minAmplitude
Signal-to-noise ratio	signalToNoiseRatio	if param.computeDrift	Yes (see below)	param.minSNR
Isolation distance	isoD	if param. computeDistanceMetrics	Yes (see below)	param.isoDmin
L-ratio	Lratio	if param. computeDistanceMetrics	Yes (see below)	param.lratioMax
Silhouette score	silhouetteScore	if param. computeDistanceMetrics	Yes (see below)	param.ssMin

Computation parameters

• General parameters:

Brief description	Parameter	Associated quality metrics	Options
Plot all quality metrics, for each unit	plotDetails	N/A
Plot global summary plots for each dataset	plotGlobal	N/A
Display progress bar and information	verbose	N/A
Re-extract raw mean waveforms	reextractRaw	N/A
Save data in .parquet files	saveAsParquet	N/A
Save a .mat structure, to be used in GUI	saveMatFileForGUI	N/A

• Ephys data parameters:

Brief description	Parameter	Associated quality metrics	Options
Ephys sample rate	ephys_sample_rate	qMetric.rawAmplitude
Number of channels recorded in ephys binary file	nChannels	qMetric.rawAmplitude
Number of sync channels recorded in ephys binary file	nSyncChannels	qMetric.rawAmplitude
Location of ephys .meta or .oebin file	ephysMetaFile	qMetric.rawAmplitude
Location of ephys .bin or .dat raw data file	rawFile	qMetric.rawAmplitude

• Quality metric parameters:

Brief description	Parameter	Associated quality metrics	Options
Number of raw spikes to extract	nRawSpikesToExtract	qMetric.rawAmplitude
Save individual raw waveform traces for each unit	saveMultipleRaw	qMetric.rawAmplitude
Decompress data or not	decompressData	qMetric.rawAmplitude
Spike width (in samples) to extract	spikeWidth	qMetric.rawAmplitude
Extract raw data or not	extractRaw	qMetric.rawAmplitude
Time samples in the baseline raw waveforms to use for signal-to-noise ratio	waveformBaselineNoiseWindow	qMetric.fractionRPVs
Refractory period time (s)	tauR_valuesMin	qMetric.fractionRPVs	If this value is different than tauR_valuesMax, bombcell will estimate the tauR value taking possible values between tauR_valuesMin:tauR_valuesStep:tauR_valuesMax
Refractory period time (s) step	tauR_valuesStep	qMetric.fractionRPVs	Only used if tauR_valuesMin and tauR_valuesMax are not equal
Refractory period time (s)	tauR_valuesMax	qMetric.fractionRPVs
Refractory period censored time (s)	tauC	qMetric.fractionRPVs
Divide the recording into time chunks or not	computeTimeChunks	qMetric.fractionRPVs, qMetric.percentageSpikesMissing_gaussian, qMetric.useTheseTimesStart and qMetric.useTheseTimesStop	If this is enabled, the recording is split into chunks of size deltaTimeChunk and the refractory period violations and percentage of spikes missing are evaluated on these time chunks
Size of recording time chunks	deltaTimeChunk	same as above
Bin size in seconds for presence ratio	driftBinSize	presenceRatio
Compute presence ratio or not	computeDrift	presenceRatio
Start time in samples to compute template waveform flatness	waveformBaselineWindowStart	qMetric.waveformBaselineFlatness
Stop time in samples to compute template waveform flatness	waveformBaselineWindowStop	qMetric.waveformBaselineFlatness
Threshold to detect template waveform peaks	minThreshDetectPeaksTroughs	qMetric.nPeaks and qMetric.nTroughs
Compute distance metrics or not	computeDistanceMetrics	qMetric.isoD, qMetric.lratio and qMetric.silhouetteScore
Number of channels to use for distance metrics	nChannelsIsoDist	qMetric.isoD, qMetric.lratio and qMetric.silhouetteScore
Use a linear or exponential fit for spatial decay	spDecayLinFit	qMetric.spDecay
Whether to normalize the spatial decay before computing the metric	normalizeSpDecay	qMetric.spDecay
Use the Hill or Llobet et al. method to compute refractory period violations	hillOrLlobetMethod	qMetric.fractionRPVs_estimatedTauR

Classification parameters (thresholds)

Brief description	Parameter	Associated quality metrics	Options
Minimum waveform amplitude (in uV)	minAmplitude	N/A
Maximum fraction of refractory period violations	maxRPVviolations	N/A
Maximum percentage of spikes missing	maxPercSpikesMissing	N/A
Minimum number of spikes	minNumSpikes	N/A
Maximum amount of drift	maxDrift	N/A
Minimum raw waveform signal-to-noise ratio	minSNR	N/A
Maximum number of template waveform peaks	maxNPeaks	N/A
Maximum number of template waveform troughs	maxNTroughs	N/A
Classify non-somatic unit into a separate class	somatic	N/A
Minimum waveform duration (in us)	minWvDuration	N/A
Maximum waveform duration (in us)	maxWvDuration	N/A
Minimum template spatial decay slope (if param.hillOrLlobetMethod == 1)	minSpatialDecaySlope	N/A
Minimum template spatial decay slope (if param.hillOrLlobetMethod == 0)	minSpatialDecaySlopeExp	N/A
Miaximum template spatial decay slope (if param.hillOrLlobetMethod == 0)	maxSpatialDecaySlopeExp	N/A
Maximum fraction of template waveform peak that baseline should not exceed	maxWvBaselineFraction	N/A
Minimum isolation distance	isoDmin	N/A
Maximum L-Ratio	lratioMax	N/A
Minimum silhouette score	ssMin	N/A
'Repolarization peak'-to-trough ratio	maxScndPeakToTroughRatio_noise	N/A
'First peak'-to-'repolarization peak' ratio	maxPeak1ToPeak2Ratio_nonSomatic (conditional on unit not passing the minWidthFirstPeak_nonSomatic, minWidthMainTrough_nonSomatic and minTroughToPeak2Ratio_nonSomatic criteria)	N/A
'Main peak'-to-trough ratio	maxMainPeakToTroughRatio_nonSomatic	N/A