JRCLUST parameters¶
Common parameters¶
CARMode¶
(Formerly vcCommonRef)
The meaning of ‘average’ in ‘common average reference’.
One of the following:
- ‘mean’: Computes the mean across sites, excluding sites in ignoreSites.
- ‘median’: Computes the median across sites, excluding sites in ignoreSites.
- ‘none’: Skips CAR.
Default is ‘mean’.
RDDetrendMode¶
(Formerly vcDetrend_postclu)
Detrending mode to apply to rho-delta values in order to determine cluster centers.
One of the following:
- ‘global’: Performs the detrending for all sites together.
- ‘local’: Performs the detrending for each site separately.
- ‘logz’: Use z-scores instead of detrending.
- ‘regress’: Use a non-constant threshold to determine centers for each site.
- ‘none’: Skips detrending.
Default is ‘global’.
autoMergeBy¶
(Formerly autoMergeCriterion)
Metric to use for automerging clusters based on average waveform.
One of the following:
- ‘pearson’: Use the Pearson correlation coefficient to compute similarity.
- ‘dist’: Define similarity as \(1 - \frac{\|\text{tr}_i - \text{tr}_j\|}{\max(\|\text{tr}_i\|, \|\text{tr}_j\|)}\), where \(\text{tr}_k\) is the mean waveform for cluster \(k\).
Default is ‘pearson’.
bitScaling¶
(Formerly uV_per_bit)
ADC bit scaling factor (Conversion factor for ADC bit values to μV).
Default is 0.30518.
blankPeriod¶
(Formerly blank_period_ms)
Duration of blanking period (in ms) when the common mean exceeds blankThresh.
Default is 5.
blankThresh¶
(Formerly blank_thresh)
Threshold (in MADs) above which to reject samples exceeding channel median after filtering.
Default is empty.
clusterFeature¶
(Formerly vcFet)
The feature to extract from your spike waveforms in order to cluster them.
One of the following:
- ‘cov’: Covariance feature.
- ‘energy’: Standard deviation of spike waveform.
- ‘gpca’: Global PCA.
- ‘pca’: Projection of spike waveforms onto principal components.
- ‘vmin’: Minimum spike amplitude.
- ‘vminmax’: Minimum and maximum spike amplitudes (2 features/site).
- ‘vpp’: Peak-to-peak spike amplitudes.
Default is ‘pca’.
dataTypeRaw¶
(Formerly vcDataType and formerly dataType)
Format of raw recordings.
One of the following:
- ‘int16’
- ‘uint16’
- ‘int32’
- ‘uint32’
- ‘single’
- ‘double’
Default is ‘int16’.
dataTypeExtracted¶
(Formerly vcDataType and formerly dataType)
Format of raw recordings after extraction.
One of the following:
- ‘int16’
- ‘uint16’
- ‘int32’
- ‘uint32’
- ‘single’
- ‘double’
Default is ‘int16’.
distCut¶
(Formerly dc_percent)
Percentile of pairwise distances between spikes on a site to use as a cutoff distance.
Default is 2.
evtDetectRad¶
(Formerly maxDist_site_um)
Maximum distance (in μm) to search over for potential duplicates (r1 in the figure below).
This distance is used to determine the number of sites to extract features if nSiteDir is empty.
Default is 50.
evtGroupRad¶
(Formerly maxDist_site_spk_um)
Maximum distance (in μm) for extracting spike waveforms
(r2 in the figure below).
Default is 75.
evtMergeRad¶
(Formerly maxDist_site_merge_um)
Maximum distance (in μm) between sites to consider merging a pair of units.
Default is 35.
evtWindow¶
(Formerly spkLim_ms)
Time range (in ms) of filtered spike waveforms, centered at the peak.
Must be an array with 2 elements, the first negative and the second positive.
For example, if evtWindow is set to [-0.5, 0.5], then 1/2 ms worth of samples
are extracted before and after the spiking event.
Default is [-0.25, 0.75].
filterType¶
(Formerly vcFilter)
Type of filter to use on raw data.
One of the following:
- ‘ndiff’: Applies a differentiation filter, choosing a kernel depending on the order given in nDiffOrder.
- ‘sgdiff’: Applies a Savitzky-Golay filter depending on the order given in nDiffOrder.
- ‘bandpass’
- ‘fir1’
- ‘user’: Convolves your raw samples with a kernel of your choosing.
- ‘none’: Skips filtering (not recommended).
Default is ‘ndiff’.
headerOffset¶
(Formerly header_offset)
Recording file header offset (in bytes).
JRCLUST will skip this many bytes at the beginning of your recording file.
Default is 0.
ignoreChans¶
(Formerly viChanZero)
Channel numbers to ignore manually. Should be an array of integers between 1 and nChans. These values will be merged into ignoreSites.
Default is empty.
ignoreSites¶
(Formerly viSiteZero)
Site IDs to ignore manually. Should be an array of integers between 1 and nSites.
Default is empty.
log10DeltaCut¶
(Formerly delta1_cut)
\(\log_{10}\) of delta cutoff (Spikes with delta values below this cutoff will not be considered as cluster centers).
Default is 0.6.
log10RhoCut¶
(Formerly rho_cut)
\(\log_{10}\) of rho cutoff (Spikes with rho values below this cutoff will not be considered as cluster centers).
Default is -2.5.
maxUnitSim¶
(Formerly maxWavCor)
Threshold for merging two units having similar spike waveforms (Units with a similiarity score above this value will be merged).
See autoMergeBy for how “similarity” is defined.
Default is 0.98.
minClusterSize¶
(Formerly min_count)
Minimum number of spikes per cluster (Automatically set to the maximum of this value and twice the number of features).
Default is 30.
nChans¶
Number of channels stored in recording file (Distinct from the number of AP sites).
Default is 384.
nClusterIntervals¶
(Formerly nTime_clu)
Number of intervals to divide the recording into around a spike.
When clustering, take the \(\frac{1}{\text{nClusterIntervals}}\) fraction of all spikes around a spiking event to compute distance.
For example, if nClusterIntervals = 1, all spikes will be used;
if nClusterIntervals = 2, JRCLUST will take the half of all spikes which are closest
in time to compute distances.
Increasing this value will take fewer and fewer spikes to compare at the risk of
oversplitting clusters (you might want to do this if you observe fast drift in your
recording).
However, automated merging based on the waveform correlation
can merge most of the units initially split by drift.
Default is 4.
nPCsPerSite¶
(Formerly nPcPerChan)
Number of principal components to compute per site.
Default is 1.
nSiteDir¶
(Formerly maxSite)
Number of neighboring sites to group in either direction.
The total number of sites per spike group (nSitesEvt) is 1 + 2*``nSiteDir``.
In other words, a spike group includes the site on which the spike occurs, along with nSiteDir
sites in the horizontal direction and nSiteDir in the vertical direction.
If empty, the number of sites per spike group is determined from evtGroupRad.
Warning
This parameter may be deprecated in an upcoming release in favor of evtGroupRad.
Default is empty.
nSitesExcl¶
(Formerly nSites_ref)
Number of sites to exclude from the spike waveform group for feature extraction.
Default is empty.
nSpikesFigProj¶
(Formerly nShow_proj)
Maximum number of spikes per cluster to display in the feature projection view.
Default is 500.
nSpikesFigWav¶
(Formerly nSpk_show)
Maximum number of spikes per cluster to display generally.
Default is 30.
outputDir¶
Directory in which to place output files (Will output to the same directory as this file if empty).
Default is an empty string.
probePad¶
(Formerly vrSiteHW)
Recording contact pad size (in μm) (Height x width).
Default is empty.
psthTimeLimits¶
(Formerly tlim_psth)
Time range (in s) over which to display PSTH.
Default is empty.
qqFactor¶
Spike detection threshold.
Multiplier of the estimate \(\sigma_{\text{noise}}^{(i)}\) of standard deviation of noise distribution on each site to compute the threshold for that site. In other words,
is the spike detection threshold for site \(i\).
Default is 5.
recordingFormat¶
Format of raw recordings.
One of the following:
- ‘SpikeGLX’: A flat [binary file])(https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/UserManual.md#output-file-format) with no header, stored in channels x samples order.
- ‘Intan’: Traditional [Intan file format](http://www.intantech.com/files/Intan_RHD2000_data_file_formats.pdf).
Default is ‘SpikeGLX’.
siteLoc¶
(Formerly mrSiteXY)
Site locations (in μm) (x values in the first column, y values in the second column).
Default is empty.
siteMap¶
(Formerly viSite2Chan)
Map of channel index to site ID (The mapping siteMap(i) = j corresponds to the statement ‘site i is stored as channel j in the recording’).
Default is empty.
trialFile¶
(Formerly vcFile_trial)
Path to file containing trial data (Can be .mat or .csv, must contain timestamps of trials in units of s).
Default is an empty string.
Advanced parameters¶
auxFile¶
(Formerly vcFile_aux)
Path to file containing auxiliary channel.
Default is an empty string.
colorMap¶
(Formerly mrColor_proj)
RGB color map for background, primary selected, and secondary selected spikes (The first three values are the R values, the next three are the G values, and the last three are the B values.).
Default is [0.83203, 0, 0.9375, 0.85547, 0.50781, 0.46484, 0.91797, 0.76563, 0.085938].
corrRange¶
(Formerly corrLim)
Correlation score range to distinguish by color map.
Default is [0.9, 1].
detectBipolar¶
(Formerly fDetectBipolar)
Detect positive as well as negative peaks.
Default is false.
dispFeature¶
(Formerly vcFet_show)
Feature to display in the feature projection plot.
One of the following:
- ‘cov’
- ‘pca’
- ‘ppca’
- ‘vpp’
- ‘template’ (only supported for template-based clusterings, e.g., Kilosort)
Default is ‘vpp’.
dispFilter¶
(Formerly vcFilter_show)
Filter to apply in traces plot.
One of the following:
- ‘ndiff’
- ‘sgdiff’
- ‘bandpass’
- ‘fir1’
- ‘user’
- ‘none’
Default is ‘none’.
driftMerge¶
(Formerly fDrift_merge)
Compute multiple waveforms at three drift locations based on the spike position if true.
Default is true.
evtManualThresh¶
(Formerly spkThresh_uV)
Manually-set spike detection threshold (in μV).
Default is empty.
evtWindowMergeFactor¶
(Formerly spkLim_factor_merge)
Ratio of samples to take when computing correlation.
Default is 1.
evtWindowRaw¶
(Formerly spkLim_raw_ms)
Time range (in ms) of raw spike waveforms, centered at the peak.
Must be an array with 2 elements, the first negative and the second positive.
For example, if evtWindowRaw is set to [-1, 1], then 1 ms worth of samples
are extracted before and after the spiking event.
Default is [-0.5, 1.5].
extractAfterDetect¶
Extract features only after detecting all spikes across all files if true. Otherwise, features will be computed on a per-chunk, per-file basis, which may not be what you want.
This is effectively set to true if you specify clusterFeature = ‘gpca’.
Default is false.
fftThresh¶
(Formerly fft_thresh)
Threshold (in MADs of power-frequency product) above which to remove frequency outliers when denoising. Frequencies with power-frequency product above this threshold will be zeroed out as noise.
Setting to 0 disables this notch filtering. If you choose to enable, the recommended value is 10.
Default is 0.
figList¶
List of tags of figures to display in feature view.
One of the following:
- ‘FigCorr’
- ‘FigHist’
- ‘FigISI’
- ‘FigMap’
- ‘FigPos’
- ‘FigProj’
- ‘FigRD’
- ‘FigSim’
- ‘FigTime’
- ‘FigWav’
Default is [“FigCorr”, “FigHist”, “FigISI”, “FigMap”, “FigPos”, “FigProj”, “FigRD”, “FigSim”, “FigTime”, “FigWav”].
frFilterShape¶
(Formerly filter_shape_rate)
Kernel shape for temporal averaging (Used in estimation of the firing rate of a given unit).
One of the following:
- ‘triangle’
- ‘rectangle’
Default is ‘triangle’.
frPeriod¶
(Formerly filter_sec_rate)
Time period (in s) over which to determine firing rate (Used in estimation of the firing rate of a given unit).
Default is 2.
frSampleRate¶
(Formerly sRateHz_rate)
Resampling rate (in Hz) for estimating the firing rate (Used in estimation of the firing rate of a given unit).
Default is 1000.
gainBoost¶
(Formerly gain_boost)
Scale factor to boost gain in raw recording (Used in filtering operation).
Default is 1.
interpPC¶
(Formerly fInterp_fet)
Interpolate 1st principal vector to maximize projection of spikes if true.
Default is true.
loadTimeLimits¶
(Formerly tlim_load)
Time range (in s) of samples to load at once (All samples are loaded if empty).
Default is empty.
maxBytesLoad¶
(Formerly MAX_BYTES_LOAD)
Maximum number of bytes to load into memory.
Default is empty.
maxClustersSite¶
(Formerly maxCluPerSite)
Maximum number of cluster centers computed per site (Used if RDDetrendMode is ‘local’).
Default is 20.
maxSecLoad¶
(Formerly MAX_LOAD_SEC)
Maximum sample duration (in s) to load into memory (Overrides maxBytesLoad if nonempty).
Default is empty.
meanInterpFactor¶
(Formerly nInterp_merge)
Interpolation factor for mean unit waveforms (Set to 1 to disable).
Default is 1.
minNeighborsDetect¶
(Formerly nneigh_min_detect)
Minimum number of sample neighbors exceeding threshold for a sample to be considered a peak.
For example, consider a potential peak occurring at sample \(t_i\).
If minNeighborsDetect is set to 1, then either sample \(t_{i-1}\) or \(t_{i+1}\)
must also exceed the detection threshold.
If minNeighborsDetect is set to 2, then both sample \(t_{i-1}\) and \(t_{i+1}\)
must also exceed the detection threshold.
If minNeighborsDetect is set to 0, then samples \(t_{i-1}\) and \(t_{i+1}\)
are not considered.
Must be one of 0, 1, or 2.
Default is 0.
minSitesWeightFeatures¶
(Formerly min_sites_mask)
Minimum number of sites to have if using weightFeatures (Ignored if weightFeatures is false).
Default is 5.
nClustersShowAux¶
(Formerly nClu_show_aux)
Number of clusters to show in the aux vs. firing rate correlation.
Default is 10.
nDiffOrder¶
(Formerly nDiff_filt)
Order for differentiator filter (Used if and only if filterType is ‘sgdiff’ or ‘ndiff’).
Default is 2.
nLoadsMaxPreview¶
(Formerly nLoads_max_preview)
Number of time segments to load in preview.
Default is 30.
nPassesMerge¶
(Formerly nRepeat_merge)
Number of times to repeat automatic waveform-based merging.
Default is 10.
nPeaksFeatures¶
(Formerly nFet_use)
Number of potential peaks to use when computing features.
Default is 2.
nSamplesPad¶
(Formerly nPad_filt)
Number of samples to overlap between chunks in large files.
Default is 100.
nSecsLoadPreview¶
(Formerly sec_per_load_preview)
Number of seconds to load in preview.
Default is 1.
nSegmentsTraces¶
(Formerly nTime_traces)
Number of time segments to display in traces view (A value of 1 shows one continuous time segment).
Default is 1.
outlierThresh¶
(Formerly thresh_mad_clu)
Threshold (in MADs) to remove outlier spikes for each cluster.
Default is 7.5.
projTimeLimits¶
(Formerly tLimFigProj)
Time range (in s) to display in feature projection view.
Default is empty.
realignTraces¶
Realign spike traces after subtracting local CAR (Realign if 1, perform subpixel interpolation if 2).
Default is 0.
siteCorrThresh¶
(Formerly thresh_corr_bad_site)
Threshold to reject bad sites based on maximum correlation with neighboring sites (Set to 0 to disable).
Default is 0.
spikeThreshMax¶
(Formerly spkThresh_max_uV)
Maximum absolute amplitude (in μV) permitted for spikes.
Default is empty.
tallSkinny¶
(Formerly fTranspose_bin)
Recording will be interpreted as nChannels x nSamples if true.
Default is true.
threshFile¶
(Formerly vcFile_thresh)
Path to .mat file storing the spike detection threshold (Created by preview GUI).
Default is an empty string.
useElliptic¶
(Formerly fEllip)
Use elliptic (bandpass) filter if true (Uses Butterworth filter if false).
Default is true.
useGlobalDistCut¶
(Formerly fDc_global)
Use a global distance cutoff for all sites if true.
Default is false.
userFiltKernel¶
(Formerly vnFilter_user)
User-specified filter kernel (Ignored unless filterType is ‘user’).
Your filtered samples will be the output of a convolution of your raw samples
with this kernel.
You must specify this if and only if your filterType is 'user'.
Default is empty.
weightFeatures¶
(Formerly fSpatialMask_clu)
Weight display features by distance from site if true.
Default is false.