default.prm

% JRCLUST parameters (default parameter set)
% For a description of these parameters, including default and legal values, see https://jrclust.readthedocs.io/en/latest/parameters/index.html

% USAGE PARAMETERS
outputDir = ''; % Directory in which to place output files (Will output to the same directory as this file if empty)

% PROBE PARAMETERS
probePad = [12, 12]; % (formerly vrSiteHW) Recording contact pad size (in μm) (Height x width)
shankMap = []; % (formerly viShank_site) Shank ID of each site
siteLoc = []; % (formerly mrSiteXY) Site locations (in μm) (x values in the first column, y values in the second column)
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')

% RECORDING FILE PARAMETERS
bitScaling = 0.30518; % (formerly uV_per_bit) ADC bit scaling factor (Conversion factor for ADC bit values to μV)
dataType = 'int16'; % (formerly vcDataType) Format of raw recordings
headerOffset = 0; % (formerly header_offset) Recording file header offset (in bytes)
nChans = 384; % Number of channels stored in recording file (Distinct from the number of AP sites)
rawRecordings = {''}; % Path or paths to raw recordings to sort
recordingFormat = 'SpikeGLX'; % Format of raw recording
sampleRate = 30000; % (formerly sRateHz) Sampling rate (in Hz) of raw recording

% PREPROCESSING PARAMETERS
blankThresh = []; % (formerly blank_thresh) Threshold (in MADs) above which to reject samples exceeding channel median after filtering
filtOrder = 3; % Bandpass filter order
filterType = 'ndiff'; % (formerly vcFilter) Type of filter to use on raw data
freqLimBP = [300, 3000]; % (formerly freqLim) Frequency cutoffs for bandpass filter
ignoreChans = []; % (formerly viChanZero) Channel numbers to ignore manually
ignoreSites = []; % (formerly viSiteZero) Site IDs to ignore manually

% SPIKE DETECTION PARAMETERS
CARMode = 'mean'; % (formerly vcCommonRef) The meaning of 'average' in 'common average reference'
blankPeriod = 5; % (formerly blank_period_ms) Duration of blanking period (in ms) when the common mean exceeds blankThresh
evtDetectRad = 50; % (formerly maxDist_site_um) Maximum distance (in μm) to search over for duplicate peaks
evtWindow = [-0.25, 0.75]; % (formerly spkLim_ms) Time range (in ms) of filtered spike waveforms, centered at the peak
nSiteDir = []; % (formerly maxSite) Number of neighboring sites to group in either direction (nSitesEvt is set to 1 + 2*nSiteDir - nSitesExcl)
nSitesExcl = []; % (formerly nSites_ref) Number of sites to exclude from the spike waveform group for feature extraction
qqFactor = 5; % Spike detection threshold factor (Thr = qqFactor*med(abs(x-med(x)))/0.6745)
refracInt = 0.25; % (formerly spkRefrac_ms) Spike refractory period (in ms)

% FEATURE EXTRACTION PARAMETERS
clusterFeature = 'pca'; % (formerly vcFet) The feature to extract from your spike waveforms in order to cluster them
evtGroupRad = 75; % (formerly maxDist_site_spk_um) Maximum distance (in μm) for extracting spike waveforms
nPCsPerSite = 1; % (formerly nPcPerChan) Number of principal components to compute per site

% CLUSTERING PARAMETERS
RDDetrendMode = 'global'; % (formerly vcDetrend_postclu) Detrending mode to apply to rho-delta values in order to determine cluster centers
autoMergeBy = 'pearson'; % (formerly autoMergeCriterion) Metric to use for automerging clusters based on average waveform
distCut = 2; % (formerly dc_percent) Percentile of pairwise distances between spikes on a site to use as a cutoff distance
evtMergeRad = 35; % (formerly maxDist_site_merge_um) Maximum distance (in μm) to consider for merging spike waveforms
log10DeltaCut = 0.6; % (formerly delta1_cut) Log10 of delta cutoff (Spikes with delta values below this cutoff will not be considered as cluster centers)
log10RhoCut = -2.5; % (formerly rho_cut) Log10 of rho cutoff (Spikes with rho values below this cutoff will not be considered as cluster centers)
maxUnitSim = 0.98; % (formerly maxWavCor) Threshold for merging two units having similar spike waveforms (Units with a similiarity score above this value will be merged)
minClusterSize = 30; % (formerly min_count) Minimum number of spikes per cluster (Automatically set to the maximum of this value and twice the number of features)
nClusterIntervals = 4; % (formerly nTime_clu) Number of intervals to divide the recording into around a spike (When clustering, take the 1/nClusterIntervals fraction of all spikes around a spiking event to compute distance)

% DISPLAY PARAMETERS
dispTimeLimits = [0, 0.2]; % (formerly tlim) Time range (in ms) to display
nSpikesFigProj = 500; % (formerly nShow_proj) Maximum number of spikes per cluster to display in the feature projection view
nSpikesFigWav = 30; % (formerly nSpk_show) Maximum number of spikes per cluster to display generally

% TRIAL PARAMETERS
psthTimeLimits = []; % (formerly tlim_psth) Time range (in s) over which to display PSTH
trialFile = ''; % (formerly vcFile_trial) Path to file containing trial data (Can be .mat or .csv, must contain timestamps of trials in units of s)