Tutorial

Installing JRCLUST

JRCLUST is hosted on GitHub. If you’d like to test the latest development code, you can clone the repository to your computer. If you want to stay on a release, head to the releases page and download the latest release.

You may want to add something like the following to your startup script:

addpath('/path/to/JRCLUST');

You may also need to recompile your CUDA codes if you’re not on Windows. Do this with

jrclust.CUDA.compileCUDA();

Warning

You may get this error on recent versions of Ubuntu: Call to sgemv in CUBLAS failed with error status: CUBLAS_STATUS_EXECUTION_FAILED. This is a known issue, but unfortunately the suggested workaround doesn’t seem to work.

Setting up your config file

JRCLUST requires a configuration file specifying a number of parameters. How some of these parameters are used is explained in the pipeline section. You may set this up with

jrc bootstrap

or

jrc bootstrap /path/to/metafile.meta

See the bootstrap documentation for details.

You will be guided through a series of prompts in setting up your config file.

Selecting a meta file

If you specify a meta file with jrc bootstrap /path/to/metafile.meta, then you will not be asked to select one; you can skip to the next section. After typing jrc bootstrap, you should get a prompt asking if you have a meta file:

If you select “Yes”, you will be prompted to select one or more with a file dialog:

If you select “No” instead, you will be prompted to select one or more raw recordings with a similar dialog. You may select from among SpikeGLX .bin/.dat files, or Intan .rhd traditional-format files.

In either case, your working directory will be set to the directory containing the file or files you selected.

Selecting a probe file

You will next be asked if you have a probe file you want to specify:

If you select “Yes”, you will be prompted to select exactly one probe file with a file dialog:

Note

If you have a probe file in your working directory, then the dialog will search there first. If you do not have a probe file in your working directory, the dialog will search in the default location, JRCLUST/probes, as shown above.

Confirmation

Next, you will be asked to confirm some salient data:

Finishing up

Once you are satisfied, JRCLUST will open up your parameter file for editing:

You should end up with a parameter file that looks something like this (see the parameters page for details):

% 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)
dataTypeRaw = 'int16'; % (formerly vcDataType) Format of raw recordings
dataTypeExtracted = 'int16'; % (formerly vcDataType) Format of extracted 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)

Look over your parameters and ensure they are satisfactory.

Displaying your probe

You might wish to plot your probe to ensure that it’s modeled as expected. This can be done with

jrc probe /path/to/your/configfile.prm

You will get a plot similar to this:

In this example, we have a two-shank probe model, each shank having 32 active electrodes for a total of 64 sites. The shanks are spaced 250 μm apart, with the leftmost shank being considered the origin. (Your probe will almost certainly look different.)

The labels on the patch plots are site number/channel number. This is handy for visualizing the channel-site correspondence. You can use this graphic to verify that the sites you gave to JRCLUST are in their proper positions. You can zoom in and out with the scroll wheel to increase or decrease resolution as necessary.

Close this plot and proceed to the next section.

Showing raw traces

You will probably want to take a look at your raw traces. Do this with

jrc traces /path/to/your/configfile.prm

You will get an interactive plot that looks like this:

Here you can page through your raw data, adjusting your scale and applying various filters. Later, after you have detected and clustered your spikes, you can highlight spikes like so:

You can also plot the power spectral density by hitting the P key in this plot. You may select a single site or show the mean power vs. frequency as shown below:

The preview GUI

A more advanced view on your raw traces is the preview GUI. Invoke it like so:

jrc preview /path/to/your/configfile.prm

This will take a look at your recording and do some preliminary spike detection with the parameters you’ve specified. (Spikes are circled in red below). You can view the maximum site-to-site correlation and set a threshold for bad sites (i.e., sites to ignore) if they come below that threshold. In the figure below, site 46 is poorly correlated with the other sites, so you might choose to ignore it. You can also view the common average across sites at each time step, expressed in units of MAD, to set a threshold for blanking out that period. There are many other parameters to set from the preview GUI. Take some time to explore these in the Edit menu, and see the effects they have by changing views in the View menu. (You can see the manual page for details.) Once you are satisfied with these parameters, you can select “Save to [your parameter file here]” from the File menu and start to detect spikes.

Detecting spikes

Now it’s time to detect spikes in your file. This can be done with

jrc detect /path/to/your/configfile.prm

If you want to cluster your spikes immediately afterward, use

jrc detect-sort /path/to/your/configfile.prm

instead.

Depending on your choice of parameters, you should see something like the following output:

>> jrc detect test.prm
2019-08-30 14:04:09 Clearing GPU memory...
2019-08-30 14:04:09 GPU memory cleared (took 0.16 s)
2019-08-30 14:04:09 Detecting spikes in recordings...
2019-08-30 14:04:09 Processing file F:\Misc\Tests\JRCLUST\single\test.bin (1/1)...
2019-08-30 14:04:10 Processing load 1/1...
2019-08-30 14:04:10 Filtering samples...
2019-08-30 14:04:10 Finished filtering samples (took 0.10 s)
2019-08-30 14:04:11 Detecting spikes from each site...
2019-08-30 14:04:11 Detected 19 spikes on site 1
2019-08-30 14:04:11 Detected 17 spikes on site 2
2019-08-30 14:04:11 Detected 69 spikes on site 3
2019-08-30 14:04:11 Detected 127 spikes on site 4
2019-08-30 14:04:11 Detected 29 spikes on site 5
2019-08-30 14:04:11 Detected 22 spikes on site 6
2019-08-30 14:04:11 Detected 51 spikes on site 7
2019-08-30 14:04:11 Detected 61 spikes on site 8
2019-08-30 14:04:11 Detected 52 spikes on site 9
2019-08-30 14:04:11 Detected 31 spikes on site 10
2019-08-30 14:04:11 Detected 113 spikes on site 11
2019-08-30 14:04:11 Detected 139 spikes on site 12
2019-08-30 14:04:11 Detected 61 spikes on site 13
2019-08-30 14:04:11 Detected 122 spikes on site 14
2019-08-30 14:04:11 Detected 274 spikes on site 15
2019-08-30 14:04:11 Detected 1156 spikes on site 16
2019-08-30 14:04:11 Detected 223 spikes on site 17
2019-08-30 14:04:11 Detected 83 spikes on site 18
2019-08-30 14:04:11 Detected 167 spikes on site 19
2019-08-30 14:04:11 Detected 362 spikes on site 20
2019-08-30 14:04:11 Detected 528 spikes on site 21
2019-08-30 14:04:11 Detected 248 spikes on site 22
2019-08-30 14:04:11 Detected 282 spikes on site 23
2019-08-30 14:04:11 Detected 331 spikes on site 24
2019-08-30 14:04:11 Detected 213 spikes on site 25
2019-08-30 14:04:11 Detected 207 spikes on site 26
2019-08-30 14:04:11 Detected 112 spikes on site 27
2019-08-30 14:04:11 Detected 426 spikes on site 28
2019-08-30 14:04:11 Detected 368 spikes on site 29
2019-08-30 14:04:11 Detected 227 spikes on site 30
2019-08-30 14:04:11 Detected 323 spikes on site 31
2019-08-30 14:04:11 Detected 404 spikes on site 32
2019-08-30 14:04:11 Detected 2047 spikes on site 33
2019-08-30 14:04:11 Detected 150 spikes on site 34
2019-08-30 14:04:11 Detected 69 spikes on site 35
2019-08-30 14:04:11 Detected 68 spikes on site 36
2019-08-30 14:04:11 Detected 121 spikes on site 37
2019-08-30 14:04:11 Detected 97 spikes on site 38
2019-08-30 14:04:11 Detected 102 spikes on site 39
2019-08-30 14:04:11 Detected 89 spikes on site 40
2019-08-30 14:04:11 Detected 114 spikes on site 41
2019-08-30 14:04:11 Detected 215 spikes on site 42
2019-08-30 14:04:11 Detected 251 spikes on site 43
2019-08-30 14:04:11 Detected 457 spikes on site 44
2019-08-30 14:04:11 Detected 645 spikes on site 45
2019-08-30 14:04:11 Detected 182 spikes on site 46
2019-08-30 14:04:11 Detected 278 spikes on site 47
2019-08-30 14:04:11 Detected 408 spikes on site 48
2019-08-30 14:04:11 Detected 337 spikes on site 49
2019-08-30 14:04:11 Detected 347 spikes on site 50
2019-08-30 14:04:11 Detected 168 spikes on site 51
2019-08-30 14:04:11 Detected 118 spikes on site 52
2019-08-30 14:04:11 Detected 196 spikes on site 53
2019-08-30 14:04:11 Detected 185 spikes on site 54
2019-08-30 14:04:11 Detected 105 spikes on site 55
2019-08-30 14:04:11 Detected 275 spikes on site 56
2019-08-30 14:04:11 Detected 121 spikes on site 57
2019-08-30 14:04:11 Detected 116 spikes on site 58
2019-08-30 14:04:11 Detected 250 spikes on site 59
2019-08-30 14:04:11 Detected 232 spikes on site 60
2019-08-30 14:04:11 Detected 62 spikes on site 61
2019-08-30 14:04:11 Detected 139 spikes on site 62
2019-08-30 14:04:11 Detected 51 spikes on site 63
2019-08-30 14:04:11 Detected 41 spikes on site 64
2019-08-30 14:04:11 Finished detecting spikes (took 0.15 s)
2019-08-30 14:04:11 Merging duplicate spiking events...
2019-08-30 14:04:11 9891 spiking events found (took 0.10 s)
2019-08-30 14:04:11 Finished load 1/1 (took 1.46 s)
2019-08-30 14:04:11 Finished processing file F:\Misc\Tests\JRCLUST\single\test.bin (1/1) (took 2.04 s)
2019-08-30 14:04:11 Extracting features...
2019-08-30 14:04:12 Finished extracting features (took 0.31 s)
2019-08-30 14:04:12 Finished detecting (took 2.50 s)
2019-08-30 14:04:15 Saving results to F:\Misc\Tests\JRCLUST\single\test_res.mat...
2019-08-30 14:04:15 Results saved to F:\Misc\Tests\JRCLUST\single\test_res.mat (took 0.02 s)

====DETECTION SUMMARY====
Detection completed in 2.50 s
Spike count: 9891
Spike counts per site: min 8 (site 2), max 2036 (site 33), median 85

Your detection results will be exported to the workspace in the form of a struct called res for inspection. See Input and output files for a description of the contents. For a detailed description of the detect step, see Spike detection.

Clustering spikes

Once you have detected your spikes, it’s time to cluster them:

jrc sort /path/to/your/configfile.prm

You should see something like the following output:

>> jrc sort test.prm
2019-08-30 14:06:37 Loading F:\Misc\Tests\JRCLUST\single\test_res.mat...
2019-08-30 14:06:37 Finished loading F:\Misc\Tests\JRCLUST\single\test_res.mat (took 0.01 s)
2019-08-30 14:06:37 Loading F:\Misc\Tests\JRCLUST\single\test_raw.jrc...
2019-08-30 14:06:37 Finished loading F:\Misc\Tests\JRCLUST\single\test_raw.jrc (took 0.01 s)
2019-08-30 14:06:37 Loading F:\Misc\Tests\JRCLUST\single\test_filt.jrc...
2019-08-30 14:06:37 Finished loading F:\Misc\Tests\JRCLUST\single\test_filt.jrc (took 0.01 s)
2019-08-30 14:06:37 Loading F:\Misc\Tests\JRCLUST\single\test_features.jrc...
2019-08-30 14:06:37 Finished loading F:\Misc\Tests\JRCLUST\single\test_features.jrc (took 0.00 s)
2019-08-30 14:06:37 Using spikes detected on 30-Aug-2019 14:04:12
2019-08-30 14:06:37 Clearing GPU memory...
2019-08-30 14:06:37 GPU memory cleared (took 0.16 s)
2019-08-30 14:06:37 Sorting detected spikes...
2019-08-30 14:06:37 Computing rho...
2019-08-30 14:06:38 Site 1: rho cutoff, 731869.75; average rho: 0.00016 (15 spikes)
2019-08-30 14:06:38 Site 2: rho cutoff, 1367942.13; average rho: 0.00036 (8 spikes)
2019-08-30 14:06:38 Site 3: rho cutoff, 371085.19; average rho: 0.00059 (44 spikes)
2019-08-30 14:06:38 Site 4: rho cutoff, 454989.97; average rho: 0.00098 (110 spikes)
2019-08-30 14:06:38 Site 5: rho cutoff, 818252.50; average rho: 0.00114 (21 spikes)
2019-08-30 14:06:38 Site 6: rho cutoff, 1096531.38; average rho: 0.00129 (8 spikes)
2019-08-30 14:06:38 Site 7: rho cutoff, 575589.00; average rho: 0.00151 (34 spikes)
2019-08-30 14:06:38 Site 8: rho cutoff, 481210.56; average rho: 0.00175 (29 spikes)
2019-08-30 14:06:38 Site 9: rho cutoff, 636892.19; average rho: 0.00193 (40 spikes)
2019-08-30 14:06:38 Site 10: rho cutoff, 2221163.75; average rho: 0.00211 (12 spikes)
2019-08-30 14:06:38 Site 11: rho cutoff, 692781.94; average rho: 0.00248 (91 spikes)
2019-08-30 14:06:38 Site 12: rho cutoff, 503940.38; average rho: 0.00293 (103 spikes)
2019-08-30 14:06:38 Site 13: rho cutoff, 745752.50; average rho: 0.00311 (39 spikes)
2019-08-30 14:06:38 Site 14: rho cutoff, 1094450.50; average rho: 0.00332 (43 spikes)
2019-08-30 14:06:38 Site 15: rho cutoff, 855698.94; average rho: 0.00402 (222 spikes)
2019-08-30 14:06:38 Site 16: rho cutoff, 308155.81; average rho: 0.00683 (1007 spikes)
2019-08-30 14:06:38 Site 17: rho cutoff, 829652.13; average rho: 0.00736 (161 spikes)
2019-08-30 14:06:38 Site 18: rho cutoff, 783599.13; average rho: 0.00758 (32 spikes)
2019-08-30 14:06:38 Site 19: rho cutoff, 698739.75; average rho: 0.00802 (85 spikes)
2019-08-30 14:06:38 Site 20: rho cutoff, 778769.88; average rho: 0.00854 (168 spikes)
2019-08-30 14:06:38 Site 21: rho cutoff, 894751.50; average rho: 0.00948 (369 spikes)
2019-08-30 14:06:38 Site 22: rho cutoff, 895366.63; average rho: 0.00986 (113 spikes)
2019-08-30 14:06:38 Site 23: rho cutoff, 811321.75; average rho: 0.01045 (141 spikes)
2019-08-30 14:06:38 Site 24: rho cutoff, 961806.00; average rho: 0.01101 (211 spikes)
2019-08-30 14:06:38 Site 25: rho cutoff, 917075.13; average rho: 0.01133 (74 spikes)
2019-08-30 14:06:38 Site 26: rho cutoff, 685997.25; average rho: 0.01184 (150 spikes)
2019-08-30 14:06:38 Site 27: rho cutoff, 1064097.88; average rho: 0.01209 (47 spikes)
2019-08-30 14:06:38 Site 28: rho cutoff, 539079.56; average rho: 0.01316 (250 spikes)
2019-08-30 14:06:38 Site 29: rho cutoff, 1070611.50; average rho: 0.01401 (261 spikes)
2019-08-30 14:06:38 Site 30: rho cutoff, 827772.50; average rho: 0.01425 (59 spikes)
2019-08-30 14:06:38 Site 31: rho cutoff, 1146530.88; average rho: 0.01492 (153 spikes)
2019-08-30 14:06:38 Site 32: rho cutoff, 970855.06; average rho: 0.01557 (241 spikes)
2019-08-30 14:06:38 Site 33: rho cutoff, 251356.16; average rho: 0.02157 (2036 spikes)
2019-08-30 14:06:38 Site 34: rho cutoff, 260651.09; average rho: 0.02213 (139 spikes)
2019-08-30 14:06:38 Site 35: rho cutoff, 714987.13; average rho: 0.02235 (45 spikes)
2019-08-30 14:06:38 Site 36: rho cutoff, 631074.38; average rho: 0.02262 (52 spikes)
2019-08-30 14:06:38 Site 37: rho cutoff, 453064.25; average rho: 0.02289 (60 spikes)
2019-08-30 14:06:38 Site 38: rho cutoff, 805470.44; average rho: 0.02323 (71 spikes)
2019-08-30 14:06:38 Site 39: rho cutoff, 660921.75; average rho: 0.02345 (45 spikes)
2019-08-30 14:06:38 Site 40: rho cutoff, 685622.75; average rho: 0.02372 (39 spikes)
2019-08-30 14:06:38 Site 41: rho cutoff, 1017240.00; average rho: 0.02414 (79 spikes)
2019-08-30 14:06:38 Site 42: rho cutoff, 724510.81; average rho: 0.02464 (129 spikes)
2019-08-30 14:06:39 Site 43: rho cutoff, 1318095.13; average rho: 0.02502 (85 spikes)
2019-08-30 14:06:39 Site 44: rho cutoff, 810584.25; average rho: 0.02592 (312 spikes)
2019-08-30 14:06:39 Site 45: rho cutoff, 913448.50; average rho: 0.02711 (374 spikes)
2019-08-30 14:06:39 Site 46: rho cutoff, 928920.94; average rho: 0.02750 (67 spikes)
2019-08-30 14:06:39 Site 47: rho cutoff, 1020212.25; average rho: 0.02830 (236 spikes)
2019-08-30 14:06:39 Site 48: rho cutoff, 465102.56; average rho: 0.02917 (257 spikes)
2019-08-30 14:06:39 Site 49: rho cutoff, 804615.63; average rho: 0.02972 (188 spikes)
2019-08-30 14:06:39 Site 50: rho cutoff, 559785.13; average rho: 0.03033 (187 spikes)
2019-08-30 14:06:39 Site 51: rho cutoff, 557701.31; average rho: 0.03050 (16 spikes)
2019-08-30 14:06:39 Site 52: rho cutoff, 371283.31; average rho: 0.03069 (39 spikes)
2019-08-30 14:06:39 Site 53: rho cutoff, 542745.94; average rho: 0.03103 (94 spikes)
2019-08-30 14:06:39 Site 54: rho cutoff, 498734.75; average rho: 0.03148 (137 spikes)
2019-08-30 14:06:39 Site 55: rho cutoff, 1296482.13; average rho: 0.03166 (20 spikes)
2019-08-30 14:06:39 Site 56: rho cutoff, 377575.56; average rho: 0.03241 (241 spikes)
2019-08-30 14:06:39 Site 57: rho cutoff, 347963.09; average rho: 0.03268 (59 spikes)
2019-08-30 14:06:39 Site 58: rho cutoff, 849382.00; average rho: 0.03297 (58 spikes)
2019-08-30 14:06:39 Site 59: rho cutoff, 531617.50; average rho: 0.03337 (102 spikes)
2019-08-30 14:06:39 Site 60: rho cutoff, 354038.84; average rho: 0.03401 (177 spikes)
2019-08-30 14:06:39 Site 61: rho cutoff, 357702.53; average rho: 0.03422 (26 spikes)
2019-08-30 14:06:39 Site 62: rho cutoff, 881595.94; average rho: 0.03482 (123 spikes)
2019-08-30 14:06:39 Site 63: rho cutoff, 457689.47; average rho: 0.03507 (36 spikes)
2019-08-30 14:06:39 Site 64: rho cutoff, 699817.06; average rho: 0.03532 (21 spikes)
2019-08-30 14:06:39 Finished computing rho (took 1.27 s)
2019-08-30 14:06:39 Computing delta...
2019-08-30 14:06:39 Site 1: median delta: 1.27137 (15 spikes)
2019-08-30 14:06:39 Site 2: median delta: 1.66295 (8 spikes)
2019-08-30 14:06:39 Site 3: median delta: 1.00265 (44 spikes)
2019-08-30 14:06:39 Site 4: median delta: 0.85708 (110 spikes)
2019-08-30 14:06:39 Site 5: median delta: 1.58162 (21 spikes)
2019-08-30 14:06:39 Site 6: median delta: 1.52481 (8 spikes)
2019-08-30 14:06:39 Site 7: median delta: 1.24786 (34 spikes)
2019-08-30 14:06:39 Site 8: median delta: 1.22150 (29 spikes)
2019-08-30 14:06:39 Site 9: median delta: 1.08609 (40 spikes)
2019-08-30 14:06:39 Site 10: median delta: 1.10892 (12 spikes)
2019-08-30 14:06:39 Site 11: median delta: 0.87843 (91 spikes)
2019-08-30 14:06:39 Site 12: median delta: 0.86909 (103 spikes)
2019-08-30 14:06:39 Site 13: median delta: 1.10214 (39 spikes)
2019-08-30 14:06:39 Site 14: median delta: 1.15297 (43 spikes)
2019-08-30 14:06:39 Site 15: median delta: 0.73530 (222 spikes)
2019-08-30 14:06:39 Site 16: median delta: 0.55511 (1007 spikes)
2019-08-30 14:06:39 Site 17: median delta: 0.75445 (161 spikes)
2019-08-30 14:06:39 Site 18: median delta: 1.07030 (32 spikes)
2019-08-30 14:06:39 Site 19: median delta: 0.90345 (85 spikes)
2019-08-30 14:06:39 Site 20: median delta: 0.80473 (168 spikes)
2019-08-30 14:06:39 Site 21: median delta: 0.66820 (369 spikes)
2019-08-30 14:06:39 Site 22: median delta: 0.91149 (113 spikes)
2019-08-30 14:06:39 Site 23: median delta: 0.76094 (141 spikes)
2019-08-30 14:06:39 Site 24: median delta: 0.75902 (211 spikes)
2019-08-30 14:06:39 Site 25: median delta: 0.97118 (74 spikes)
2019-08-30 14:06:39 Site 26: median delta: 0.81842 (150 spikes)
2019-08-30 14:06:39 Site 27: median delta: 0.95115 (47 spikes)
2019-08-30 14:06:39 Site 28: median delta: 0.72237 (250 spikes)
2019-08-30 14:06:39 Site 29: median delta: 0.69283 (261 spikes)
2019-08-30 14:06:39 Site 30: median delta: 1.03695 (59 spikes)
2019-08-30 14:06:39 Site 31: median delta: 0.75059 (153 spikes)
2019-08-30 14:06:39 Site 32: median delta: 0.74415 (241 spikes)
2019-08-30 14:06:39 Site 33: median delta: 0.47524 (2036 spikes)
2019-08-30 14:06:39 Site 34: median delta: 0.83504 (139 spikes)
2019-08-30 14:06:39 Site 35: median delta: 1.03859 (45 spikes)
2019-08-30 14:06:39 Site 36: median delta: 0.97808 (52 spikes)
2019-08-30 14:06:39 Site 37: median delta: 0.98207 (60 spikes)
2019-08-30 14:06:39 Site 38: median delta: 0.94462 (71 spikes)
2019-08-30 14:06:39 Site 39: median delta: 1.00673 (45 spikes)
2019-08-30 14:06:39 Site 40: median delta: 0.99713 (39 spikes)
2019-08-30 14:06:39 Site 41: median delta: 0.87949 (79 spikes)
2019-08-30 14:06:39 Site 42: median delta: 0.84302 (129 spikes)
2019-08-30 14:06:39 Site 43: median delta: 0.90183 (85 spikes)
2019-08-30 14:06:39 Site 44: median delta: 0.68221 (312 spikes)
2019-08-30 14:06:39 Site 45: median delta: 0.66591 (374 spikes)
2019-08-30 14:06:39 Site 46: median delta: 0.92985 (67 spikes)
2019-08-30 14:06:39 Site 47: median delta: 0.70058 (236 spikes)
2019-08-30 14:06:39 Site 48: median delta: 0.73736 (257 spikes)
2019-08-30 14:06:39 Site 49: median delta: 0.76567 (188 spikes)
2019-08-30 14:06:39 Site 50: median delta: 0.80459 (187 spikes)
2019-08-30 14:06:39 Site 51: median delta: 1.46500 (16 spikes)
2019-08-30 14:06:39 Site 52: median delta: 1.09898 (39 spikes)
2019-08-30 14:06:39 Site 53: median delta: 0.92572 (94 spikes)
2019-08-30 14:06:39 Site 54: median delta: 0.81506 (137 spikes)
2019-08-30 14:06:39 Site 55: median delta: 1.22181 (20 spikes)
2019-08-30 14:06:39 Site 56: median delta: 0.73346 (241 spikes)
2019-08-30 14:06:39 Site 57: median delta: 1.03142 (59 spikes)
2019-08-30 14:06:39 Site 58: median delta: 0.98693 (58 spikes)
2019-08-30 14:06:39 Site 59: median delta: 0.86694 (102 spikes)
2019-08-30 14:06:39 Site 60: median delta: 0.83345 (177 spikes)
2019-08-30 14:06:39 Site 61: median delta: 1.02984 (26 spikes)
2019-08-30 14:06:39 Site 62: median delta: 0.77846 (123 spikes)
2019-08-30 14:06:39 Site 63: median delta: 1.04947 (36 spikes)
2019-08-30 14:06:39 Site 64: median delta: 1.07382 (21 spikes)
2019-08-30 14:06:39 Finished computing delta (took 0.27 s)
2019-08-30 14:06:39 Assigning clusters (nClusters: 528)...
2019-08-30 14:06:39 9363/9891 spikes unassigned, 709 can be assigned
2019-08-30 14:06:39 8654/9891 spikes unassigned, 1015 can be assigned
2019-08-30 14:06:39 7639/9891 spikes unassigned, 1144 can be assigned
2019-08-30 14:06:39 6495/9891 spikes unassigned, 1065 can be assigned
2019-08-30 14:06:39 5430/9891 spikes unassigned, 977 can be assigned
2019-08-30 14:06:39 4453/9891 spikes unassigned, 866 can be assigned
2019-08-30 14:06:39 3587/9891 spikes unassigned, 740 can be assigned
2019-08-30 14:06:39 2847/9891 spikes unassigned, 620 can be assigned
2019-08-30 14:06:39 2227/9891 spikes unassigned, 519 can be assigned
2019-08-30 14:06:39 1708/9891 spikes unassigned, 438 can be assigned
2019-08-30 14:06:39 1270/9891 spikes unassigned, 333 can be assigned
2019-08-30 14:06:39 937/9891 spikes unassigned, 247 can be assigned
2019-08-30 14:06:39 690/9891 spikes unassigned, 218 can be assigned
2019-08-30 14:06:39 472/9891 spikes unassigned, 148 can be assigned
2019-08-30 14:06:39 324/9891 spikes unassigned, 103 can be assigned
2019-08-30 14:06:39 221/9891 spikes unassigned, 58 can be assigned
2019-08-30 14:06:39 163/9891 spikes unassigned, 34 can be assigned
2019-08-30 14:06:39 129/9891 spikes unassigned, 27 can be assigned
2019-08-30 14:06:39 102/9891 spikes unassigned, 28 can be assigned
2019-08-30 14:06:39 74/9891 spikes unassigned, 21 can be assigned
2019-08-30 14:06:39 53/9891 spikes unassigned, 15 can be assigned
2019-08-30 14:06:39 38/9891 spikes unassigned, 18 can be assigned
2019-08-30 14:06:39 20/9891 spikes unassigned, 12 can be assigned
2019-08-30 14:06:39 8/9891 spikes unassigned, 4 can be assigned
2019-08-30 14:06:39 4/9891 spikes unassigned, 1 can be assigned
2019-08-30 14:06:39 3/9891 spikes unassigned, 2 can be assigned
2019-08-30 14:06:39 1/9891 spikes unassigned, 1 can be assigned
2019-08-30 14:06:39 9826/9891 spikes unassigned, 272 can be assigned
2019-08-30 14:06:39 9554/9891 spikes unassigned, 589 can be assigned
2019-08-30 14:06:39 8965/9891 spikes unassigned, 867 can be assigned
2019-08-30 14:06:39 8098/9891 spikes unassigned, 958 can be assigned
2019-08-30 14:06:39 7140/9891 spikes unassigned, 1008 can be assigned
2019-08-30 14:06:39 6132/9891 spikes unassigned, 976 can be assigned
2019-08-30 14:06:39 5156/9891 spikes unassigned, 872 can be assigned
2019-08-30 14:06:39 4284/9891 spikes unassigned, 726 can be assigned
2019-08-30 14:06:39 3558/9891 spikes unassigned, 618 can be assigned
2019-08-30 14:06:39 2940/9891 spikes unassigned, 529 can be assigned
2019-08-30 14:06:39 2411/9891 spikes unassigned, 416 can be assigned
2019-08-30 14:06:39 1995/9891 spikes unassigned, 325 can be assigned
2019-08-30 14:06:39 1670/9891 spikes unassigned, 284 can be assigned
2019-08-30 14:06:39 1386/9891 spikes unassigned, 185 can be assigned
2019-08-30 14:06:39 1201/9891 spikes unassigned, 122 can be assigned
2019-08-30 14:06:39 1079/9891 spikes unassigned, 69 can be assigned
2019-08-30 14:06:39 1010/9891 spikes unassigned, 39 can be assigned
2019-08-30 14:06:39 971/9891 spikes unassigned, 27 can be assigned
2019-08-30 14:06:39 944/9891 spikes unassigned, 28 can be assigned
2019-08-30 14:06:39 916/9891 spikes unassigned, 22 can be assigned
2019-08-30 14:06:39 894/9891 spikes unassigned, 17 can be assigned
2019-08-30 14:06:39 877/9891 spikes unassigned, 19 can be assigned
2019-08-30 14:06:39 858/9891 spikes unassigned, 13 can be assigned
2019-08-30 14:06:39 845/9891 spikes unassigned, 4 can be assigned
2019-08-30 14:06:39 841/9891 spikes unassigned, 1 can be assigned
2019-08-30 14:06:39 840/9891 spikes unassigned, 3 can be assigned
2019-08-30 14:06:39 837/9891 spikes unassigned, 1 can be assigned
2019-08-30 14:06:39 836/9891 spikes unassigned, 1 can be assigned
2019-08-30 14:06:39 Finished initial assignment (65 clusters) (took 0.11 s)
2019-08-30 14:06:39 Computing cluster mean waveforms...
2019-08-30 14:06:39 Finished computing cluster mean waveforms (took 0.17 s)
2019-08-30 14:06:39 Computing waveform correlation...
2019-08-30 14:06:40 Finished computing waveform correlation (took 0.19 s)
2019-08-30 14:06:40 Computing cluster self-similarity...
2019-08-30 14:06:40 Finished computing cluster self-similarity (took 0.05 s)
2019-08-30 14:06:40 Computing cluster quality scores...
2019-08-30 14:06:40 Finished computing cluster quality scores (took 0.06 s)
2019-08-30 14:06:40 Merging clusters by similarity...
2019-08-30 14:06:40 No clusters to merge (took 0.00 s)
2019-08-30 14:06:40 Finished sorting (took 2.52 s)
2019-08-30 14:06:42 Saving results to F:\Misc\Tests\JRCLUST\single\test_res.mat...
2019-08-30 14:06:43 Results saved to F:\Misc\Tests\JRCLUST\single\test_res.mat (took 0.13 s)

====SORTING SUMMARY====
Sorting completed in 2.51 s
Clusters: 65 (no merges)
Spike count per cluster: min 31 (cluster 24), max 2036 (cluster 37), median 80
Site count per cluster: min 1 (cluster 1), max 1 (cluster 1), median 1

JRCLUST will tell you when your spikes were detected and perform clustering and postprocessing. As in the detect step, JRCLUST will export the results structure to the workspace for inspection.

Curating your clustering

You will now want to inspect the results of your clustering. Do this with

jrc manual /path/to/your/configfile.prm

You will be greeted with the following screen:

Each of these figures contains a different view onto the data. Here you will be able to annotate, delete, merge, or split clusters. For a description of what each figure does and how to perform these operations, see the Cluster curation section. When you are satisfied with your clustering, you may save and exit.