Command listing

JRCLUST Command listing

jrc command arg1 arg2 ...

Documentation and help

help: Display a help menu or open a manual page (jrc help command-name)

doc: Open a PDF manual

version: Display the version number and the last updated date

about: Display about information

wiki: Open a JRCLUST Wiki on GitHub or open a specific topic (jrc wiki command-name)

wiki-download: Download the JRCLUST Wiki on GitHub to ./wiki/'

issue: Post an issue at GitHub (log-in with your GitHub account)

Main commands

edit: Edit the .prm file (P) that a user is currently working on

clear: Clear cached memory (jrc clear) or previously generated output (jrc clear myparam.prm)

spikesort: Run detect spike, sort spike, auto-merging

detect: Run detect spike and save spike waveforms (_spkwav.jrc, _spkraw.jrc), feature values (_spkfet.jrc), and the rest (_jrc.mat)

sort: Run sort spike, auto-merging (after detect spike) and save S_clu struct in _jrc.mat

auto: auto-merge clusters after sorting

download: Download sample data

probe: Plot a probe layout and channel and site numbers

makeprm: Create a new parameter file based on the default template file (default.prm) and probe file

traces: Plot traces

describe: Display information about the dataset

manual: Run the manual clustering GUI

auto-manual: Run the auto clustering and do the manual clustering next

plot-activity: Show firing rate as a function of time and depth

verify: Compares against ground truth file (_gt.mat)

drift: Plot drift view

plot-rd: Rho vs. Delta plot used in DPCLUS clustering (Rodriguez-Laio)

batch: Batch process list of .prm files

Import and export

export: Export the Master struct (S0) to the Workspace, which is also saved _jrc.mat output file. (see Input and output files.

export-csv: Export clustered information to a .csv file (spike time, cluster #, max site#)

export-quality: Export the unit quality information to a .csv file (ends with "_quality.csv")

export-jrc1: Export to version 1 format (write to _evt.mat and _clu.mat)

import-jrc1: Import from version 1 format

export-imec-sync: Export Sync channel (uint16) to the workspace (vnSync)

export-wav: Export the entire raw traces (mnWav) to the Workpace

export-spkwav: Export spike waveforms organized by clusters to the Workspace

export-spk: Export spike waveforms to the Workspace, sorted by the time of spike

export-spkamp: Export spike amplitudes to the Workspace

export-fet: Export feature matrix (trFet) and sites (miFet_sites) to the Workspace

export-prm: Export complete list of parameters to a new file

import-intan: Import from intan recordings, which saved each channel as -A###.dat file in int16 format

import-nsx: Imports Neuroshare format and export the analog channels to .bin file

import-lfp: save LFP (local field potential) data by subsampling the raw waveform.

Sorting multiple recordings together

dir: List all recording files to be clustered together (csFile_merge)

traces: List all recording files and select which one to display

traces: Direcly specify the file number to display

Deployment

git-pull: Get the latest version from git or revert to a specific version.
update: Update code by copying from the Dropbox location ("path_dropbox" must be specified in user.cfg)
unit-test: Run a suite of unit test.
install: Install JRCLUST by compiling CUDA and Kilosort
compile: Recompile CUDA codes (.cu) to .ptx file