Command line interface

Usage

jrc command arg1 arg2 ...

• jrc.m function calls the latest JRCLUST version (currently jrc3.m).
• You can also explicitly state the version number for JRCLUST (e.g. jrc3 command ...)

Documentation and help

• jrc help: Display a help menu
• jrc doc: Open a help document (pdf)
• jrc version: Display the version number and the updated date
• jrc about: Display about information
• jrc which: Display the file path for the jrclust code called
• jrc wiki: Open a JRCLUST Wiki on GitHub
• jrc wiki-download: Download the JRCLUST Wiki on GitHub to ./wiki/
• jrc issue: Post an issue at GitHub (log-in with your GitHub account)

Main commands

• jrc edit (myparam.prm): Edit .prm file currently working on
• jrc setprm myparam.prm: Select a .prm file to use
• jrc clear: Clear cache
• jrc clear myparam.prm: Delete previous results (files: _jrc.mat, _spkwav.jrc, _spkraw.jrc, _spkfet.jrc)
• jrc spikesort myparams.prm: Run the whole suite (spike detection and clustering)
• jrc detect myparams.prm: Run spike detection and extract spike waveforms
  • Output files: _jrc.mat, _spkwav.jrc (filtered spike waveforms), _spkraw.jrc (raw spike waveforms), _spkfet.jrc (features)
• jrc sort myparams.prm: Cluster spikes (after spike detection). "_jrc.mat" file gets updated with S_clu field.
• jrc auto myparams.prm: Recluster spikes after updating post-clustering paramters
• jrc download sample: Download sample data from Neuropix phase 2 probe
• jrc probe {myprobe.prb, myparams.prm}: Plot probe layout
• jrc makeprm myrecording.bin myprobe.prb: Create a new parameter file based on the default template file (default.prm) and probe file
• jrc makeprm myrecording.bin myprobe.prb mytemplate.prm: Create a new parameter file based on the specified template file and probe file
• jrc traces myparams.prm: Displays raw trace
• jrc describe myparams.prm: Display information about a clu dataset
• jrc manual myparams.prm: Run the manual clustering GUI
• jrc auto-manual myparams.prm: Run the auto clustering and do the manual clustering next
• jrc plot-activity myparams.prm: Show firing rate as a function of time and depth
• jrc verify myparams.prm: Compares against ground truth file (_gt.mat)
• jrc drift myparams.prm: Visualize the probe drift
• jrc plot-rd myparams.prm: Rho vs. Delta plot used in DPCLUS clustering (Rodriguez-Laio)
• jrc batch myparam.batch (command): Batch process list of prm files
• jrc batch myparam.batch template.prm: Batch process list of .bin files using a template prm file

Import and export

• jrc export myparams.prm: Export the global struct (S0) to the workspace. This is also contained in _jrc.mat output file.
• jrc export-csv myparams.prm: Export clustered information to a csv file (spike time, cluster #, max site#)
• jrc export-jrc1 myparams.prm: Export to version 1 format (write to _evt.mat and _clu.mat)
• jrc import-jrc1 myparams.prm: Import from version 1 format
• jrc export-imec-sync myparams.prm: Export Sync channel (uint16) to the workspace (vnSync)
• jrc export-wav myparams.prm: Export the entire raw traces (mnWav) to the Workpace
• jrc export-spkwav myparams.prm (clu#): Export spike waveforms organized by clusters to the Workspace
• jrc export-spk myparams.prm: Export spike waveforms to the Workspace, sorted by the time of spike
• jrc export-spkamp myparams.prm (clu#): Export spike amplitudes to the Workspace
• jrc export-fet myparams.prm: Export feature matrix (trFet) and sites (miFet_sites) to the Workspace
• jrc export-prm myparams.prm (myparam_full.prm): Export complete list of parameters to a new file
  • If the second argument is omitted, the current parameter file is updated
  • If some parameter values are missing, they will be copied from the default template file (default.prm).
• jrc import-intan intanrec*.dat myprobe.prb: Import from intan recordings, which saved each channel as -A###.dat file in int16 format.
  • Output: Single .bin file that combines multiple .dat files, saved in a directory above the .dat files.
  • Output: .prm file by combining the .bin and .prb file names (e.g. binfile_prbfile.prm).
• jrc import-nsx myrec.ns5 myprobe.prb: Imports Neuroshare format and export the analog channels to .bin file.
  • Output: .prm file by combining the .bin and .prb file names (e.g. binfile_prbfile.prm).

Combine and sort multiple recordings

• jrc dir myparam.prm: List all recording files to be clustered together (csFile_merge)
• jrc traces myparam.prm: List all recording files and select which one to display
• jrc traces myparam.prm File#: Direcly specify the file number to display

Deployment

• jrc update: Update code by copying from the dropbox location (specified in user.cfg or default.cfg)
• `jrc git-pull: Update to the latest version from GitHub (valid only if installed by "git checkout" command)
• jrc git-pull version_tag: Revert to a specific release version ("version_tag") from GitHub (valid only if installed by "git checkout" command)
• jrc unit-test: Run a suite of unit teste
• jrc install: Install jrc by compiling codes
• jrc compile: Recompile CUDA code (GPU codes, *.cu)