Command line interface

Usage

jrc command arg1 arg2 ...

• jrc.m function calls the latest JRCLUST version (currently jrc3.m).
• You can also run jrc3 command ... by explicitly specifying the version number.

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)'; ' Output files: _jrc.mat';
• `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 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.';
  ' Combine .dat files to a single .bin file and saves to the directory above.'; ' Generate .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.'; ' Generates .prm file by combining the .bin and .prb file names (e.g. binfile_prbfile.prm).'; '';

Sorting multiple recordings together

• 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)';