Function listing

Spike sorting

• makeprm_(): Create a new parameter file. Called by "jrc makeprm myrecording.bin myprobe.prb".
• clear_(): Clear memory used by JRCLUST. Called by "jrc clear" or "jrc clear myparam.prm"
• edit_(): Edit .prm file. Called by "jrc edit myparam.prm".
• detect_(): Spike detection and feature extraction. Called by "jrc detect myparam.prm"
• auto_(): Post-cluster automated merging. Called by "jrc auto myparam.prm".
• describe_(): Describe the clustered data. Called by "jrc describe myparam.prm".
• sort_(): Cluster spikes. Called by "jrc sort myparam.prm"

Installation

• compile_cuda_(): Compile CUDA codes.
• compile_ksort_(): Compile Kilosort codes.
• install_(): Install JRCLUST and compile C codes.

Documentation and help functions

• wiki_(): Open a Github Wiki page. Called by "jrc wiki" or "jrc wiki command page_name".
• wiki_download_(): Download the entire Github wiki page. Called by "jrc wiki-download".
• doc_(): Open a PDF manual ("JRCLUST manual.pdf"). Called by "jrc doc". To be removed since Github Wiki contains the latest documentation.
• help_(): Print a help text. Called by "jrc help"

Batch process

• batch_(): Batch process. Called by "jrc batch mylist.batch".
• batch_mat_(): Batch process a .mat file containing .
• batch_plot_(): Plot spiking activities from multiple sessions. Called by "jrc batch-plot mylist.batch".
• batch_verify_(): Batch process and verify ground truth.
• dir_files_(): Find list of files that matches the wild card. Called by "jrc dir e:\myfiles*.bin".

Deployment

• update_(): Download the latest version by copying from the local Dropbox folder location. Called by "jrc download". Dropbox location must be specified in "user.cfg\path_dropbox".
• jrc_version_(): Display JRCLUST version number and last updated date. Called by "jrc version".
• about_(): Display version, author, and requirements. Called by "jrc about".
• git_pull_(): Download the latest version from Github. Called by "jrc git-pull" or "jrc git-pull version_name".
• disp_dependencies_(): Display code and toolbox dependencies. Called by "jrc dependencies".
• download_(): Download sample data. Called by "jrc download sample".
• issue_(): Leave an issue on Github. Called by "jrc issue"

GUI functions

• traces_(): Plot traces GUi. Called by "jrc traces myparam.prm".
• plot_drift_(): Plot spike position vs. time. Called by "jrc drift myparam.prm".
• plot_rd_(): Plot Rho vs. Delta plot (Rodriguez-Laio). Called by "jrc plot-rd".
• probe_(): Plot probe layout. Called by "jrc probe myprobe.prb".
• preview_(): preview GUI. Called by "jrc preview myparam.prm".
• manual_(): manual sorting GUI. Called by "jrc manual myparam.prm"
• plot_activity_(): Plot activity rate vs. time. Called by "jrc plot-activity myparam.prm".
• gui_(): Launch a main GUI. Called by "jrc gui".

Developer's functions

• validate_(): Ground-truth validation function. Called by "jrc validate myparam.rpm".
• test_(): Test an internal function. See jrc3_test.m.
• traces_test_(): Test "traces" GUI.
• commit_(): commit the code (developer use only)
• call_(): Call internal functions within jrc3. Called by "jrc3('call_', 'func_name_', nOutput)"
• manual_test_(): Automated testing for manual GUI
• unit_test_(): Launch automated unit test. Called by "jrc unit-test".
• gui_test_():

Other spike sorting

• kilosort_(): Run Kilosort. Called by "jrc kilosort myparam.prm".

Export

• assignWorkspace_(): assign a variable to workspace. Called by "jrc export var_name".
• export_(): Called by "jrc export".
• export_csv_(): Export cluster info to csv format. Called by "jrc export-csv myparam.prm".
• export_fet_(): Export spike features to the workspace.
• export_imec_sync_():
• export_jrc1_():
• export_prm_():
• export_spkamp_():
• export_spkwav_():

Import

• import_gt_silico_():
• import_h5_():
• import_intan_():
• import_jrc1_():
• import_ksort_():
• import_nsx_():
• import_silico_():
• import_tsf_():

Utility functions

• contains_():
• get0_:
• is_detected_():
• is_sorted_():
• loadParam_():
• load_bin_():
• load_file_():
• load_nsx_():
• matchFileExt_():
• nsx_info_():
• setpath_():

find_site_spk23_ mn2tn_wav_spk2_ disp_cs_ find_prb_ jrcpath_ keyPressFcn_Fig_traces_ str_toggle_ key_modifier_ spk_pos_ trWav2fet_cov_ spkwav_car_ tr_sort_ref_ mr2vr_sub2ind_ mem_max_ plan_load_ setlim_ load_file_preview_ load_file_ get_ loadParam_ calc_maxSite_ get_filter_ spikeMerge_ spikeMerge_single_ findNearSite_ car_reject_ expand_vr_ find_peak_ cell2mat_ findRange_ centroid_mr_ fet2clu_ partition_vi_ eucl2_dist_ cluster_spacetime_ cuda_rho_ cuda_delta_ compute_dc2_ quantile_ fet12_site_ fet12_site_1_ validate_ load_gt_ gt2spk_ sgfilt4_ sgfilt_init_ mr2rms_ post_merge_

Struct

struct_get_ remove_struct_ write_struct_

File handling

fopen_ read_cfg_ load_cached_ load_prb_ search_file_ subsDir_ write_bin_ load_bin_multi_

GUI support

change_amp_