Index

_

_apply_unit_refine_labels() (cibrrig.sorting.export_to_alf.ALFExporter method) _clean_3d_axes() (in module cibrrig.plot) _create_ax() (in module cibrrig.plot) _crop_traces() (in module cibrrig.preprocess.extract_physiology) _describe_framerate() (in module cibrrig.preprocess.extract_frame_times) _extract_ds_chan() (in module cibrrig.preprocess.nidq_utils) _get_eta_squareds() (in module cibrrig.postprocess.extract_resp_modulation) _get_phase_max() (in module cibrrig.postprocess.extract_resp_modulation) _get_phase_modulation() (in module cibrrig.postprocess.extract_resp_modulation) _get_probe_number() (in module cibrrig.archiving.ephys_data_to_alf) _get_trigger_from_SR() (in module cibrrig.preprocess.extract_physiology) _load_opto_calibration_fn() (in module cibrrig.preprocess.extract_opto_times) _log (in module cibrrig.analysis.population) (in module cibrrig.archiving.backup) (in module cibrrig.archiving.ephys_data_to_alf) (in module cibrrig.postprocess.extract_chronux) (in module cibrrig.postprocess.extract_resp_modulation) (in module cibrrig.postprocess.synchronize_sorting_to_aux) (in module cibrrig.preprocess.extract_frame_times) (in module cibrrig.preprocess.extract_opto_times) (in module cibrrig.preprocess.extract_physiology) (in module cibrrig.preprocess.extract_sync_times) (in module cibrrig.preprocess.nidq_utils) (in module cibrrig.preprocess.preproc_pipeline) (in module cibrrig.sorting.export_to_alf) (in module cibrrig.sorting.spikeinterface_ks4) (in module cibrrig.utils.alf_utils) (in module cibrrig.utils.utils) (in module cibrrig.videos)

_plot_all_planes() (in module cibrrig.videos) _plot_laser_alf() (in module cibrrig.plot) _plot_laser_intervals() (in module cibrrig.plot) _plot_laser_log() (in module cibrrig.plot) _plot_projection_line_2D() (in module cibrrig.plot) _plot_projection_line_3D() (in module cibrrig.plot) _plot_xy_plane() (in module cibrrig.videos) _remove_EKG_explicit() (in module cibrrig.preprocess.physiology) _remove_EKG_inferred() (in module cibrrig.preprocess.physiology) _setup_colorbar() (in module cibrrig.plot) _subset_raster() (in module cibrrig.analysis.population) _trim_axes() (in module cibrrig.videos)

A

add_new_column() (cibrrig.gui.InsertionTableAppBase method) add_new_row() (cibrrig.gui.InsertionTableAppBase method) add_row() (cibrrig.gui.InsertionTableAppBase method) (cibrrig.gui.NpxInsertionTableApp method) (cibrrig.gui.OptoInsertionTableApp method) adjust_chronux_phi() (in module cibrrig.postprocess.extract_chronux) ALF (cibrrig.main_pipeline.DataOrganization attribute) alf_objects (cibrrig.utils.alf_utils.Recording attribute) alf_path (cibrrig.sorting.export_to_alf.ALFExporter attribute) (cibrrig.utils.alf_utils.Recording attribute), [1]

ALFExporter (class in cibrrig.sorting.export_to_alf) AMP_THRESH (in module cibrrig.sorting.export_to_alf) AMPLITUDE_CUTOFF (in module cibrrig.sorting.export_to_alf) analog_entries (cibrrig.gui.WiringEditor attribute) analyzer (cibrrig.sorting.export_to_alf.ALFExporter attribute) apply_preprocessing() (in module cibrrig.sorting.spikeinterface_ks4) archive() (in module cibrrig.archiving.backup) ARCHIVED (cibrrig.main_pipeline.DataOrganization attribute) archiver (cibrrig.archiving.backup.RecordingInfoUI attribute), [1] Archiver (class in cibrrig.archiving.backup) AUX_KWARGS (in module cibrrig.videos)

B

ba (in module cibrrig.gui) BAKER_DEST (in module cibrrig.run_sasquatch) BAKER_DEST_RSS (in module cibrrig.run_sasquatch) bin_path (cibrrig.sorting.export_to_alf.ALFExporter attribute) binary_onsets() (in module cibrrig.preprocess.nidq_utils) binsize (cibrrig.analysis.population.Population attribute), [1]

BM_PATH (in module cibrrig.preprocess.extract_physiology), [1] brain_xyz_path (in module cibrrig.gui) breaks (cibrrig.utils.alf_utils.Recording attribute) browse_run_clicked() (cibrrig.archiving.backup.RecordingInfoUI method) browse_subjects_clicked() (cibrrig.archiving.backup.RecordingInfoUI method) burst_stats_dia() (in module cibrrig.preprocess.physiology)

C

CACHE_DIR (in module cibrrig.videos) cbins (cibrrig.analysis.population.Population attribute), [1] check_backup_flag() (in module cibrrig.archiving.ephys_data_to_alf) check_data_organization() (in module cibrrig.main_pipeline) check_is_alf() (in module cibrrig.main_pipeline) check_is_gate() (in module cibrrig.utils.utils) check_unit_refine() (in module cibrrig.main_pipeline) check_wiring() (in module cibrrig.archiving.ephys_data_to_alf) cibrrig module cibrrig.analysis module cibrrig.analysis.population module cibrrig.analysis.singlecell module cibrrig.archiving module cibrrig.archiving.backup module cibrrig.archiving.ephys_data_to_alf module cibrrig.archiving.tarball_spikeinterface module cibrrig.gui module cibrrig.main_pipeline module cibrrig.plot module cibrrig.postprocess module cibrrig.postprocess.concatenate_triggers module cibrrig.postprocess.extract_chronux module cibrrig.postprocess.extract_resp_modulation module cibrrig.postprocess.optotag module cibrrig.postprocess.synchronize_sorting_to_aux module cibrrig.preprocess module cibrrig.preprocess.compress_video module cibrrig.preprocess.extract_frame_times module cibrrig.preprocess.extract_opto_times module cibrrig.preprocess.extract_physiology module cibrrig.preprocess.extract_sync_times module cibrrig.preprocess.nidq_utils module cibrrig.preprocess.physiology module cibrrig.preprocess.preproc_pipeline module

cibrrig.run_sasquatch module cibrrig.sorting module cibrrig.sorting.export_to_alf module cibrrig.sorting.spikeinterface_ks4 module cibrrig.utils module cibrrig.utils.alf_utils module cibrrig.utils.utils module cibrrig.videos module clean_linear_radial_axis() (in module cibrrig.plot) clean_polar_axis() (in module cibrrig.plot) cli() (in module cibrrig.archiving.ephys_data_to_alf) (in module cibrrig.main_pipeline) (in module cibrrig.preprocess.preproc_pipeline) (in module cibrrig.sorting.spikeinterface_ks4) COLORS (in module cibrrig.gui) compress_ephys_files_local() (cibrrig.archiving.backup.Archiver method) compress_ephys_files_remote() (cibrrig.archiving.backup.Archiver method) compress_video_in_place() (cibrrig.archiving.backup.Archiver method) compute_avg_hr() (in module cibrrig.preprocess.physiology) compute_dia_phase() (in module cibrrig.preprocess.physiology) COMPUTE_MOTION_SI (in module cibrrig.sorting.spikeinterface_ks4) compute_obstructive_apneas() (in module cibrrig.preprocess.physiology) compute_path_lengths() (cibrrig.analysis.population.Population method) (in module cibrrig.analysis.population) compute_pre_post_raster() (in module cibrrig.postprocess.optotag) compute_projection() (cibrrig.analysis.population.Population method) compute_projection_speed() (cibrrig.analysis.population.Population method) (in module cibrrig.analysis.population) compute_raster() (cibrrig.analysis.population.Population method) compute_resp_mod() (in module cibrrig.postprocess.extract_resp_modulation) compute_sighs() (in module cibrrig.preprocess.physiology) compute_tagging_summary() (in module cibrrig.postprocess.optotag) concatenate_alf_objects() (cibrrig.utils.alf_utils.Recording method) concatenate_log() (cibrrig.utils.alf_utils.Recording method) concatenate_recording() (in module cibrrig.sorting.spikeinterface_ks4) concatenate_session() (cibrrig.utils.alf_utils.Recording method) concatenate_triggers() (cibrrig.utils.alf_utils.Recording method) CONCATENATED (cibrrig.main_pipeline.Status attribute) convert2ccf() (in module cibrrig.gui) convert_and_export() (cibrrig.gui.InsertionTableAppBase method) (cibrrig.gui.NpxInsertionTableApp method) (cibrrig.gui.OptoInsertionTableApp method) copy_binary (cibrrig.sorting.export_to_alf.ALFExporter attribute) copy_previous_row() (cibrrig.gui.InsertionTableAppBase method) copy_run_level_files() (cibrrig.archiving.backup.Archiver method) copy_sessions() (cibrrig.archiving.backup.Archiver method) copy_sessions_alf() (cibrrig.archiving.backup.Archiver method) create_dataframe() (cibrrig.gui.InsertionTableAppBase method) create_full_metrics() (cibrrig.sorting.export_to_alf.ALFExporter method) create_pca_features() (cibrrig.sorting.export_to_alf.ALFExporter method)

D

DataOrganization (class in cibrrig.main_pipeline) DEFAULT_ARCHIVE_PATH (in module cibrrig.gui) DEFAULT_IMEC (in module cibrrig.archiving.ephys_data_to_alf) DEFAULT_NIDQ (in module cibrrig.archiving.ephys_data_to_alf) DEFAULT_SESSION_PATH (in module cibrrig.archiving.backup) DEFAULT_SUBJECTS_PATH (in module cibrrig.archiving.backup) (in module cibrrig.gui)

DEFAULT_VIDEO_DIRECTORY (in module cibrrig.archiving.backup) DEFAULT_WIRING (in module cibrrig.gui) DEFAULT_WORKING_PATH (in module cibrrig.gui) delete_last_row() (cibrrig.gui.InsertionTableAppBase method) df (cibrrig.gui.InsertionTableAppBase attribute) digital_entries (cibrrig.gui.WiringEditor attribute) DirectorySelector (class in cibrrig.gui) do_correction (in module cibrrig.sorting.spikeinterface_ks4), [1]

E

ephys_files_local (cibrrig.archiving.backup.Archiver attribute), [1] ephys_files_remote (cibrrig.archiving.backup.Archiver attribute) ephys_files_target (cibrrig.archiving.backup.Archiver attribute) ERR (in module cibrrig.postprocess.extract_chronux) event_counts_per_epochs() (in module cibrrig.utils.utils) export_to_dataframe() (cibrrig.gui.InsertionTableAppBase method)

EXTENSIONS (in module cibrrig.sorting.spikeinterface_ks4) extract_breath_events() (in module cibrrig.sorting.spikeinterface_ks4) extract_hr_channel() (in module cibrrig.preprocess.nidq_utils) extract_hr_from_ekg() (in module cibrrig.preprocess.physiology) extract_tagging_from_logs() (in module cibrrig.postprocess.optotag) extract_temp() (in module cibrrig.preprocess.nidq_utils)

F

filt_int_ds_arbitrary() (in module cibrrig.preprocess.nidq_utils) filt_int_ds_dia() (in module cibrrig.preprocess.nidq_utils) from_baker() (in module cibrrig.run_sasquatch)

from_NPX() (in module cibrrig.run_sasquatch) full_archive() (cibrrig.archiving.backup.Archiver method) full_archive_with_local_compression() (cibrrig.archiving.backup.Archiver method)

G

gates (cibrrig.archiving.ephys_data_to_alf.Run attribute) gen_sbatch_script() (in module cibrrig.run_sasquatch) gen_tarball_script() (in module cibrrig.run_sasquatch) get_all_phase_curves() (in module cibrrig.analysis.singlecell) get_ap_breaks_samps() (in module cibrrig.postprocess.synchronize_sorting_to_aux) get_breaks_times() (cibrrig.utils.alf_utils.Recording method) get_camera_chans() (in module cibrrig.preprocess.extract_frame_times) get_channel_indices() (cibrrig.sorting.export_to_alf.ALFExporter method) get_ephys_files_local() (cibrrig.archiving.backup.Archiver method) get_ephys_files_remote() (cibrrig.archiving.backup.Archiver method) get_eta() (in module cibrrig.utils.utils) get_gate_number() (in module cibrrig.archiving.ephys_data_to_alf) get_gates() (cibrrig.archiving.ephys_data_to_alf.Run method) (cibrrig.gui.DirectorySelector method) (in module cibrrig.utils.utils) get_good_spikes() (in module cibrrig.analysis.population) (in module cibrrig.utils.utils) get_headers() (cibrrig.gui.InsertionTableAppBase method) (cibrrig.gui.OptoInsertionTableApp method) get_hr_from_dia() (in module cibrrig.preprocess.physiology) get_insertion_types() (cibrrig.gui.InsertionTableAppBase method) (cibrrig.gui.NpxInsertionTableApp method) (cibrrig.gui.OptoInsertionTableApp method)

get_insertions() (cibrrig.gui.InsertionTableAppBase method) get_laser_chans() (in module cibrrig.preprocess.extract_opto_times) get_lfp_recording() (cibrrig.sorting.export_to_alf.ALFExporter method) get_opto_df() (in module cibrrig.preprocess.extract_opto_times) get_opto_df_digital() (in module cibrrig.preprocess.extract_opto_times) get_opto_file() (cibrrig.gui.OptoFileFinder method) get_output_wiring() (cibrrig.gui.WiringEditor method) get_paths() (cibrrig.gui.DirectorySelector method) get_pct_diff() (in module cibrrig.utils.utils) get_phase_curve() (in module cibrrig.analysis.singlecell) get_record_date() (cibrrig.archiving.backup.Archiver method) (in module cibrrig.archiving.ephys_data_to_alf) get_session_info() (cibrrig.gui.DirectorySelector method) get_sessions_local() (cibrrig.archiving.backup.Archiver method) get_status() (in module cibrrig.main_pipeline) get_tip() (in module cibrrig.gui) get_trig_string() (in module cibrrig.preprocess.nidq_utils) get_triggers() (in module cibrrig.preprocess.nidq_utils) get_tvec() (in module cibrrig.preprocess.nidq_utils) get_tvec_from_fn() (in module cibrrig.preprocess.nidq_utils) get_tvec_from_SR() (in module cibrrig.preprocess.nidq_utils) get_vector_means() (in module cibrrig.postprocess.extract_resp_modulation) get_videos_in_sessions() (cibrrig.archiving.backup.Archiver method) guess_subject_ID() (cibrrig.archiving.backup.Archiver method)

H

has_audio (cibrrig.archiving.backup.Archiver attribute) has_brainbox (in module cibrrig.plot) has_imec (cibrrig.archiving.backup.Archiver attribute) has_insertions (cibrrig.archiving.backup.Archiver attribute) has_log (cibrrig.archiving.backup.Archiver attribute) has_nidq (cibrrig.archiving.backup.Archiver attribute)

has_notes (cibrrig.archiving.backup.Archiver attribute) has_ssm (cibrrig.analysis.population.Population attribute), [1] has_video (cibrrig.archiving.backup.Archiver attribute) HELENS_DEST (in module cibrrig.run_sasquatch) HISTORY_KWARGS (in module cibrrig.videos) HUGGING_FACE_LOCAL (in module cibrrig.sorting.export_to_alf)

I

improve_opto_log() (cibrrig.utils.alf_utils.Recording method) infer_num_probes() (cibrrig.gui.DirectorySelector method) init_ui() (cibrrig.archiving.backup.RecordingInfoUI method) (cibrrig.gui.DirectorySelector method)

initUI() (cibrrig.gui.WiringEditor method) insertion2IBL() (in module cibrrig.gui) INSERTION_TYPES (in module cibrrig.gui) InsertionTableAppBase (class in cibrrig.gui)

J

job_kwargs (cibrrig.sorting.export_to_alf.ALFExporter attribute) (in module cibrrig.sorting.spikeinterface_ks4)

job_params (in module cibrrig.run_sasquatch)

K

keep_raw (cibrrig.archiving.backup.Archiver attribute), [1]

kstest_optotag() (in module cibrrig.postprocess.optotag)

L

label_sighs() (in module cibrrig.preprocess.extract_physiology) LAMBDA_IBL (in module cibrrig.gui) laser_colors (in module cibrrig.plot) list_all_alf_objects() (cibrrig.utils.alf_utils.Recording method) load_csv() (cibrrig.gui.InsertionTableAppBase method) load_dia_emg() (in module cibrrig.preprocess.nidq_utils) load_ds_pdiff() (in module cibrrig.preprocess.nidq_utils)

load_mmap() (in module cibrrig.preprocess.nidq_utils) load_notes() (cibrrig.gui.NotesDialog method) load_opto_calibration() (in module cibrrig.preprocess.extract_opto_times) load_rslds() (cibrrig.analysis.population.Population method) load_spikes() (cibrrig.utils.alf_utils.Recording method) local_run_path (cibrrig.gui.DirectorySelector attribute), [1] log_elapsed_time() (in module cibrrig.sorting.spikeinterface_ks4)

M

main() (in module cibrrig.archiving.backup) (in module cibrrig.archiving.tarball_spikeinterface) (in module cibrrig.main_pipeline) (in module cibrrig.postprocess.concatenate_triggers) (in module cibrrig.postprocess.extract_chronux) (in module cibrrig.postprocess.extract_resp_modulation) (in module cibrrig.postprocess.optotag) (in module cibrrig.postprocess.synchronize_sorting_to_aux) (in module cibrrig.preprocess.compress_video) (in module cibrrig.preprocess.extract_frame_times) (in module cibrrig.preprocess.extract_opto_times) (in module cibrrig.preprocess.extract_physiology) (in module cibrrig.preprocess.extract_sync_times) (in module cibrrig.run_sasquatch) make_aux_raster_projection_with_stims() (in module cibrrig.videos) make_plots() (in module cibrrig.postprocess.optotag) make_pre_post_trial() (in module cibrrig.utils.utils) make_projection() (in module cibrrig.videos) make_rec_date_target() (cibrrig.archiving.backup.Archiver method) make_rotating_projection() (in module cibrrig.videos) MAP_TO_INTERVALS (in module cibrrig.preprocess.extract_sync_times) mark_backup() (cibrrig.archiving.backup.Archiver method) MIN_PCT_TAGS_WITH_SPIKES (in module cibrrig.postprocess.optotag) MIN_SPIKES (in module cibrrig.sorting.export_to_alf) module cibrrig cibrrig.analysis cibrrig.analysis.population cibrrig.analysis.singlecell cibrrig.archiving cibrrig.archiving.backup cibrrig.archiving.ephys_data_to_alf cibrrig.archiving.tarball_spikeinterface cibrrig.gui cibrrig.main_pipeline cibrrig.plot cibrrig.postprocess cibrrig.postprocess.concatenate_triggers cibrrig.postprocess.extract_chronux cibrrig.postprocess.extract_resp_modulation cibrrig.postprocess.optotag cibrrig.postprocess.synchronize_sorting_to_aux cibrrig.preprocess cibrrig.preprocess.compress_video cibrrig.preprocess.extract_frame_times cibrrig.preprocess.extract_opto_times cibrrig.preprocess.extract_physiology cibrrig.preprocess.extract_sync_times cibrrig.preprocess.nidq_utils cibrrig.preprocess.physiology cibrrig.preprocess.preproc_pipeline cibrrig.run_sasquatch cibrrig.sorting cibrrig.sorting.export_to_alf cibrrig.sorting.spikeinterface_ks4 cibrrig.utils cibrrig.utils.alf_utils cibrrig.utils.utils cibrrig.videos

MOTION_PRESET (in module cibrrig.sorting.spikeinterface_ks4) move_gates() (cibrrig.archiving.ephys_data_to_alf.Run method) move_motion_info() (in module cibrrig.sorting.spikeinterface_ks4) move_ni_files() (in module cibrrig.archiving.ephys_data_to_alf) move_run_files() (cibrrig.archiving.ephys_data_to_alf.Run method) move_sorted_to_alf() (in module cibrrig.sorting.spikeinterface_ks4)

N

n_gates (cibrrig.gui.InsertionTableAppBase attribute) N_JOBS (in module cibrrig.sorting.spikeinterface_ks4) n_recs (cibrrig.utils.alf_utils.Recording attribute), [1] name (cibrrig.gui.InsertionTableAppBase attribute) ndims (cibrrig.analysis.population.Population attribute), [1] ni_fns (cibrrig.utils.alf_utils.Recording attribute), [1]

no_gui() (in module cibrrig.archiving.backup) NONE (cibrrig.main_pipeline.Status attribute) notes_fn (cibrrig.gui.NotesDialog attribute) NotesDialog (class in cibrrig.gui) NpxInsertionTableApp (class in cibrrig.gui) num_sessions (cibrrig.archiving.backup.Archiver attribute), [1]

O

OCCIPITAL_APEX (in module cibrrig.gui) OCCIPITAL_NADIR (in module cibrrig.gui) OMIT_SIGNALS (in module cibrrig.preprocess.extract_sync_times) on_analog_value_changed() (cibrrig.gui.WiringEditor method) on_digital_value_changed() (cibrrig.gui.WiringEditor method) open_file_dialog() (cibrrig.archiving.backup.RecordingInfoUI method)

opto_file (cibrrig.gui.OptoFileFinder attribute), [1] opto_file_selected (cibrrig.gui.OptoFileFinder attribute) OPTO_OBJECTS (in module cibrrig.sorting.spikeinterface_ks4) OptoFileFinder (class in cibrrig.gui) OptoInsertionTableApp (class in cibrrig.gui) output_wiring (cibrrig.gui.WiringEditor attribute) overall_notes_text (cibrrig.gui.NotesDialog attribute)

P

parse_opto_log() (in module cibrrig.utils.utils) pca (cibrrig.analysis.population.Population attribute), [1] PITCH_CORRECTION (in module cibrrig.gui) plot_2D_projection() (in module cibrrig.plot) plot_3D_projection() (in module cibrrig.plot) plot_by_speed() (cibrrig.analysis.population.Population method) plot_driftmap_with_trace() (in module cibrrig.plot) plot_insertion_layout() (in module cibrrig.gui) plot_laser() (in module cibrrig.plot) plot_most_likely_dynamics() (in module cibrrig.plot) plot_most_likely_dynamics_3D() (in module cibrrig.plot) plot_motion() (in module cibrrig.sorting.spikeinterface_ks4) plot_peth_and_raster() (in module cibrrig.plot) plot_polar_average() (in module cibrrig.plot) plot_probe_insertion() (in module cibrrig.gui) plot_probe_insertion_ibl() (in module cibrrig.gui) plot_probe_insertion_urchin() (in module cibrrig.gui) plot_projection() (cibrrig.analysis.population.Population method) (in module cibrrig.plot)

plot_projection_line() (cibrrig.analysis.population.Population method) (in module cibrrig.plot) plot_projection_line_multicondition() (in module cibrrig.plot) plot_QC() (in module cibrrig.preprocess.preproc_pipeline) plot_reset_curve() (in module cibrrig.plot) plot_sweeps() (in module cibrrig.plot) plot_vectorfield() (cibrrig.analysis.population.Population method) populate_table() (cibrrig.gui.InsertionTableAppBase method) Population (class in cibrrig.analysis.population) POSSIBLE_WIRINGS (in module cibrrig.gui) postprocess_sorting() (in module cibrrig.sorting.spikeinterface_ks4) PREPROC (cibrrig.main_pipeline.Status attribute) preprocess_pca() (in module cibrrig.analysis.population) process_rec() (in module cibrrig.preprocess.extract_opto_times) process_rec_extracted() (in module cibrrig.preprocess.extract_frame_times) process_rec_ni() (in module cibrrig.preprocess.extract_frame_times) project_pca() (in module cibrrig.analysis.population) projection (cibrrig.analysis.population.Population attribute), [1] PROJECTION_KWARGS (in module cibrrig.videos) projection_speed (cibrrig.analysis.population.Population attribute), [1]

R

raster (cibrrig.analysis.population.Population attribute), [1] raster_smoothed (cibrrig.analysis.population.Population attribute), [1] rasterize() (in module cibrrig.analysis.population) RATIO (in module cibrrig.postprocess.optotag) RAW (cibrrig.main_pipeline.DataOrganization attribute) raw_ephys_path (cibrrig.utils.alf_utils.Recording attribute), [1] record_date (cibrrig.archiving.backup.Archiver attribute) Recording (class in cibrrig.utils.alf_utils) RecordingInfoUI (class in cibrrig.archiving.backup) remap_time_basis() (in module cibrrig.utils.utils) remote_archive_path (cibrrig.gui.DirectorySelector attribute), [1] remote_working_path (cibrrig.gui.DirectorySelector attribute), [1] remove_and_interpolate() (in module cibrrig.sorting.spikeinterface_ks4) remove_backup_flag() (in module cibrrig.archiving.ephys_data_to_alf) remove_EKG() (in module cibrrig.preprocess.physiology) remove_empty_folders() (in module cibrrig.run_sasquatch) remove_opto_artifact (cibrrig.gui.DirectorySelector attribute), [1] remove_opto_artifacts() (in module cibrrig.sorting.spikeinterface_ks4) rename_and_move_video() (in module cibrrig.archiving.ephys_data_to_alf) rename_flat_probe() (in module cibrrig.archiving.ephys_data_to_alf) rename_nested_probes() (in module cibrrig.archiving.ephys_data_to_alf) rename_probe_folders() (in module cibrrig.archiving.ephys_data_to_alf) rename_session() (in module cibrrig.archiving.ephys_data_to_alf) replace_timeaxis_with_scalebar() (in module cibrrig.plot) reshape_chronux_output() (in module cibrrig.postprocess.extract_chronux) RESP_MOD_COMPUTED (cibrrig.main_pipeline.Status attribute) Run (class in cibrrig.archiving.ephys_data_to_alf) run() (cibrrig.sorting.export_to_alf.ALFExporter method) (in module cibrrig.archiving.ephys_data_to_alf) (in module cibrrig.main_pipeline) (in module cibrrig.preprocess.extract_frame_times) (in module cibrrig.preprocess.extract_opto_times) (in module cibrrig.preprocess.extract_physiology) (in module cibrrig.preprocess.extract_sync_times) (in module cibrrig.preprocess.preproc_pipeline) (in module cibrrig.sorting.spikeinterface_ks4)

run_chronux() (in module cibrrig.postprocess.extract_chronux) run_ephys_qc (cibrrig.gui.DirectorySelector attribute), [1] run_ephys_qc_session() (in module cibrrig.preprocess.preproc_pipeline) run_file() (in module cibrrig.preprocess.extract_frame_times) (in module cibrrig.preprocess.extract_opto_times) run_one() (in module cibrrig.preprocess.extract_physiology) run_path (cibrrig.archiving.backup.Archiver attribute) (cibrrig.archiving.ephys_data_to_alf.Run attribute), [1] run_path_source (cibrrig.archiving.backup.Archiver attribute) run_phy_probe() (in module cibrrig.postprocess.extract_chronux) run_probe() (in module cibrrig.postprocess.extract_chronux) (in module cibrrig.postprocess.extract_resp_modulation) (in module cibrrig.postprocess.optotag) (in module cibrrig.sorting.spikeinterface_ks4) run_salt() (in module cibrrig.postprocess.optotag) run_session() (in module cibrrig.postprocess.extract_chronux) (in module cibrrig.postprocess.extract_resp_modulation) (in module cibrrig.postprocess.optotag) (in module cibrrig.postprocess.synchronize_sorting_to_aux) (in module cibrrig.preprocess.extract_frame_times) (in module cibrrig.preprocess.extract_opto_times) runQC() (in module cibrrig.preprocess.preproc_pipeline)

S

SALT_P_CUTOFF (in module cibrrig.postprocess.optotag) sanity_check_plots() (in module cibrrig.postprocess.extract_resp_modulation) SASQUATCH_WORKING_DIR (in module cibrrig.run_sasquatch) save_depths() (cibrrig.sorting.export_to_alf.ALFExporter method) save_extracted_waveforms() (cibrrig.sorting.export_to_alf.ALFExporter method) save_fn (cibrrig.gui.InsertionTableAppBase attribute) save_notes() (cibrrig.gui.NotesDialog method) save_templates() (cibrrig.sorting.export_to_alf.ALFExporter method) save_values() (cibrrig.gui.WiringEditor method) scale_raster() (in module cibrrig.analysis.population) SCRATCH_NAME (in module cibrrig.sorting.spikeinterface_ks4) select_button (cibrrig.gui.OptoFileFinder attribute) select_file() (cibrrig.gui.OptoFileFinder method) select_local_run_path() (cibrrig.gui.DirectorySelector method) select_remote_archive_path() (cibrrig.gui.DirectorySelector method) select_remote_working_path() (cibrrig.gui.DirectorySelector method) session_list_source (cibrrig.archiving.backup.Archiver attribute) session_path (cibrrig.utils.alf_utils.Recording attribute), [1] set_clicked() (cibrrig.archiving.backup.RecordingInfoUI method) set_status() (in module cibrrig.main_pipeline) set_subjects_path() (cibrrig.archiving.backup.Archiver method) setup_logging() (in module cibrrig.main_pipeline) si_motion() (in module cibrrig.sorting.spikeinterface_ks4)

sigma (cibrrig.analysis.population.Population attribute), [1] sim_rslds() (cibrrig.analysis.population.Population method) skip_file() (cibrrig.gui.OptoFileFinder method) SLIDING_RP (in module cibrrig.sorting.export_to_alf) smooth_raster() (in module cibrrig.analysis.population) SORTER (in module cibrrig.sorting.spikeinterface_ks4) sorter_params (in module cibrrig.sorting.spikeinterface_ks4) sparse_templates (cibrrig.sorting.export_to_alf.ALFExporter attribute) spike_clusters (cibrrig.analysis.population.Population attribute), [1] spike_times (cibrrig.analysis.population.Population attribute), [1] SPIKESORTED (cibrrig.main_pipeline.Status attribute) split_shanks_and_spatial_filter() (in module cibrrig.sorting.spikeinterface_ks4) Status (class in cibrrig.main_pipeline) subject_ID (cibrrig.archiving.backup.Archiver attribute), [1] subject_path_target (cibrrig.archiving.backup.Archiver attribute) subjects_path (cibrrig.archiving.backup.Archiver attribute) subjects_path_target (cibrrig.archiving.backup.Archiver attribute) submit() (cibrrig.gui.DirectorySelector method) (cibrrig.gui.NotesDialog method) sync2alf() (in module cibrrig.preprocess.extract_sync_times) sync_spikes() (in module cibrrig.postprocess.synchronize_sorting_to_aux) sync_var() (cibrrig.analysis.population.Population method) SYNCHRONIZED (cibrrig.main_pipeline.Status attribute)

T

t0 (cibrrig.analysis.population.Population attribute), [1] table (cibrrig.gui.InsertionTableAppBase attribute) TAPERS (in module cibrrig.postprocess.extract_chronux) tbins (cibrrig.analysis.population.Population attribute), [1] templates (cibrrig.sorting.export_to_alf.ALFExporter attribute) TEMPORAL_FEATURES (in module cibrrig.utils.alf_utils) test_unit_refine_model_import() (in module cibrrig.sorting.export_to_alf) testing (cibrrig.sorting.export_to_alf.ALFExporter attribute) text_fields (cibrrig.gui.NotesDialog attribute) tf (cibrrig.analysis.population.Population attribute), [1]

time_to_interval() (in module cibrrig.utils.utils) title (cibrrig.gui.WiringEditor attribute) to_csv() (cibrrig.gui.InsertionTableAppBase method) today_path (cibrrig.archiving.backup.Archiver attribute) today_path_target (cibrrig.archiving.backup.Archiver attribute) toggle_remove_opto_artifact() (cibrrig.gui.DirectorySelector method) TRAIL_KWARGS (in module cibrrig.videos) transform (cibrrig.analysis.population.Population attribute), [1] transform_rslds() (cibrrig.analysis.population.Population method) trim_yscale_to_lims() (in module cibrrig.plot)

U

update_angles() (cibrrig.gui.InsertionTableAppBase method) update_has_video_state() (cibrrig.archiving.backup.RecordingInfoUI method)

USE_MOTION_SI (in module cibrrig.sorting.spikeinterface_ks4) used_sparsity (cibrrig.sorting.export_to_alf.ALFExporter attribute)

V

validate_intervals() (in module cibrrig.utils.utils)

video_files (cibrrig.archiving.backup.Archiver attribute), [1] video_path_target (cibrrig.archiving.backup.Archiver attribute)

W

WAVELENGTH_COLOR (in module cibrrig.postprocess.optotag) weighted_histogram() (in module cibrrig.utils.utils)

WIN (in module cibrrig.postprocess.extract_chronux) WiringEditor (class in cibrrig.gui) write_params() (cibrrig.sorting.export_to_alf.ALFExporter method)