Index

A

a_little_spike() (in module ibllib.tests.test_ephys) acorr() (in module brainbox.singlecell) acquisition_description_legacy_session() (in module ibllib.pipes.dynamic_pipeline) acronym (BrainRegions attribute) (FranklinPaxinosRegions attribute) add_lines() (DefaultPlot method) (in module brainbox.plot_base) add_training_lines() (in module ibllib.pipes.training_status) adjust_extremes_linear() (EphysAlignment method) adjust_extremes_uniform() (EphysAlignment static method) aggregate_device() (in module ibllib.io.session_params) align_all_trials() (MotionAlignment method) align_motion() (MotionAlignment method) align_with_audio() (in module ibllib.io.extractors.camera) AlignmentQC (class in ibllib.qc.alignment_qc) allen_gene_expression() (in module ibllib.atlas.genes) AllenAtlas (class in ibllib.atlas.atlas)

amp_heatmap() (in module brainbox.plot) annotate_swanson() (in module ibllib.atlas.flatmaps) ApPlots (class in ibllib.plots.figures) apply_sync() (in module ibllib.ephys.sync_probes) arrange_channels2banks() (in module brainbox.plot_base) arrange_into_regions() (EphysAlignment static method) as_globus_path() (in module ibllib.io.globus) assert_expected() (Task method) assert_expected_inputs() (Task method) assert_expected_outputs() (Task method) assert_valid_label() (in module ibllib.io.video) assign_task() (in module ibllib.pipes) atlas (SpikeSortingLoader attribute) attribute_times() (in module ibllib.io.extractors.camera) AudioCompress (class in ibllib.pipes.audio_tasks) AudioSync (class in ibllib.pipes.audio_tasks) AudioTask (class in ibllib.pipes.base_tasks) average_drift() (in module brainbox.metrics.single_units)

B

backend (TestCameraQC attribute) backup_session() (in module ibllib.pipes.misc) BadChannelsAp (class in ibllib.plots.figures) BaseBpodTrialsExtractor (class in ibllib.io.extractors.base) BaseExtractor (class in ibllib.io.extractors.base) bbox (DlcQC attribute) behavior_exists() (in module ibllib.pipes.misc) BehaviourPlots (class in ibllib.plots.figures) beta (Insertion attribute) bin_spikes() (in module brainbox.processing) (in module brainbox.singlecell) bin_spikes2D() (in module brainbox.singlecell) bin_spikes_trials() (in module brainbox.population.cca) bincount2D() (in module brainbox.processing) bpod_fields (FpgaTrials attribute) bpod_rsync_fields (FpgaTrials attribute) bpod_trials (BaseBpodTrialsExtractor attribute) BrainAtlas (class in ibllib.atlas.atlas) brainbox module brainbox.atlas module brainbox.behavior module brainbox.behavior.dlc module brainbox.behavior.pyschofit module brainbox.behavior.training module brainbox.behavior.wheel module brainbox.core module brainbox.ephys_plots module brainbox.io module brainbox.io.one module brainbox.io.spikeglx module brainbox.lfp module brainbox.metrics module brainbox.metrics.electrode_drift module brainbox.metrics.single_units module brainbox.plot module brainbox.plot_base module brainbox.population module

brainbox.population.cca module brainbox.population.decode module brainbox.processing module brainbox.quality module brainbox.quality.lfp_qc module brainbox.quality.permutation_test module brainbox.singlecell module brainbox.spike_features module brainbox.task module brainbox.task.closed_loop module brainbox.task.passive module brainbox.task.trials module brainbox.tests module brainbox.tests.test_behavior module brainbox.tests.test_cca module brainbox.tests.test_io module brainbox.tests.test_metrics module brainbox.tests.test_passive module brainbox.tests.test_plot_base module brainbox.tests.test_population module brainbox.tests.test_processing module brainbox.tests.test_singlecell module brainbox.tests.test_task module brainbox.tests.test_trials module brainbox.tests.test_video module brainbox.video module BrainCoordinates (class in ibllib.atlas.atlas) BrainRegions (class in ibllib.atlas.regions) butter_filter() (in module brainbox.lfp)

C

calculate_peths() (in module brainbox.singlecell) CameraQC (class in ibllib.qc.camera) CameraQCCamlog (class in ibllib.qc.camera) CameraTimestampsBpod (class in ibllib.io.extractors.camera) CameraTimestampsCamlog (class in ibllib.io.extractors.camera) CameraTimestampsFPGA (class in ibllib.io.extractors.camera) cart2sph() (in module ibllib.atlas.atlas) ccf2xyz() (AllenAtlas method) channel_locations_interpolation() (in module brainbox.io.one) check_audio_pre_trial() (in module ibllib.qc.task_metrics) check_brightness() (CameraQC method) check_camera_times() (CameraQC method) (CameraQCCamlog method) check_correct_trial_event_sequence() (in module ibllib.qc.task_metrics) check_create_raw_session_flag() (in module ibllib.pipes.misc) check_detected_wheel_moves() (in module ibllib.qc.task_metrics) check_dropped_frames() (CameraQC method) check_error_trial_event_sequence() (in module ibllib.qc.task_metrics) check_errorCue_delays() (in module ibllib.qc.task_metrics) check_file_headers() (CameraQC method) check_focus() (CameraQC method) check_framerate() (CameraQC method) check_goCue_delays() (in module ibllib.qc.task_metrics) check_iti_delays() (in module ibllib.qc.task_metrics) check_lick_detection() (DlcQC method) check_mean_in_bbox() (DlcQC method) check_n_trial_events() (in module ibllib.qc.task_metrics) check_negative_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) check_nvidia_driver() (in module ibllib.misc.misc) check_paw_close_nan() (DlcQC method) check_paw_far_nan() (DlcQC method) check_pin_state() (CameraQC method) check_position() (CameraQC method) check_positive_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) check_pupil_blocked() (DlcQC method) check_pupil_diameter_snr() (DlcQC method) check_resolution() (CameraQC method) check_response_feedback_delays() (in module ibllib.qc.task_metrics) check_response_stimFreeze_delays() (in module ibllib.qc.task_metrics) check_reward_volume_set() (in module ibllib.qc.task_metrics) check_reward_volumes() (in module ibllib.qc.task_metrics) check_stimFreeze_delays() (in module ibllib.qc.task_metrics) check_stimOff_delays() (in module ibllib.qc.task_metrics) check_stimOff_itiIn_delays() (in module ibllib.qc.task_metrics) check_stimOn_delays() (in module ibllib.qc.task_metrics) check_stimOn_goCue_delays() (in module ibllib.qc.task_metrics) check_stimulus_move_before_goCue() (in module ibllib.qc.task_metrics) check_time_trace_length_match() (DlcQC method) check_timestamps() (CameraQC method) (in module ibllib.io.extractors.fibrephotometry) check_trace_all_nan() (DlcQC method) check_transfer() (in module ibllib.pipes.misc) check_trial_length() (in module ibllib.qc.task_metrics) check_up_to_date() (in module ibllib.pipes.training_status) check_wheel_alignment() (CameraQC method) check_wheel_freeze_during_quiescence() (in module ibllib.qc.task_metrics) check_wheel_integrity() (in module ibllib.qc.task_metrics) check_wheel_move_before_feedback() (in module ibllib.qc.task_metrics) check_wheel_move_during_closed_loop() (in module ibllib.qc.task_metrics) check_wheel_move_during_closed_loop_bpod() (in module ibllib.qc.task_metrics) Choice (class in ibllib.io.extractors.training_trials) ChoiceWorldTrialsBpod (class in ibllib.pipes.behavior_tasks) ChoiceWorldTrialsNidq (class in ibllib.pipes.behavior_tasks) circles() (in module ibllib.atlas.flatmaps) classify() (in module brainbox.population.decode) cleanUp() (DataHandler method) (RemoteAwsDataHandler method) (SDSCDataHandler method) (ServerGlobusDataHandler method) (Task method) cli_ask_default() (in module ibllib.pipes.misc) cli_ask_options() (in module ibllib.pipes.misc) cm_to_deg() (in module brainbox.behavior.wheel) cm_to_rad() (in module brainbox.behavior.wheel) code_to_outcome() (QC static method) coherence() (in module brainbox.lfp) collection (SpikeSortingLoader attribute) collections (SpikeSortingLoader attribute) color_cycle() (in module ibllib.plots.misc) compress() (in module ibllib.io.ffmpeg) compute() (AlignmentQC method) (HabituationQC method) (TaskQC method) compute_alignment_status() (AlignmentQC method) compute_bias_info() (in module brainbox.behavior.training) compute_boundaries() (BrainAtlas method)

compute_cluster_average() (in module brainbox.processing) compute_comparison_statistics() (in module brainbox.task.closed_loop) compute_hierarchy() (BrainRegions method) compute_labels() (in module brainbox.metrics.single_units) compute_median_reaction_time() (in module brainbox.behavior.training) compute_metrics() (SpikeSortingLoader static method) compute_n_trials() (in module brainbox.behavior.training) compute_outcome_from_extended_qc() (QC method) compute_performance() (in module brainbox.behavior.training) compute_performance_easy() (in module brainbox.behavior.training) compute_psychometric() (in module brainbox.behavior.training) compute_reaction_time() (in module brainbox.behavior.training) compute_session_duration_delay_location() (in module ibllib.pipes.training_status) compute_session_status() (TaskQC method) compute_session_status_from_dict() (TaskQC static method) compute_similarity_matrix() (AlignmentQC method) compute_surface() (BrainAtlas method) compute_training_info() (in module brainbox.behavior.training) compute_training_status() (in module ibllib.pipes.training_status) compute_volume_from_points() (in module ibllib.atlas.plots) concatenate_trials() (in module brainbox.behavior.training) confirm_ephys_remote_folder() (in module ibllib.pipes.misc) contamination() (in module brainbox.metrics.single_units) contamination_alt() (in module brainbox.metrics.single_units) ContrastLR (class in ibllib.io.extractors.biased_trials) (class in ibllib.io.extractors.training_trials) convert2dict() (DefaultPlot method) convert_pgts() (in module ibllib.time) copy() (TimeSeries method) copy_wiring_files() (in module ibllib.pipes.misc) copy_with_check() (in module ibllib.pipes.misc) coverage() (in module ibllib.pipes.histology) coverage_grid() (in module ibllib.pipes.histology) cpu (AudioCompress attribute) (AudioSync attribute) (EphysAudio attribute) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysDLC attribute) (EphysPassive attribute) (EphysPulses attribute), [1] (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (RawEphysQC attribute), [1] (SyncMtscomp attribute) (SyncPulses attribute) (Task attribute) (TrainingAudio attribute) create_alyx_probe_insertions() (in module ibllib.pipes.misc) create_alyx_tasks() (Pipeline method) create_audio_flags() (in module ibllib.io.flags) create_basic_transfer_params() (in module ibllib.pipes.misc) create_channel_dict() (in module ibllib.pipes.histology) create_compress_video_flags() (in module ibllib.io.flags) create_create_flags() (in module ibllib.io.flags) create_custom_ephys_wirings() (in module ibllib.pipes.misc) create_dataset() (FTPPatcher method) create_dlc_flags() (in module ibllib.io.flags) create_ephys_flags() (in module ibllib.pipes.misc) create_ephys_transfer_done_flag() (in module ibllib.pipes.misc) create_ephyspc_params() (in module ibllib.pipes.misc) create_extract_flags() (in module ibllib.io.flags) create_fake_alf_folder_dlc_data() (in module ibllib.tests.fixtures.utils) create_fake_complete_ephys_session() (in module ibllib.tests.fixtures.utils) create_fake_ephys_recording_bad_passive_transfer_sessions() (in module ibllib.tests.fixtures.utils) create_fake_raw_behavior_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_ephys_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_video_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_session_folder() (in module ibllib.tests.fixtures.utils) create_flags() (in module ibllib.io.flags) create_other_flags() (in module ibllib.io.flags) create_register_flags() (in module ibllib.io.flags) create_session() (RegistrationClient method) create_sessions() (RegistrationClient method) create_tasks_list_from_pipeline() (Pipeline method) create_trajectory_dict() (in module ibllib.pipes.histology) create_transfer_done_flag() (in module ibllib.pipes.misc) create_transfer_flags() (in module ibllib.io.flags) create_video_transfer_done_flag() (in module ibllib.pipes.misc) create_videopc_params() (in module ibllib.pipes.misc) criteria (TaskQC attribute) criterion_1a() (in module brainbox.behavior.training) criterion_1b() (in module brainbox.behavior.training) criterion_delay() (in module brainbox.behavior.training) criterion_ephys() (in module brainbox.behavior.training)

D

data_for_keys() (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.qc.camera) data_info (EphysSessionLoader attribute) (SessionLoader attribute) DataHandler (class in ibllib.oneibl.data_handlers) datasets (SpikeSortingLoader attribute) date2isostr() (in module ibllib.time) default_path (BaseExtractor attribute) DefaultPlot (class in brainbox.plot_base) delete_empty_folders() (in module ibllib.io.misc) delete_flags() (in module ibllib.io.flags) Density (class in ibllib.plots.misc) depth (Insertion attribute) depth() (in module brainbox.spike_features) detect_missing_histology_tracks() (in module ibllib.pipes.histology) detect_ready_tone() (in module ibllib.io.extractors.training_audio) detection() (in module ibllib.ephys.spikes)

differentiate_units() (in module brainbox.task.closed_loop) display_status() (in module brainbox.behavior.training) dlc_qc_plot() (in module ibllib.plots.figures) dlcenv (EphysDLC attribute) DlcQC (class in ibllib.qc.dlc) download_spike_sorting() (SpikeSortingLoader method) download_spike_sorting_object() (SpikeSortingLoader method) driftmap() (in module brainbox.plot) driftmap_color() (in module brainbox.plot) dset (TestAlyx2Path attribute) dstypes (CameraQC attribute) (CameraQCCamlog attribute) (DlcQC attribute) dstypes_fpga (CameraQC attribute) (CameraQCCamlog attribute) dxyz (BrainCoordinates property) DynamicTask (class in ibllib.pipes.base_tasks)

E

eid (SessionLoader attribute) (SpikeSortingLoader attribute) ensure_required_data() (CameraQC method) (CameraQCCamlog method) entry (Insertion property) ephys_bad_channels() (in module ibllib.plots.figures) EphysAlignment (class in ibllib.pipes.ephys_alignment) EphysAudio (class in ibllib.pipes.ephys_preprocessing) EphysCellsQc (class in ibllib.pipes.ephys_preprocessing) (class in ibllib.pipes.ephys_tasks) EphysCompressNP1 (class in ibllib.pipes.ephys_tasks) EphysCompressNP21 (class in ibllib.pipes.ephys_tasks) EphysCompressNP24 (class in ibllib.pipes.ephys_tasks) EphysDLC (class in ibllib.pipes.ephys_preprocessing) EphysExtractionPipeline (class in ibllib.pipes.ephys_preprocessing) EphysMtscomp (class in ibllib.pipes.ephys_preprocessing) EphysPassive (class in ibllib.pipes.ephys_preprocessing) EphysPostDLC (class in ibllib.pipes.ephys_preprocessing) EphysPulses (class in ibllib.pipes.ephys_preprocessing) (class in ibllib.pipes.ephys_tasks) EphysQC (class in ibllib.ephys.ephysqc) EphysRegisterRaw (class in ibllib.pipes.ephys_tasks) EphysSessionLoader (class in brainbox.io.one) EphysSyncPulses (class in ibllib.pipes.ephys_tasks) EphysSyncRegisterRaw (class in ibllib.pipes.ephys_tasks) EphysTask (class in ibllib.pipes.base_tasks) EphysTrials (class in ibllib.pipes.ephys_preprocessing) EphysVideoCompress (class in ibllib.pipes.ephys_preprocessing) EphysVideoSyncQc (class in ibllib.pipes.ephys_preprocessing) erf_psycho() (in module brainbox.behavior.pyschofit) erf_psycho_2gammas() (in module brainbox.behavior.pyschofit) ErrorCueTriggerTimes (class in ibllib.io.extractors.training_trials) ES_CONTINUOUS (WindowsInhibitor attribute) ES_SYSTEM_REQUIRED (WindowsInhibitor attribute) estimate_drift() (in module brainbox.metrics.electrode_drift) eval_x() (Trajectory method) eval_y() (Trajectory method)

eval_z() (Trajectory method) excise_flag_file() (in module ibllib.io.flags) execute() (in module ibllib.pipes.scan_fix_passive_files) exit_points() (Trajectory method) ExperimentDescriptionRegisterRaw (class in ibllib.pipes.base_tasks) explanation (IblError attribute) (Neuropixel3BSyncFrontsNonMatching attribute) (NvidiaDriverNotReady attribute) (SyncBpodFpgaException attribute) (SyncBpodWheelException attribute) (WidefieldWiringException attribute) extent() (BrainAtlas method) extent_flmap() (FlatMap method) extract() (BaseBpodTrialsExtractor method) (BaseExtractor method) extract_all() (in module ibllib.io.extractors.biased_trials) (in module ibllib.io.extractors.bpod_trials) (in module ibllib.io.extractors.camera) (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.io.extractors.habituation_trials) (in module ibllib.io.extractors.opto_trials) (in module ibllib.io.extractors.training_trials) (in module ibllib.io.extractors.training_wheel) extract_behaviour_sync() (in module ibllib.io.extractors.ephys_fpga) extract_camera_sync() (in module ibllib.io.extractors.camera) extract_data() (TaskQCExtractor method) extract_first_movement_times() (in module ibllib.io.extractors.training_wheel) extract_passive_periods() (in module ibllib.io.extractors.ephys_passive) extract_replay_debug() (in module ibllib.io.extractors.ephys_passive) extract_rfmapping() (in module ibllib.io.extractors.ephys_passive) extract_rmsmap() (in module ibllib.ephys.ephysqc) extract_sound() (in module ibllib.io.extractors.training_audio) extract_sync() (in module ibllib.io.extractors.ephys_fpga) extract_task_replay() (in module ibllib.io.extractors.ephys_passive) extract_timestamps() (FibrePhotometry method) extract_waveforms() (in module brainbox.io.spikeglx) extract_wheel_moves() (in module ibllib.io.extractors.training_wheel) extract_wheel_sync() (in module ibllib.io.extractors.ephys_fpga)

F

feat_vars() (in module brainbox.plot) feature2track() (EphysAlignment static method) feature2track_lin() (EphysAlignment static method) FeedbackTimes (class in ibllib.io.extractors.training_trials) FeedbackType (class in ibllib.io.extractors.training_trials) FibrePhotometry (class in ibllib.io.extractors.fibrephotometry) FibrePhotometryExtractionPipeline (class in ibllib.pipes.photometry_tasks) files (SpikeSortingLoader attribute) filter_by_trial() (in module brainbox.task.trials) filter_correct_incorrect() (in module brainbox.task.trials) filter_correct_incorrect_left_right() (in module brainbox.task.trials) filter_left_right() (in module brainbox.task.trials) filter_trials() (in module brainbox.task.trials) filter_units() (in module brainbox.processing) find_earliest_recompute_date() (in module ibllib.pipes.training_status) find_face() (CameraQC method) find_nearest() (in module ibllib.io.extractors.video_motion) find_pairs() (in module ibllib.pipes.scan_fix_passive_files) find_trial_ids() (in module brainbox.task.trials) firing_rate() (in module brainbox.plot) (in module brainbox.singlecell) firing_rate_coeff_var() (in module brainbox.metrics.single_units) firing_rate_fano_factor() (in module brainbox.metrics.single_units) fit() (Trajectory static method) fit_cca() (in module brainbox.population.cca)

FlatMap (class in ibllib.atlas.atlas) force (EphysAudio attribute) (EphysCellsQc attribute) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPassive attribute) (EphysPostDLC attribute) (EphysPulses attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (EphysVideoSyncQc attribute) (RawEphysQC attribute) (SpikeSorting attribute), [1] (Task attribute) (TrainingStatus attribute) (TrainingTrials attribute) format_date_range() (in module ibllib.time) FpgaTrials (class in ibllib.io.extractors.ephys_fpga) frame_diff() (in module brainbox.video) frame_diffs() (in module brainbox.video) FranklinPaxinosAtlas (class in ibllib.atlas.atlas) FranklinPaxinosRegions (class in ibllib.atlas.regions) from_dict() (Insertion static method) from_track() (Insertion static method) FTPPatcher (class in ibllib.oneibl.patcher)

G

generate_image() (Snapshot method) generate_pseudo_blocks() (in module brainbox.task.closed_loop) generate_pseudo_session() (in module brainbox.task.closed_loop) generate_pseudo_stimuli() (in module brainbox.task.closed_loop) generate_spike_train() (in module brainbox.tests.test_metrics) get_acquisition_description() (in module ibllib.pipes.dynamic_pipeline) get_active_wheel_period() (CameraQC static method) get_aligned_channels() (in module ibllib.qc.alignment_qc) get_bpodqc_metrics_frame() (in module ibllib.qc.task_metrics) get_brain_entry() (Insertion static method) get_brain_exit() (Insertion static method) get_brain_locations() (EphysAlignment method) get_brain_regions() (in module ibllib.pipes.histology) get_cameras() (in module ibllib.io.session_params) get_cca_projection() (in module brainbox.population.cca) get_channel_locations() (EphysAlignment method) get_channels() (ReportSnapshotProbe method) get_collections() (in module ibllib.io.session_params) get_correlations() (in module brainbox.population.cca) get_data_handler() (Task method) get_device_collection() (DynamicTask method) get_directory_size() (in module ibllib.pipes.misc) get_dlc_everything() (in module brainbox.behavior.dlc) get_event_aligned_raster() (in module brainbox.task.trials) get_event_bin_indexes() (in module brainbox.population.cca) get_feature_event_times() (in module brainbox.behavior.dlc) get_feedback_times_ge5() (FeedbackTimes static method) get_feedback_times_lt5() (FeedbackTimes static method) get_frame() (VideoStreamer method), [1] get_histology_regions() (EphysAlignment static method) get_histology_status() (ReportSnapshotProbe method) get_ibl_sync_map() (in module ibllib.io.extractors.ephys_fpga) get_iblscripts_folder() (in module ibllib.pipes.misc) get_impostor_target() (in module brainbox.task.closed_loop) get_included_trials_ge5() (IncludedTrials static method) get_included_trials_lt5() (IncludedTrials static method) get_insertion_track() (EphysAlignment method) get_lab_training_status() (in module brainbox.behavior.training) get_labels() (BrainAtlas method) get_latest_training_information() (in module ibllib.pipes.training_status) get_licks() (in module brainbox.behavior.dlc) get_local_data_repository() (in module ibllib.oneibl.data_handlers) (in module ibllib.oneibl.registration) get_local_endpoint() (in module ibllib.io.globus) get_main_probe_sync() (in module ibllib.io.extractors.ephys_fpga) get_micro_manipulator_data() (in module ibllib.pipes.histology) get_nearest_boundary() (EphysAlignment static method) get_new_filename() (in module ibllib.pipes.misc) get_nshanks() (EphysTask method) get_on_off_times_and_positions() (in module brainbox.task.passive) get_perp_vector() (EphysAlignment method) get_picked_tracks() (in module ibllib.pipes.histology) get_pipeline() (in module ibllib.io.extractors.base) get_pname() (EphysTask method) get_port_events() (in module ibllib.io.raw_data_loaders) get_pregenerated_events() (ProbaContrasts static method) get_probe_signature() (ApPlots method) (BadChannelsAp method) (HistologySlices method) (LfpPlots method) (ReportSnapshotProbe method) (SpikeSorting method) get_protocol() (DynamicTask method) get_psth() (in module brainbox.task.trials) get_pupil_diameter() (in module brainbox.behavior.dlc) get_remote_stub_name() (in module ibllib.io.session_params)

get_rf_map_over_depth() (in module brainbox.task.passive) get_scale_factor() (EphysAlignment method) get_session_extractor_type() (in module ibllib.io.extractors.base) get_session_numbers_from_date_path() (in module ibllib.pipes.misc) get_sessions() (in module brainbox.behavior.training) get_signatures() (EphysCellsQc method) (EphysMtscomp method) (EphysPassive method) (EphysPulses method) (EphysTrials method) (EphysVideoCompress method) (EphysVideoSyncQc method) (RawEphysQC method) (SpikeSorting method), [1] (Task method) get_signed_contrast() (in module brainbox.behavior.training) get_smooth_pupil_diameter() (in module brainbox.behavior.dlc) get_sniffs() (in module brainbox.behavior.dlc) get_speed() (in module brainbox.behavior.dlc) get_speed_for_features() (in module brainbox.behavior.dlc) get_spike_counts_in_bins() (in module brainbox.population.decode) get_stim_aligned_activity() (in module brainbox.task.passive) get_stimOn_times_ge5() (StimOnTimes_deprecated static method) get_stimOn_times_lt5() (StimOnTimes_deprecated static method) get_subject_training_status() (in module brainbox.behavior.training) get_svd_map() (in module brainbox.task.passive) get_sync() (DynamicTask method) (in module ibllib.io.session_params) get_sync_and_chn_map() (in module ibllib.io.extractors.ephys_fpga) get_sync_collection() (DynamicTask method) (in module ibllib.io.session_params) get_sync_extension() (DynamicTask method) (in module ibllib.io.session_params) get_sync_fronts() (in module ibllib.io.extractors.ephys_fpga) get_sync_namespace() (DynamicTask method) (in module ibllib.io.session_params) get_task_collection() (DynamicTask method) (in module ibllib.io.session_params) get_task_extractor_type() (in module ibllib.io.extractors.base) get_task_protocol() (in module ibllib.io.extractors.base) (in module ibllib.io.session_params) get_track_and_feature() (EphysAlignment method) get_training_info_for_session() (in module ibllib.pipes.training_status) get_training_status() (in module brainbox.behavior.training) get_trial_start_times() (in module ibllib.io.extractors.training_wheel) get_trials_task() (in module ibllib.pipes.training_status) get_units_bunch() (in module brainbox.processing) get_video_compressed() (in module ibllib.io.session_params) get_video_frame() (in module ibllib.io.video) get_video_frames_preload() (in module ibllib.io.video) get_video_length() (in module ibllib.io.extractors.camera) get_video_meta() (in module ibllib.io.video) get_wheel_position() (in module ibllib.io.extractors.training_wheel) get_wheel_positions() (in module ibllib.io.extractors.ephys_fpga) getData() (DataHandler method) globus_path_from_dataset() (in module ibllib.oneibl.patcher) GlobusPatcher (class in ibllib.oneibl.patcher) GoCueTimes (class in ibllib.io.extractors.training_trials) GoCueTriggerTimes (class in ibllib.io.extractors.training_trials) gpu (EphysDLC attribute) (GpuTask attribute) (SpikeSorting attribute), [1] (Task attribute) (TaskGpuLock attribute) GpuTask (class in ibllib.tests.test_tasks) groom_pin_state() (in module ibllib.io.extractors.camera)

H

HabituationQC (class in ibllib.qc.task_metrics) HabituationRegisterRaw (class in ibllib.pipes.behavior_tasks) HabituationTrials (class in ibllib.io.extractors.habituation_trials)

HabituationTrialsBpod (class in ibllib.pipes.behavior_tasks) histology (SpikeSortingLoader attribute) HistologySlices (class in ibllib.plots.figures)

I

i2x() (BrainCoordinates method) i2xyz() (BrainCoordinates method) i2y() (BrainCoordinates method) i2z() (BrainCoordinates method) IblError ibllib module ibllib.atlas module ibllib.atlas.atlas module ibllib.atlas.flatmaps module ibllib.atlas.genes module ibllib.atlas.plots module ibllib.atlas.regions module ibllib.ephys module ibllib.ephys.ephysqc module ibllib.ephys.spikes module ibllib.ephys.sync_probes module ibllib.exceptions module ibllib.graphic module ibllib.io module ibllib.io.extractors module ibllib.io.extractors.base module ibllib.io.extractors.biased_trials module ibllib.io.extractors.bpod_trials module ibllib.io.extractors.camera module ibllib.io.extractors.default_channel_maps module ibllib.io.extractors.ephys_fpga module ibllib.io.extractors.ephys_passive module ibllib.io.extractors.fibrephotometry module ibllib.io.extractors.habituation_trials module ibllib.io.extractors.opto_trials module ibllib.io.extractors.passive_plotting module ibllib.io.extractors.signatures module ibllib.io.extractors.training_audio module ibllib.io.extractors.training_trials module ibllib.io.extractors.training_wheel module ibllib.io.extractors.video_motion module ibllib.io.extractors.widefield module ibllib.io.ffmpeg module ibllib.io.flags module ibllib.io.globus module ibllib.io.misc module ibllib.io.npy_header module ibllib.io.raw_daq_loaders module ibllib.io.raw_data_loaders module ibllib.io.session_params module ibllib.io.video module ibllib.misc module ibllib.misc.misc module ibllib.oneibl module ibllib.oneibl.data_handlers module ibllib.oneibl.patcher module ibllib.oneibl.registration module ibllib.oneibl.stream module ibllib.pipes module ibllib.pipes.audio_tasks module ibllib.pipes.base_tasks module ibllib.pipes.behavior_tasks module ibllib.pipes.dynamic_pipeline module ibllib.pipes.ephys_alignment module ibllib.pipes.ephys_preprocessing module ibllib.pipes.ephys_tasks module ibllib.pipes.histology module ibllib.pipes.local_server module ibllib.pipes.misc module ibllib.pipes.photometry_tasks module ibllib.pipes.purge_rig_data module ibllib.pipes.remote_server module ibllib.pipes.scan_fix_passive_files module

ibllib.pipes.sync_tasks module ibllib.pipes.tasks module ibllib.pipes.training_preprocessing module ibllib.pipes.training_status module ibllib.pipes.transfer_rig_data module ibllib.pipes.video_tasks module ibllib.pipes.widefield_tasks module ibllib.plots module ibllib.plots.figures module ibllib.plots.misc module ibllib.plots.snapshot module ibllib.qc module ibllib.qc.alignment_qc module ibllib.qc.base module ibllib.qc.camera module ibllib.qc.critical_reasons module ibllib.qc.dlc module ibllib.qc.qcplots module ibllib.qc.task_extractors module ibllib.qc.task_metrics module ibllib.tests module ibllib.tests.extractors module ibllib.tests.extractors.test_ephys_fpga module ibllib.tests.extractors.test_ephys_passive module ibllib.tests.extractors.test_ephys_trials module ibllib.tests.extractors.test_extractors module ibllib.tests.fixtures module ibllib.tests.fixtures.utils module ibllib.tests.qc module ibllib.tests.qc.test_alignment_qc module ibllib.tests.qc.test_base_qc module ibllib.tests.qc.test_camera_qc module ibllib.tests.qc.test_critical_reasons module ibllib.tests.qc.test_dlc_qc module ibllib.tests.qc.test_task_metrics module ibllib.tests.test_atlas module ibllib.tests.test_dynamic_pipeline module ibllib.tests.test_ephys module ibllib.tests.test_histology module ibllib.tests.test_io module ibllib.tests.test_oneibl module ibllib.tests.test_pipes module ibllib.tests.test_plots module ibllib.tests.test_tasks module ibllib.tests.test_time module ibllib.tests.test_widefield module ibllib.time module iblrig_video_compression() (in module ibllib.io.ffmpeg) id (BrainRegions attribute) (FranklinPaxinosRegions attribute) image_crosscorr_plot() (in module brainbox.ephys_plots) image_fr_plot() (in module brainbox.ephys_plots) image_lfp_spectrum_plot() (in module brainbox.ephys_plots) image_raw_data() (in module brainbox.ephys_plots) image_rms_plot() (in module brainbox.ephys_plots) ImagePlot (class in brainbox.plot_base) imshow() (CameraQC static method) IncludedTrials (class in ibllib.io.extractors.training_trials) infer_wheel_units() (in module ibllib.io.extractors.training_wheel) inhibit() (WindowsInhibitor method) insert_idx() (in module brainbox.behavior.dlc) Insertion (class in ibllib.atlas.atlas) interpolate_along_track() (in module ibllib.pipes.histology) interpolate_position() (in module brainbox.behavior.wheel) Intervals (class in ibllib.io.extractors.training_trials) io_charge (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysDLC attribute) (EphysPassive attribute) (EphysPostDLC attribute) (EphysPulses attribute), [1] (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (EphysVideoCompress attribute) (RawEphysQC attribute), [1] (SpikeSorting attribute), [1] (SyncMtscomp attribute) (SyncPulses attribute) (Task attribute) (TrainingVideoCompress attribute) is_locked() (Task method) isostr2date() (in module ibllib.time) ItiDuration (class in ibllib.io.extractors.training_trials) ItiInTimes (class in ibllib.io.extractors.training_trials)

J

job_creator() (in module ibllib.pipes.local_server) job_run_ks2() (in module ibllib.pipes.remote_server) job_size (AudioCompress attribute) (AudioSync attribute) (ChoiceWorldTrialsBpod attribute) (ChoiceWorldTrialsNidq attribute) (EphysCellsQc attribute) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysDLC attribute) (EphysPulses attribute) (EphysRegisterRaw attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (EphysVideoCompress attribute) (HabituationRegisterRaw attribute) (HabituationTrialsBpod attribute) (PassiveRegisterRaw attribute) (PassiveTask attribute) (RawEphysQC attribute) (RegisterRawDataTask attribute) (SpikeSorting attribute), [1] (SyncMtscomp attribute) (SyncPulses attribute) (SyncRegisterRaw attribute) (Task attribute) (TaskFibrePhotometryRegisterRaw attribute) (TrainingStatus attribute) (TrainingVideoCompress attribute) (TrialRegisterRaw attribute) (VideoCompress attribute) (VideoConvert attribute) (VideoRegisterRaw attribute) (VideoSyncQcBpod attribute) (VideoSyncQcCamlog attribute) (VideoSyncQcNidq attribute) (WidefieldCompress attribute) (WidefieldFOV attribute) (WidefieldPreprocess attribute) (WidefieldRegisterRaw attribute) (WidefieldSync attribute)

job_transfer_ks2() (in module ibllib.pipes.remote_server)

K

ks2_to_alf() (in module ibllib.ephys.spikes)

ks2_to_tar() (in module ibllib.ephys.spikes)

L

label (EphysExtractionPipeline attribute) (FibrePhotometryExtractionPipeline attribute) (Insertion attribute) (TrainingExtractionPipeline attribute) label_from_path() (in module ibllib.io.video) LaserBool (class in ibllib.io.extractors.opto_trials) last_movement_onset() (in module brainbox.behavior.wheel) launch_transfers() (GlobusPatcher method) launch_transfers_secondary() (GlobusPatcher method) lda_project() (in module brainbox.population.decode) level (BrainRegions attribute) (EphysAudio attribute) (EphysCellsQc attribute) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPassive attribute) (EphysPostDLC attribute) (EphysPulses attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (EphysVideoSyncQc attribute) (FranklinPaxinosRegions attribute) (RawEphysQC attribute) (SpikeSorting attribute) (Task attribute) (Task10 attribute) (Task11 attribute) (TaskFibrePhotometryPreprocess attribute) (TrainingAudio attribute) (TrainingStatus attribute) (TrainingTrials attribute) LfpPlots (class in ibllib.plots.figures) likelihood_threshold() (in module brainbox.behavior.dlc) lim() (BrainCoordinates method) line_amp_plot() (in module brainbox.ephys_plots) line_fr_plot() (in module brainbox.ephys_plots) LinePlot (class in brainbox.plot_base) load_ambient_sensor() (in module ibllib.io.raw_data_loaders) load_bpod() (in module ibllib.io.raw_data_loaders) load_bpod_fronts() (in module ibllib.io.raw_data_loaders) load_camera_frame_count() (in module ibllib.io.raw_data_loaders) load_camera_frameData() (in module ibllib.io.raw_data_loaders) load_camera_gpio() (in module ibllib.io.raw_data_loaders) load_camera_ssv_times() (in module ibllib.io.raw_data_loaders) load_channel_locations() (in module brainbox.io.one) load_channel_map() (in module ibllib.io.extractors.ephys_fpga) load_channels() (SpikeSortingLoader method) load_channels_from_insertion() (in module brainbox.io.one) load_channels_tdms() (in module ibllib.io.raw_daq_loaders) load_combined_trials() (in module ibllib.pipes.training_status) load_data() (AlignmentQC method) (CameraQC method) (CameraQCCamlog method) (DlcQC method) (EphysQC method) (in module ibllib.io.raw_data_loaders) (MotionAlignment method) (QC method) (TaskQC method)

load_embedded_frame_data() (in module ibllib.io.raw_data_loaders) load_encoder_events() (in module ibllib.io.raw_data_loaders) load_encoder_positions() (in module ibllib.io.raw_data_loaders) load_encoder_trial_info() (in module ibllib.io.raw_data_loaders) load_ephys_session() (in module brainbox.io.one) load_ephyspc_params() (in module ibllib.pipes.misc) load_existing_dataframe() (in module ibllib.pipes.training_status) load_fake_bpod_data() (TestHabituationQC static method) (TestTaskMetrics static method) load_fake_wheel_data() (TestTaskMetrics static method) load_lfp() (in module brainbox.io.one) load_licks() (SessionLoader method) load_mic() (in module ibllib.io.raw_data_loaders) load_motion_energy() (SessionLoader method) load_params_dict() (in module ibllib.pipes.misc) load_passive_rfmap() (in module brainbox.io.one) load_pipeline_dict() (in module ibllib.pipes.dynamic_pipeline) load_pose() (SessionLoader method) load_pupil() (SessionLoader method) load_raw_daq_tdms() (in module ibllib.io.raw_daq_loaders) load_raw_data() (TaskQCExtractor method) load_reference_frames() (CameraQC static method) load_session_data() (EphysSessionLoader method) (SessionLoader method) load_settings() (in module ibllib.io.raw_data_loaders) load_settings_file() (in module ibllib.pipes.scan_fix_passive_files) load_spike_sorting() (EphysSessionLoader method) (in module brainbox.io.one) (SpikeSortingLoader method) load_spike_sorting_fast() (in module brainbox.io.one) load_spike_sorting_with_channel() (in module brainbox.io.one) load_stim_position_screen() (in module ibllib.io.raw_data_loaders) load_sync() (in module ibllib.io.extractors.ephys_fpga) load_sync_tdms() (in module ibllib.io.raw_daq_loaders) load_track_csv() (in module ibllib.pipes.histology) load_trials() (in module ibllib.pipes.training_status) (SessionLoader method) load_video_data() (CameraQC method) load_videopc_params() (in module ibllib.pipes.misc) load_wheel() (SessionLoader method) load_wheel_reaction_times() (in module brainbox.io.one) load_widefield_mmap() (in module ibllib.io.raw_data_loaders) LocalDataHandler (class in ibllib.oneibl.data_handlers) log (Task attribute) login() (in module ibllib.io.globus) login_auto() (in module ibllib.io.globus)

M

main() (in module ibllib.pipes.transfer_rig_data) (in module ibllib.qc.critical_reasons) main_gui() (in module ibllib.qc.critical_reasons) make_graph() (Pipeline method) make_lock_file() (Task static method) make_pipeline() (in module ibllib.pipes.dynamic_pipeline) make_pipeline_dict() (in module ibllib.pipes.dynamic_pipeline) make_plots() (in module ibllib.pipes.training_status) make_synthetic_data() (in module ibllib.tests.test_ephys) merge_clusters() (SpikeSortingLoader static method) merge_clusters_channels() (in module brainbox.io.one) mgrid (BrainCoordinates property) mindist() (Trajectory method) missed_spikes_est() (in module brainbox.metrics.single_units) (in module brainbox.plot) mktree() (FTPPatcher method) mle_fit_psycho() (in module brainbox.behavior.pyschofit) mock_input() (in module ibllib.tests.qc.test_critical_reasons) (TestFTPPatcher static method) MockExtracor (class in ibllib.tests.extractors.test_extractors) module brainbox brainbox.atlas brainbox.behavior brainbox.behavior.dlc brainbox.behavior.pyschofit brainbox.behavior.training brainbox.behavior.wheel brainbox.core brainbox.ephys_plots brainbox.io brainbox.io.one brainbox.io.spikeglx brainbox.lfp brainbox.metrics brainbox.metrics.electrode_drift brainbox.metrics.single_units brainbox.plot brainbox.plot_base brainbox.population brainbox.population.cca brainbox.population.decode brainbox.processing brainbox.quality brainbox.quality.lfp_qc brainbox.quality.permutation_test brainbox.singlecell brainbox.spike_features brainbox.task brainbox.task.closed_loop brainbox.task.passive brainbox.task.trials brainbox.tests brainbox.tests.test_behavior brainbox.tests.test_cca brainbox.tests.test_io brainbox.tests.test_metrics brainbox.tests.test_passive brainbox.tests.test_plot_base brainbox.tests.test_population brainbox.tests.test_processing brainbox.tests.test_singlecell brainbox.tests.test_task brainbox.tests.test_trials brainbox.tests.test_video brainbox.video ibllib ibllib.atlas ibllib.atlas.atlas ibllib.atlas.flatmaps ibllib.atlas.genes ibllib.atlas.plots ibllib.atlas.regions ibllib.ephys ibllib.ephys.ephysqc ibllib.ephys.spikes ibllib.ephys.sync_probes ibllib.exceptions ibllib.graphic ibllib.io ibllib.io.extractors ibllib.io.extractors.base ibllib.io.extractors.biased_trials ibllib.io.extractors.bpod_trials ibllib.io.extractors.camera ibllib.io.extractors.default_channel_maps ibllib.io.extractors.ephys_fpga ibllib.io.extractors.ephys_passive ibllib.io.extractors.fibrephotometry ibllib.io.extractors.habituation_trials ibllib.io.extractors.opto_trials ibllib.io.extractors.passive_plotting ibllib.io.extractors.signatures ibllib.io.extractors.training_audio ibllib.io.extractors.training_trials ibllib.io.extractors.training_wheel ibllib.io.extractors.video_motion ibllib.io.extractors.widefield ibllib.io.ffmpeg ibllib.io.flags ibllib.io.globus ibllib.io.misc ibllib.io.npy_header ibllib.io.raw_daq_loaders ibllib.io.raw_data_loaders ibllib.io.session_params ibllib.io.video ibllib.misc ibllib.misc.misc ibllib.oneibl ibllib.oneibl.data_handlers ibllib.oneibl.patcher ibllib.oneibl.registration ibllib.oneibl.stream ibllib.pipes ibllib.pipes.audio_tasks ibllib.pipes.base_tasks ibllib.pipes.behavior_tasks ibllib.pipes.dynamic_pipeline ibllib.pipes.ephys_alignment ibllib.pipes.ephys_preprocessing ibllib.pipes.ephys_tasks ibllib.pipes.histology ibllib.pipes.local_server ibllib.pipes.misc ibllib.pipes.photometry_tasks ibllib.pipes.purge_rig_data ibllib.pipes.remote_server ibllib.pipes.scan_fix_passive_files ibllib.pipes.sync_tasks ibllib.pipes.tasks ibllib.pipes.training_preprocessing ibllib.pipes.training_status ibllib.pipes.transfer_rig_data ibllib.pipes.video_tasks ibllib.pipes.widefield_tasks ibllib.plots ibllib.plots.figures ibllib.plots.misc ibllib.plots.snapshot ibllib.qc ibllib.qc.alignment_qc ibllib.qc.base ibllib.qc.camera ibllib.qc.critical_reasons ibllib.qc.dlc ibllib.qc.qcplots ibllib.qc.task_extractors ibllib.qc.task_metrics ibllib.tests ibllib.tests.extractors ibllib.tests.extractors.test_ephys_fpga ibllib.tests.extractors.test_ephys_passive ibllib.tests.extractors.test_ephys_trials ibllib.tests.extractors.test_extractors ibllib.tests.fixtures ibllib.tests.fixtures.utils ibllib.tests.qc ibllib.tests.qc.test_alignment_qc ibllib.tests.qc.test_base_qc ibllib.tests.qc.test_camera_qc ibllib.tests.qc.test_critical_reasons ibllib.tests.qc.test_dlc_qc ibllib.tests.qc.test_task_metrics ibllib.tests.test_atlas ibllib.tests.test_dynamic_pipeline ibllib.tests.test_ephys ibllib.tests.test_histology ibllib.tests.test_io ibllib.tests.test_oneibl ibllib.tests.test_pipes ibllib.tests.test_plots ibllib.tests.test_tasks ibllib.tests.test_time ibllib.tests.test_widefield ibllib.time

motion_energy (EphysSessionLoader attribute) (SessionLoader attribute) motion_energy() (in module brainbox.video) MotionAlignment (class in ibllib.io.extractors.video_motion) move_ephys_files() (in module ibllib.pipes.misc) move_rename_pairs() (in module ibllib.pipes.scan_fix_passive_files) movements() (in module brainbox.behavior.wheel) MRITorontoAtlas() (in module ibllib.atlas.atlas) multi_parts_flags_creation() (in module ibllib.pipes.misc) multiple_spike_trains() (in module brainbox.tests.test_metrics)

N

name (BrainRegions attribute) (FranklinPaxinosRegions attribute) (Pipeline property) (Task property) NeedlesAtlas() (in module ibllib.atlas.atlas)

neg_likelihood() (in module brainbox.behavior.pyschofit) Neuropixel3BSyncFrontsNonMatching noise_cutoff() (in module brainbox.metrics.single_units) NvidiaDriverNotReady nxyz (BrainCoordinates property)

O

on_key_press() (Density method) (Traces method) one (Pipeline attribute) (SessionLoader attribute) (SpikeSortingLoader attribute) (Task attribute)

order (BrainRegions attribute) (FranklinPaxinosRegions attribute) outcome (QC property) outputs (Task attribute) overall_outcome() (QC static method)

P

parent (BrainRegions attribute) (FranklinPaxinosRegions attribute) parse_version() (SpikeSorting static method) pass_through_training_hierachy() (in module ibllib.pipes.training_status) PassiveChoiceWorld (class in ibllib.io.extractors.ephys_passive) PassiveRegisterRaw (class in ibllib.pipes.behavior_tasks) PassiveTask (class in ibllib.pipes.behavior_tasks) patch_dataset() (Patcher method) patch_datasets() (GlobusPatcher method) (Patcher method) (SDSCPatcher method) Patcher (class in ibllib.oneibl.patcher) peri_event_time_histogram() (in module brainbox.plot) permut_test() (in module brainbox.quality.permutation_test) PhasePosQuiescence (class in ibllib.io.extractors.training_trials) phi (Insertion attribute) phy_model_from_ks2_path() (in module ibllib.ephys.ephysqc) pid (SpikeSortingLoader attribute) pid2ref (SpikeSortingLoader property) pid_label (ReportSnapshotProbe property) Pipeline (class in ibllib.pipes.tasks) plot() (Snapshot method) plot2d_all() (in module ibllib.pipes.histology) plot3d_all() (in module ibllib.pipes.histology) plot_alignment() (MotionAlignment method) plot_atlas() (in module brainbox.atlas) plot_audio_times() (in module ibllib.io.extractors.passive_plotting) plot_brain_regions() (in module brainbox.ephys_plots) plot_cdf() (in module brainbox.ephys_plots) plot_correlations() (in module brainbox.population.cca) plot_cslice() (BrainAtlas method) plot_fit_params() (in module ibllib.pipes.training_status) plot_flatmap() (FlatMap method) plot_gabor_times() (in module ibllib.io.extractors.passive_plotting) plot_heatmap_performance_over_days() (in module ibllib.pipes.training_status) plot_hslice() (BrainAtlas method) plot_image() (in module brainbox.plot_base) plot_lick_hist() (in module brainbox.behavior.dlc) plot_lick_raster() (in module brainbox.behavior.dlc) plot_line() (in module brainbox.plot_base) plot_motion_energy_hist() (in module brainbox.behavior.dlc) plot_over_days() (in module ibllib.pipes.training_status) plot_pairwise_correlations() (in module brainbox.population.cca) plot_pairwise_correlations_mult() (in module brainbox.population.cca) plot_passive_periods() (in module ibllib.io.extractors.passive_plotting) plot_performance_easy_median_reaction_time() (in module ibllib.pipes.training_status) plot_permut_test() (in module brainbox.quality.permutation_test) plot_points_on_slice() (in module ibllib.atlas.plots) plot_probe() (in module brainbox.plot_base) plot_psychometric() (in module brainbox.behavior.training) plot_psychometric_curve() (in module ibllib.pipes.training_status) plot_pupil_diameter_hist() (in module brainbox.behavior.dlc) plot_reaction_time() (in module brainbox.behavior.training) plot_reaction_time_over_trials() (in module brainbox.behavior.training) plot_results() (in module ibllib.qc.qcplots) plot_rfmapping() (in module ibllib.io.extractors.passive_plotting) plot_scalar_on_barplot() (in module ibllib.atlas.plots) plot_scalar_on_flatmap() (in module ibllib.atlas.plots) plot_scalar_on_slice() (in module ibllib.atlas.plots) plot_scatter() (in module brainbox.plot_base) plot_slices() (BrainAtlas method) plot_speed_hist() (in module brainbox.behavior.dlc) plot_sslice() (BrainAtlas method) plot_stims_times() (in module ibllib.io.extractors.passive_plotting) plot_swanson() (in module ibllib.atlas.flatmaps) plot_sync_channels() (in module ibllib.io.extractors.passive_plotting) plot_tilted_slice() (BrainAtlas method) plot_top() (BrainAtlas method) plot_trace_on_frame() (in module brainbox.behavior.dlc) plot_trial_count_and_session_duration() (in module ibllib.pipes.training_status) plot_valve_times() (in module ibllib.io.extractors.passive_plotting) plot_volume_on_slice() (in module ibllib.atlas.plots) plot_wheel_position() (in module brainbox.behavior.dlc) plt_window() (in module brainbox.behavior.dlc) pname (SpikeSortingLoader attribute) point (Trajectory attribute) populate_raw_spikeglx() (in module ibllib.tests.fixtures.utils) populate_task_settings() (in module ibllib.tests.fixtures.utils)

popup() (in module ibllib.graphic) pose (EphysSessionLoader attribute) (SessionLoader attribute) power_spectrum() (in module brainbox.lfp) prepare_experiment() (in module ibllib.io.session_params) prepare_lr_data() (in module ibllib.atlas.plots) preprocess() (in module brainbox.population.cca) (Widefield method) pres_ratio() (in module brainbox.metrics.single_units) (in module brainbox.plot) prev_traj_id (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) priority (AudioCompress attribute) (AudioSync attribute) (ChoiceWorldTrialsBpod attribute) (ChoiceWorldTrialsNidq attribute) (EphysAudio attribute) (EphysCellsQc attribute), [1] (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysMtscomp attribute) (EphysPulses attribute), [1] (EphysRegisterRaw attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (EphysVideoSyncQc attribute) (HabituationRegisterRaw attribute) (HabituationTrialsBpod attribute) (PassiveRegisterRaw attribute) (PassiveTask attribute) (RawEphysQC attribute), [1] (RegisterRawDataTask attribute) (SpikeSorting attribute), [1] (SyncMtscomp attribute) (SyncPulses attribute) (SyncRegisterRaw attribute) (Task attribute) (TaskFibrePhotometryPreprocess attribute) (TaskFibrePhotometryRegisterRaw attribute) (TrainingAudio attribute) (TrainingRegisterRaw attribute) (TrainingStatus attribute), [1] (TrainingTrials attribute) (TrainingVideoCompress attribute) (TrialRegisterRaw attribute) (VideoCompress attribute) (VideoConvert attribute) (VideoRegisterRaw attribute) (VideoSyncQcBpod attribute) (VideoSyncQcCamlog attribute) (VideoSyncQcNidq attribute) (WidefieldCompress attribute) (WidefieldFOV attribute) (WidefieldPreprocess attribute) (WidefieldRegisterRaw attribute) (WidefieldSync attribute) ProbabilityLeft (class in ibllib.io.extractors.training_trials) ProbaContrasts (class in ibllib.io.extractors.biased_trials) probe00_id (TestTracingQc attribute) probe01_id (TestTracingQc attribute) probe_id (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestUploadToFlatIron attribute) probe_labels_from_session_path() (in module ibllib.pipes.misc) probe_lfp_spectrum_plot() (in module brainbox.ephys_plots) probe_rms_plot() (in module brainbox.ephys_plots) ProbePlot (class in brainbox.plot_base) probes (EphysSessionLoader property) probes_description() (in module ibllib.ephys.spikes) project() (Trajectory method) PsychofitTest (class in brainbox.tests.test_behavior) ptp_over_noise() (in module brainbox.metrics.single_units) pupil (EphysSessionLoader attribute) (SessionLoader attribute) purge_local_data() (in module ibllib.pipes.purge_rig_data) PYKILOSORT_REPO (SpikeSorting attribute), [1]

Q

QC (class in ibllib.qc.base)

qc_fpga_task() (in module ibllib.ephys.ephysqc) quick_unit_metrics() (in module brainbox.metrics.single_units)

R

r2ix() (BrainCoordinates method) r2iy() (BrainCoordinates method) r2iz() (BrainCoordinates method) ram (Task attribute) raster() (SpikeSortingLoader method) raw_destripe() (in module ibllib.plots.figures) raw_names (Widefield attribute) raw_qc_session() (in module ibllib.ephys.ephysqc) raw_widefield (TestSyncData attribute) RawEphysQC (class in ibllib.pipes.ephys_preprocessing) (class in ibllib.pipes.ephys_tasks) rdiff_install() (in module ibllib.pipes.misc) read() (in module ibllib.io.npy_header) (Streamer method) read_daq_timestamps() (in module ibllib.io.extractors.fibrephotometry) read_daq_voltage() (in module ibllib.io.extractors.fibrephotometry) read_flag_file() (in module ibllib.io.flags) read_params() (in module ibllib.io.session_params) read_params_file() (DynamicTask method) regions_from_allen_csv() (in module ibllib.atlas.regions) register_aligned_track() (in module ibllib.pipes.histology) register_dataset() (in module ibllib.oneibl.registration) (Patcher method) register_datasets() (Patcher method) (Task method) register_image() (Snapshot method) register_images() (ReportSnapshot method) (ReportSnapshotProbe method) (Snapshot method) (Task method) register_session() (RegistrationClient method) register_session_raw_data() (in module ibllib.oneibl.registration) register_snapshots() (WidefieldRegisterRaw method) register_sync() (RegistrationClient method) register_track() (in module ibllib.pipes.histology) register_track_files() (in module ibllib.pipes.histology) RegisterRawDataTask (class in ibllib.pipes.base_tasks) RegistrationClient (class in ibllib.oneibl.registration) regress() (in module brainbox.population.decode) remap() (BrainRegions method) RemoteAwsDataHandler (class in ibllib.oneibl.data_handlers) RemoteGlobusDataHandler (class in ibllib.oneibl.data_handlers)

RemoteHttpDataHandler (class in ibllib.oneibl.data_handlers) remove_axis_outline() (in module ibllib.plots.figures) remove_check() (CameraQC method) remove_files() (Widefield method) rename_data() (TaskQCExtractor static method) rename_ephys_files() (in module ibllib.pipes.misc) rename_files() (RegisterRawDataTask method) rename_files_compatibility() (in module ibllib.oneibl.registration) rename_session() (in module ibllib.pipes.misc) reorder_data() (in module ibllib.atlas.plots) RepNum (class in ibllib.io.extractors.training_trials) report_health() (in module ibllib.pipes.local_server) ReportSnapshot (class in ibllib.plots.snapshot) ReportSnapshotProbe (class in ibllib.plots.snapshot) rerun() (Pipeline method) (Task method) rerun_failed() (Pipeline method) reset_params() (TestFTPPatcher method) resolve_manual() (AlignmentQC method) ResponseTimes (class in ibllib.io.extractors.training_trials) responsive_units() (in module brainbox.task.closed_loop) RewardVolume (class in ibllib.io.extractors.training_trials) rgb (BrainRegions attribute) (FranklinPaxinosRegions attribute) rmsmap() (in module ibllib.ephys.ephysqc) roc_between_two_events() (in module brainbox.task.closed_loop) roc_single_event() (in module brainbox.task.closed_loop) roi (MotionAlignment attribute) rsync_paths() (in module ibllib.pipes.misc) run() (AlignmentQC method) (CameraQC method) (DlcQC method) (EphysQC method) (Pipeline method) (QC method) (Task method) (TaskQC method) run_all_qc() (in module ibllib.qc.camera) (in module ibllib.qc.dlc) run_alyx_task() (in module ibllib.pipes.tasks) run_count (Task02_error attribute) run_extractor_classes() (in module ibllib.io.extractors.base)

S

samples2times() (SpikeSortingLoader method) samples_to_cm() (in module brainbox.behavior.wheel) save_bool() (in module ibllib.io.raw_data_loaders) save_dataframe() (in module ibllib.pipes.training_status) save_names (BaseExtractor attribute) (CameraTimestampsBpod attribute) (Choice attribute) (ContrastLR attribute), [1] (FeedbackTimes attribute) (FeedbackType attribute) (FibrePhotometry attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (PhasePosQuiescence attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimOnOffFreezeTimes attribute) (StimOnTimes_deprecated attribute) (StimOnTriggerTimes attribute) (TrialsTable attribute) (TrialsTableBiased attribute) (TrialsTableEphys attribute) (TrialType attribute) (Wheel attribute) (Widefield attribute) save_path() (in module ibllib.pipes.training_status) scale_histology_regions() (EphysAlignment method) scatter_amp_depth_fr_plot() (in module brainbox.ephys_plots) scatter_raster_plot() (in module brainbox.ephys_plots) scatter_xyc_plot() (in module brainbox.plot_base) ScatterPlot (class in brainbox.plot_base) scripts (EphysDLC attribute) sdsc_globus_path_from_dataset() (in module ibllib.oneibl.patcher) sdsc_path_from_dataset() (in module ibllib.oneibl.patcher) SDSCDataHandler (class in ibllib.oneibl.data_handlers) SDSCPatcher (class in ibllib.oneibl.patcher) ServerDataHandler (class in ibllib.oneibl.data_handlers) ServerGlobusDataHandler (class in ibllib.oneibl.data_handlers) session_name() (in module ibllib.pipes.purge_rig_data) session_path (BaseExtractor attribute) (SessionLoader attribute) (SpikeSortingLoader attribute) SessionLoader (class in brainbox.io.one) set_axis_label_size() (in module ibllib.plots.figures) set_clim() (DefaultPlot method) set_color() (ScatterPlot method) set_labels() (DefaultPlot method) set_line_color() (ScatterPlot method) set_line_style() (ScatterPlot method) set_line_width() (ScatterPlot method) set_marker_size() (ScatterPlot method) set_marker_type() (ScatterPlot method) set_offset() (ImagePlot method) (ProbePlot method) set_opacity() (ScatterPlot method) set_roi() (MotionAlignment static method) set_scale() (ImagePlot method) (ProbePlot method) set_xlim() (DefaultPlot method) set_ylim() (DefaultPlot method) set_zlim() (DefaultPlot method) settings (BaseBpodTrialsExtractor attribute) setUp() (DataHandler method) setup() (FTPPatcher static method) (in module ibllib.io.globus) setUp() (PsychofitTest method) (RemoteAwsDataHandler method) (RemoteGlobusDataHandler method) (RemoteHttpDataHandler method) (SDSCDataHandler method) (ServerGlobusDataHandler method) (SpikeSorting method) (Task method) (TaskGpuLock method) (TestArrangeChannels2Bank method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestEphysBehaviorExtraction method) (TestEphysQC method) (TestExtractedWheelUnits method) (TestExtractTrialData method) (TestFTPPatcher method) (TestHabituationQC method) (TestHistology method) (TestIblChannelMaps method) (TestIO_ALF method) (TestPipelineAlyx method) (TestPipesMisc method) (TestPlotBase method) (TestPopulation method) (TestQC method) (TestRegistration method) (TestScanFixPassiveFiles method) (TestScatterXYC method) (TestsEphysAlignment method) (TestsEphysReconstruction method) (TestSessionParams method) (TestsFolderStructure method) (TestsGlobus method) (TestsMisc method) (TestsParams method) (TestsPassiveExtractor method) (TestsRawDataLoaders method) (TestSyncData method) (TestSyncExtraction method) (TestTask method) (TestTaskMetrics method) (TestTraining method) (TestTrials method) (TestUserPmtSess method) (TestVideo method), [1] (TestWheel method) (TestWheelExtraction method) (TestWheelLoaders method) (TestWheelMovesExtraction method) (TestWidefieldExtractor method) (TestWidefieldRegister method)

setUpClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestAtlasPlots class method) (TestAtlasSlicesConversion class method) (TestBrainRegions class method) (TestCameraQC class method) (TestDlcQC class method) (TestDlcQcPlot class method) (TestEphysQC class method) (TestFranklinPaxinos class method) (TestSnapshot class method) (TestTracingQc class method) (TestUploadToFlatIron method) (TestVideo class method) SHELL_SCRIPT (SpikeSorting attribute), [1] shuffle_analysis() (in module brainbox.population.cca) signature (AudioCompress property) (AudioSync property) (BehaviourPlots attribute) (ChoiceWorldTrialsBpod property) (ChoiceWorldTrialsNidq property) (EphysAudio attribute) (EphysCellsQc attribute) (EphysCellsQc property) (EphysCompressNP1 property) (EphysCompressNP21 property) (EphysCompressNP24 property) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPassive attribute) (EphysPostDLC attribute) (EphysPulses attribute) (EphysPulses property) (EphysRegisterRaw property) (EphysSyncPulses property) (EphysSyncRegisterRaw property) (EphysTrials attribute) (EphysVideoCompress attribute) (EphysVideoSyncQc attribute) (ExperimentDescriptionRegisterRaw property) (HabituationRegisterRaw property) (HabituationTrialsBpod property) (PassiveRegisterRaw property) (PassiveTask property) (RawEphysQC attribute) (RawEphysQC property) (ReportSnapshotProbe attribute) (SpikeSorting attribute) (SpikeSorting property) (SyncMtscomp property) (SyncPulses property) (SyncRegisterRaw property) (Task attribute) (TaskFibrePhotometryPreprocess attribute) (TaskFibrePhotometryRegisterRaw property) (TrainingStatus attribute) (TrainingStatus property) (TrainingTrials attribute) (TrialRegisterRaw property) (VideoCompress property) (VideoConvert property) (VideoRegisterRaw property) (VideoSyncQcBpod property) (VideoSyncQcCamlog property) (VideoSyncQcNidq property) (WidefieldCompress property) (WidefieldFOV property) (WidefieldPreprocess property) (WidefieldRegisterRaw property) (WidefieldSync property) sigtest_linshift() (in module brainbox.population.decode) sigtest_pseudosessions() (in module brainbox.population.decode) slice() (BrainAtlas method) slidingRP_viol() (in module brainbox.metrics.single_units) Snapshot (class in ibllib.plots.snapshot) SomePipeline (class in ibllib.tests.test_tasks) spectrum() (in module ibllib.plots.misc) sph2cart() (in module ibllib.atlas.atlas) spike_sorter (SpikeSortingLoader attribute) SPIKE_SORTER_NAME (SpikeSorting attribute), [1] spike_sorting_metrics() (in module brainbox.metrics.single_units) spike_sorting_metrics_ks2() (in module ibllib.ephys.ephysqc) spike_sorting_path (SpikeSortingLoader attribute) spike_sorting_signature() (in module ibllib.io.extractors.signatures) (SpikeSorting static method) SpikeSorting (class in ibllib.pipes.ephys_preprocessing) (class in ibllib.pipes.ephys_tasks) (class in ibllib.plots.figures) SpikeSortingLoader (class in brainbox.io.one) split_by_area() (in module brainbox.population.cca) split_timepoints() (in module brainbox.population.cca) split_trials() (in module brainbox.population.cca) squares() (in module ibllib.plots.misc) SSHPatcher (class in ibllib.oneibl.patcher) StimFreezeTriggerTimes (class in ibllib.io.extractors.training_trials) StimOffTriggerTimes (class in ibllib.io.extractors.training_trials) StimOnOffFreezeTimes (class in ibllib.io.extractors.training_trials) StimOnTimes_deprecated (class in ibllib.io.extractors.training_trials) StimOnTriggerTimes (class in ibllib.io.extractors.training_trials) Streamer (class in brainbox.io.spikeglx) structarr() (in module ibllib.misc.misc) subjects_data_folder() (in module ibllib.pipes.misc) swanson() (in module ibllib.atlas.flatmaps) sync() (in module brainbox.processing) (in module ibllib.ephys.sync_probes) sync_gen() (TestSyncExtraction method) sync_photometry_to_daq() (in module ibllib.io.extractors.fibrephotometry) sync_probe_front_times() (in module ibllib.ephys.sync_probes) sync_rotary_encoder() (in module ibllib.io.extractors.training_wheel) sync_spike_sorting() (in module ibllib.ephys.spikes) sync_timestamps() (Widefield method) sync_trials_robust() (in module ibllib.io.raw_data_loaders) SyncBpodFpgaException SyncBpodWheelException SyncMtscomp (class in ibllib.pipes.sync_tasks) SyncPulses (class in ibllib.pipes.sync_tasks) SyncRegisterRaw (class in ibllib.pipes.sync_tasks) synthetic_with_bad_channels() (in module ibllib.tests.test_ephys)

T

Task (class in ibllib.pipes.tasks) Task00 (class in ibllib.tests.test_tasks) Task01_void (class in ibllib.tests.test_tasks) Task02_error (class in ibllib.tests.test_tasks) Task10 (class in ibllib.tests.test_tasks) Task11 (class in ibllib.tests.test_tasks) task_queue() (in module ibllib.pipes.local_server) TaskFibrePhotometryPreprocess (class in ibllib.pipes.photometry_tasks) TaskFibrePhotometryRegisterRaw (class in ibllib.pipes.photometry_tasks) TaskGpuLock (class in ibllib.tests.test_tasks) TaskIncomplete (class in ibllib.tests.test_tasks) TaskQC (class in ibllib.qc.task_metrics) TaskQCExtractor (class in ibllib.qc.task_extractors) tasks (Pipeline attribute) tasks_runner() (in module ibllib.pipes.local_server) tearDown() (PsychofitTest method) (Task method) (TestAtlasPlots method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestEphysQC method) (TestExtractTrialData method) (TestIO_ALF method) (TestPipelineAlyx method) (TestPipesMisc method) (TestRegistration method) (TestScanFixPassiveFiles method) (TestsFolderStructure method) (TestsMisc method) (TestsParams method) (TestsPassiveExtractor method) (TestsRawDataLoaders method) (TestUserPmtSess method) (TestWidefieldExtractor method) (TestWidefieldRegister method) (WidefieldPreprocess method) tearDownClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestCameraQC class method) (TestDlcQC class method) (TestDlcQcPlot class method) (TestEphysQC class method) (TestSnapshot class method) (TestTracingQc class method) (TestUploadToFlatIron class method) tempdir (TestEphysQC attribute) test__set_eid_or_path() (TestQC method) test_acorr_0() (TestPopulation method) test_acorr_1() (TestPopulation method) test_acro2acro() (TestBrainRegions method) test_acro2id() (TestBrainRegions method) test_acro2index() (TestBrainRegions method) test_aggregate() (TestSessionParams method) test_align_to_trial() (TestEphysSyncExtraction method) test_alignments() (TestAlignmentQcExisting method) (TestAlignmentQcManual method) test_allen_ba() (TestAtlasSlicesConversion method) test_ancestors_descendants() (TestBrainRegions method) test_ancestors_descendants_indices() (TestBrainRegions method) test_argument_parser() (TestBrainRegions method) test_as_globus_path() (TestsGlobus method) test_assert_valid_label() (TestVideo method) test_attribute_times() (TestCameraExtractors method) test_audio_ttl_start_up_down() (TestEphysFPGA_TTLsExtraction method) test_audio_ttl_wiring_camera() (TestEphysFPGA_TTLsExtraction method) test_backup_session() (TestSyncData method) test_behavior_exists() (TestPipesMisc method) test_bincount_2d() (TestProcessing method) test_bpod_trace_extraction() (TestEphysSyncExtraction method) test_brain_coordinates() (TestsCoordinatesSimples method) test_ccf_xyz() (TestAtlasSlicesConversion method) test_channel_detections() (TestDetectBadChannels method) test_channel_locations() (TestsEphysReconstruction method) test_check_audio_pre_trial() (TestTaskMetrics method) test_check_brightness() (TestCameraQC method) test_check_camera_times() (TestCameraQC method) test_check_correct_trial_event_sequence() (TestTaskMetrics method) test_check_create_raw_session_flag() (TestPipesMisc method) test_check_detected_wheel_moves() (TestTaskMetrics method) test_check_dropped_frames() (TestCameraQC method) test_check_error_trial_event_sequence() (TestTaskMetrics method) test_check_errorCue_delays() (TestTaskMetrics method) test_check_file_headers() (TestCameraQC method) test_check_focus() (TestCameraQC method) test_check_frame_frequency() (TestTaskMetrics method) test_check_frame_updates() (TestTaskMetrics method) test_check_framerate() (TestCameraQC method) test_check_goCue_delays() (TestTaskMetrics method) test_check_iti_delays() (TestTaskMetrics method) test_check_lick_detection() (TestDlcQC method) test_check_mean_in_bbox() (TestDlcQC method) test_check_n_trial_events() (TestTaskMetrics method) test_check_negative_feedback_stimOff_delays() (TestTaskMetrics method) test_check_paw_nan() (TestDlcQC method) test_check_pin_state() (TestCameraQC method) test_check_position() (TestCameraQC method) test_check_positive_feedback_stimOff_delays() (TestTaskMetrics method) test_check_pupil_blocked() (TestDlcQC method) test_check_pupil_diameter_snr() (TestDlcQC method) test_check_resolution() (TestCameraQC method) test_check_response_feedback_delays() (TestTaskMetrics method) test_check_response_stimFreeze_delays() (TestTaskMetrics method) test_check_reward_volume_set() (TestTaskMetrics method) test_check_reward_volumes() (TestTaskMetrics method) test_check_stimFreeze_delays() (TestTaskMetrics method) test_check_stimOff_delays() (TestTaskMetrics method) test_check_stimOff_itiIn_delays() (TestTaskMetrics method) test_check_stimOn_delays() (TestTaskMetrics method) test_check_stimOn_goCue_delays() (TestTaskMetrics method) test_check_stimulus_move_before_goCue() (TestTaskMetrics method) test_check_time_trace_length_match() (TestDlcQC method) test_check_timestamps() (TestCameraQC method) test_check_trace_all_nan() (TestDlcQC method) test_check_transfer() (TestPipesMisc method) test_check_trial_length() (TestTaskMetrics method) test_check_wheel_alignment() (TestCameraQC method) test_check_wheel_freeze_during_quiescence() (TestTaskMetrics method) test_check_wheel_integrity() (TestTaskMetrics method) test_check_wheel_move_before_feedback() (TestTaskMetrics method) test_check_wheel_move_during_closed_loop() (TestTaskMetrics method) test_class_setup() (TestSnapshot method) test_classify() (TestPopulation method) test_clusters_metrics() (in module brainbox.tests.test_metrics) test_code_to_outcome() (TestQC method) test_compute() (TestHabituationQC method) test_compute_cluster_averag() (TestProcessing method) test_compute_hierarchy() (TestBrainRegions method) test_concatenate_and_computations() (TestTraining method) test_conversions() (TestFranklinPaxinos method) test_coronal_slice() (TestAtlasPlots method) test_create_alyx_probe_insertions() (TestPipesMisc method) test_create_basic_transfer_params() (TestPipesMisc method) test_create_ephys_flags() (TestPipesMisc method) test_create_ephys_transfer_done_flag() (TestPipesMisc method) test_create_multiparts_flags() (TestMultiPartsRecordings method) test_create_sessions() (TestRegistration method) test_create_video_transfer_done_flag() (TestPipesMisc method) test_data_content() (TestUploadToFlatIron method) test_date2isostr() (TestUtils method) test_default() (TestPlotBase method) test_delete_empty_folders() (TestsMisc method) test_derivative() (TestWheel method) test_differentiate_units() (TestTask method) test_direction_changes() (TestWheel method) test_drift_estimate() (in module brainbox.tests.test_metrics) test_dsets_2_path() (TestAlyx2Path method) test_encoder_events_corrupt() (TestWheelLoaders method) test_encoder_positions_clock_errors() (TestExtractTrialData method) test_encoder_positions_clock_reset() (TestExtractTrialData method) test_encoder_positions_corrupts() (TestWheelLoaders method) test_ensure_data() (TestCameraQC method) (TestDlcQC method) (TestEphysQC method) test_erf_psycho() (PsychofitTest method) test_erf_psycho_2gammas() (PsychofitTest method) test_eval_trajectory() (TestTrajectory method) test_exit_volume() (TestTrajectory method) test_extended_qc() (TestQC method) test_extract_all() (TestExtractTrialData method) test_extract_first_movement_times() (TestWheelMovesExtraction method) test_extract_wheel_moves() (TestExtractedWheelUnits method) (TestWheelMovesExtraction method) test_filename_parser() (TestHistology method) test_find_pairs() (TestScanFixPassiveFiles method) test_find_trial_ids() (TestTrials method) test_firing_rate() (in module brainbox.tests.test_singlecell) test_format_date_range() (TestUtils method) test_frame2ttl_flickers() (TestEphysFPGA_TTLsExtraction method) test_frame_diff() (TestVideo method) test_frame_diffs() (TestVideo method) test_generate_image() (TestSnapshot method) test_generate_pseudo_blocks() (TestTask method) test_generate_pseudo_session() (TestTask method) test_generate_pseudo_stimuli() (TestTask method) test_get() (TestBrainRegions method) test_get_active_wheel_period() (TestCameraQC method) test_get_brain_exit_entry() (TestHistology method) test_get_choice() (TestExtractTrialData method) test_get_collections() (TestSessionParams method) test_get_contrastLR() (TestExtractTrialData method) test_get_ephys_files() (TestsFolderStructure method) test_get_event_aligned_rasters() (TestTrials method) test_get_feedback_times_ge5() (TestExtractTrialData method) test_get_feedback_times_lt5() (TestExtractTrialData method) test_get_feedbackType() (TestExtractTrialData method) test_get_goCueOnset_times() (TestExtractTrialData method) test_get_goCueTrigger_times() (TestExtractTrialData method) test_get_impostor_target() (TestTask method) test_get_included_trials() (TestExtractTrialData method) test_get_included_trials_ge5() (TestExtractTrialData method) test_get_included_trials_lt5() (TestExtractTrialData method) test_get_intervals() (TestExtractTrialData method) test_get_new_filename() (TestPipesMisc method) test_get_probabilityLeft() (TestEphysBehaviorExtraction method) (TestExtractTrialData method) test_get_repNum() (TestExtractTrialData method) test_get_response_times() (TestExtractTrialData method) test_get_rewardVolume() (TestExtractTrialData method) test_get_spike_counts_in_bins() (TestPopulation method) test_get_stimOn_times_ge5() (TestExtractTrialData method) test_get_stimOn_times_lt5() (TestExtractTrialData method) test_get_stimOnTrigger_times() (TestExtractTrialData method) test_get_unit_bunches() (in module brainbox.tests.test_processing) test_gpu_lock_and_local_data_handler() (TestLocks method) test_groom_pin_state() (TestCameraExtractors method) test_guiinput_ins() (TestUserPmtSess method) test_histology_get_brain_regions() (TestHistology method) test_histology_insertion_from_track() (TestHistology method) test_horizontal_slice() (TestAtlasPlots method) test_ibl_sync_maps() (TestIblChannelMaps method) test_id2acro() (TestBrainRegions method) test_id2id() (TestBrainRegions method) test_id2index() (TestBrainRegions method) test_image() (TestPlotBase method) test_image_scaling() (TestSnapshot method) test_impeccable_dataset() (TestFpgaTask method) test_in_training() (TestTraining method) test_index2acronym() (TestBrainRegions method) test_index2id() (TestBrainRegions method) test_init_from_dict() (TestInsertion method) test_init_from_track() (TestInsertion method) test_interpolate_rf_mapping_stimulus() (TestsPassiveExtractor method) test_isostr2date() (TestUtils method) test_label_from_path() (TestVideo method) test_layouts() (TestNeuropixel method) test_legacy_biased() (TestCreateLegacyAcqusitionDescriptions method) test_legacy_ephys() (TestCreateLegacyAcqusitionDescriptions method) test_legacy_training() (TestCreateLegacyAcqusitionDescriptions method) test_level() (TestFranklinPaxinos method) test_line() (TestPlotBase method) test_linear_scaling() (TestsEphysAlignment method) test_load_camera_frame_count() (TestsRawDataLoaders method) test_load_camera_frameData() (TestsRawDataLoaders method) test_load_camera_gpio() (TestsRawDataLoaders method)

test_load_camera_ssv_times() (TestsRawDataLoaders method) test_load_embedded_frame_data() (TestsRawDataLoaders method) test_load_encoder_events() (TestExtractTrialData method) test_load_encoder_positions() (TestExtractTrialData method) test_load_encoder_trial_info() (TestsRawDataLoaders method) test_load_ephys() (TestIO_ALF method) test_load_passive_stim_meta() (TestsPassiveExtractor method) test_login_auto() (TestsGlobus method) test_lookups() (TestAtlasSlicesConversion method) test_lookups_probabilistic() (TestAtlasSlicesConversion method) test_mappings_lateralized() (TestBrainRegions method) test_mappings_not_lateralized() (TestBrainRegions method) test_mle_fit_psycho() (PsychofitTest method) test_move_rename_pairs() (TestScanFixPassiveFiles method) test_movement_log() (TestWheelMovesExtraction method) test_movements() (TestWheel method) test_movements_FPGA() (TestWheel method) test_neg_likelihood() (PsychofitTest method) test_new_default_param() (TestsParams method) test_no_pad() (TestArrangeChannels2Bank method) test_no_scaling() (TestsEphysAlignment method) test_noise_cut_off() (in module brainbox.tests.test_metrics) test_note_probe_ins() (TestUserPmtSess method) test_offset() (TestsEphysAlignment method) test_out_of_bounds() (TestAggregateOutcome method) test_outcome_from_dict_default() (TestAggregateOutcome method) test_outcome_from_dict_iti_delays() (TestAggregateOutcome method) test_outcome_from_dict_stimFreeze_delays() (TestAggregateOutcome method) test_outcome_setter() (TestQC method) test_overall_outcome() (TestQC method) test_pad() (TestArrangeChannels2Bank method) test_param_get_file() (TestsParams method) test_params() (TestsParams method) test_parse_version() (TestSpikeSortingTask method) test_patch_data() (TestSessionParams method) test_peths_synthetic() (TestPeths method) test_pipeline_alyx() (TestPipelineAlyx method) test_plot_slices() (TestAtlasSlicesConversion method) test_plotting() (TestBunch method) test_prepare_lr_data() (TestBrainRegions method) test_probe() (TestPlotBase method) test_probe_names_from_session_path() (TestPipesMisc method) test_project_mindist() (TestTrajectory method) test_propagate_down() (TestBrainRegions method) test_psychometric_insufficient_data() (TestTraining method) test_rdiff_install() (TestSyncData method) test_read_write_params_yaml() (in module ibllib.tests.test_dynamic_pipeline) test_read_yaml() (TestSessionParams method) test_ready4delay() (TestTraining method) test_ready4ephys() (TestTraining method) test_ready4recording() (TestTraining method) test_reason_addnumberstr() (TestUserPmtSess method) test_register_multiple() (TestSnapshot method) test_registration_datasets() (TestRegistration method) test_registration_session() (TestRegistration method) test_regress() (TestPopulation method) test_remap() (TestBrainRegions method) test_remove_files() (TestWidefieldExtractor method) test_rename_and_move() (TestPipesMisc method) test_rename_files() (TestWidefieldRegister method) test_rename_session() (TestPipesMisc method) test_reorder_data() (TestBrainRegions method) test_responsive_units() (TestTask method) test_reverse_directions() (TestsCoordinatesSimples method) test_rf_map() (TestPassive method) test_RGB_conversion() (TestScatterXYC method) test_RGB_conversion_with_clim() (TestScatterXYC method) test_rgba() (TestBrainRegions method) test_roc_between_two_events() (TestTask method) test_roc_single_event() (TestTask method) test_rsync_paths() (TestSyncData method) test_sagittal_slice() (TestAtlasPlots method) test_save_files() (TestWidefieldExtractor method) test_saving_method() (TestBaseExtractorSavingMethods method) test_scan_fix() (TestScanFixPassiveFiles method) test_scatter() (TestPlotBase method) test_setup() (TestFTPPatcher method) test_sigtest_linshift() (TestPopulation method) test_sigtest_pseudosessions() (TestPopulation method) test_size_outputs() (TestExtractTrialData method) test_slice() (TestAtlasSlicesConversion method) test_snapshot_default() (TestSnapshot method) test_sph2cart_and_back() (TestsCoordinatesSimples method) test_spike_detection() (TestDetectSpikes method) test_stim_aligned() (TestPassive method) test_stimOnOffFreeze_times() (TestExtractTrialData method) test_sync() (TestProcessing method) test_sync_3A() (TestSyncExtraction method) test_sync_3B() (TestSyncExtraction method) test_sync_bpod_bonsai_poor_quality_timestamps() (TestSyncWheelBpod method) test_sync_nidq() (TestSyncExtraction method) test_task_names_extractors() (TestExtractors2Tasks method) (TestRegistrationEndpoint method) test_task_to_pipeline() (TestExtractors2Tasks method) test_timestamp_saving() (TestWidefieldExtractor method) test_traces_by_trial() (TestWheel method) test_tracing_exists() (TestTracingQc method) test_tracing_not_exists() (TestTracingQc method) test_trained_1a() (TestTraining method) test_trained_1b() (TestTraining method) test_training_to_bias() (TestTraining method) test_trajectory() (TestTrajectory method) test_transfer_session_folders() (TestSyncData method) test_ttl_bpod_gaelle_writes_protocols_but_guido_doesnt_read_them() (TestEphysFPGA_TTLsExtraction method) test_uniform_scaling() (TestsEphysAlignment method) test_update() (TestQC method) test_upload_to_flatiron() (TestUploadToFlatIron method) test_url_from_eid() (TestVideo method) test_userinput_ins() (TestUserPmtSess method) test_userinput_sess() (TestUserPmtSess method) test_weibull() (PsychofitTest method) test_weibull50() (PsychofitTest method) test_wheel_folders() (TestExtractTrialData method) test_wheel_trace_from_sync() (TestEphysSyncExtraction method) test_with_depth() (TestArrangeChannels2Bank method) test_without_inputs() (TestDlcQcPlot method) test_without_RGB_conversion() (TestScatterXYC method) test_x1_decoding() (TestWheelExtraction method) test_x2_decoding() (TestWheelExtraction method) test_x4_decoding() (TestWheelExtraction method) test_xcorr_0() (TestPopulation method) test_xcorr_1() (TestPopulation method) test_xcorr_2() (TestPopulation method) TestAggregateOutcome (class in ibllib.tests.qc.test_task_metrics) TestAlignmentQcExisting (class in ibllib.tests.qc.test_alignment_qc) TestAlignmentQcManual (class in ibllib.tests.qc.test_alignment_qc) TestAlyx2Path (class in ibllib.tests.test_oneibl) testAppendFlagFile() (TestsRawDataLoaders method) TestArrangeChannels2Bank (class in brainbox.tests.test_plot_base) TestAtlasPlots (class in ibllib.tests.test_atlas) TestAtlasSlicesConversion (class in ibllib.tests.test_atlas) TestBaseExtractorSavingMethods (class in ibllib.tests.extractors.test_extractors) TestBrainRegions (class in ibllib.tests.test_atlas) TestBunch (class in brainbox.tests.test_cca) TestCameraExtractors (class in ibllib.tests.extractors.test_extractors) TestCameraQC (class in ibllib.tests.qc.test_camera_qc) TestCreateLegacyAcqusitionDescriptions (class in ibllib.tests.test_dynamic_pipeline) TestDetectBadChannels (class in ibllib.tests.test_ephys) TestDetectSpikes (class in ibllib.tests.test_ephys) TestDlcQC (class in ibllib.tests.qc.test_dlc_qc) TestDlcQcPlot (class in ibllib.tests.test_plots) TestEphysBehaviorExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestEphysFPGA_TTLsExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestEphysQC (class in ibllib.tests.test_ephys) TestEphysSyncExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestExtractedWheelUnits (class in ibllib.tests.extractors.test_ephys_fpga) TestExtractors2Tasks (class in ibllib.tests.test_pipes) TestExtractTrialData (class in ibllib.tests.extractors.test_extractors) testFlagFileRead() (TestsRawDataLoaders method) TestFpgaTask (class in ibllib.tests.test_ephys) TestFranklinPaxinos (class in ibllib.tests.test_atlas) TestFTPPatcher (class in ibllib.tests.test_oneibl) TestHabituationQC (class in ibllib.tests.qc.test_task_metrics) TestHistology (class in ibllib.tests.test_histology) TestIblChannelMaps (class in ibllib.tests.extractors.test_ephys_fpga) TestInsertion (class in ibllib.tests.test_atlas) TestIO_ALF (class in brainbox.tests.test_io) TestLocks (class in ibllib.tests.test_tasks) TestMultiPartsRecordings (class in ibllib.tests.test_pipes) TestNeuropixel (class in ibllib.tests.test_ephys) TestPassive (class in brainbox.tests.test_passive) TestPeths (class in brainbox.tests.test_singlecell) TestPipelineAlyx (class in ibllib.tests.test_tasks) TestPipesMisc (class in ibllib.tests.test_pipes) TestPlotBase (class in brainbox.tests.test_plot_base) TestPopulation (class in brainbox.tests.test_population) (class in brainbox.tests.test_singlecell) TestProcessing (class in brainbox.tests.test_processing) TestQC (class in ibllib.tests.qc.test_base_qc) TestRegistration (class in ibllib.tests.test_oneibl) TestRegistrationEndpoint (class in ibllib.tests.test_oneibl) tests_headers() (TestNeuropixel method) TestScanFixPassiveFiles (class in ibllib.tests.test_pipes) TestScatterXYC (class in brainbox.tests.test_plot_base) TestsCoordinatesSimples (class in ibllib.tests.test_atlas) TestsEphysAlignment (class in ibllib.tests.test_histology) TestsEphysReconstruction (class in ibllib.tests.test_histology) TestSessionParams (class in ibllib.tests.test_io) TestsFolderStructure (class in ibllib.tests.extractors.test_ephys_fpga) TestsGlobus (class in ibllib.tests.test_io) TestsMisc (class in ibllib.tests.test_io) TestSnapshot (class in ibllib.tests.test_plots) TestsParams (class in ibllib.tests.test_io) TestsPassiveExtractor (class in ibllib.tests.extractors.test_ephys_passive) TestSpikeSortingTask (class in ibllib.tests.test_pipes) TestsRawDataLoaders (class in ibllib.tests.test_io) TestSyncData (class in ibllib.tests.test_pipes) TestSyncExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestSyncWheelBpod (class in ibllib.tests.extractors.test_extractors) TestTask (class in brainbox.tests.test_task) TestTaskMetrics (class in ibllib.tests.qc.test_task_metrics) TestTracingQc (class in ibllib.tests.qc.test_alignment_qc) TestTraining (class in brainbox.tests.test_behavior) TestTrajectory (class in ibllib.tests.test_atlas) TestTrials (class in brainbox.tests.test_trials) TestUploadToFlatIron (class in ibllib.tests.qc.test_alignment_qc) TestUserPmtSess (class in ibllib.tests.qc.test_critical_reasons) TestUtils (class in ibllib.tests.test_time) TestVideo (class in brainbox.tests.test_video) (class in ibllib.tests.test_io) TestWheel (class in brainbox.tests.test_behavior) TestWheelExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestWheelLoaders (class in ibllib.tests.extractors.test_extractors) TestWheelMovesExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestWidefieldExtractor (class in ibllib.tests.test_widefield) TestWidefieldRegister (class in ibllib.tests.test_widefield) theta (Insertion attribute) tilted_slice() (BrainAtlas method) time_elapsed_secs (Task attribute) time_out_secs (Task attribute) TimeSeries (class in brainbox.core) tip (Insertion property) Traces (class in ibllib.plots.misc) traces_by_trial() (in module brainbox.behavior.wheel) track2feature() (EphysAlignment static method) TrainingAudio (class in ibllib.pipes.training_preprocessing) TrainingDLC (class in ibllib.pipes.training_preprocessing) TrainingExtractionPipeline (class in ibllib.pipes.training_preprocessing) TrainingRegisterRaw (class in ibllib.pipes.training_preprocessing) TrainingStatus (class in ibllib.pipes.behavior_tasks) (class in ibllib.pipes.training_preprocessing) TrainingTrials (class in ibllib.pipes.training_preprocessing) TrainingVideoCompress (class in ibllib.pipes.training_preprocessing) Trajectory (class in ibllib.atlas.atlas) trajectory (Insertion property) transfer_folder() (in module ibllib.pipes.misc) transfer_session_folders() (in module ibllib.pipes.misc) trial_times_to_times() (in module ibllib.io.raw_data_loaders) TrialRegisterRaw (class in ibllib.pipes.behavior_tasks) trials (EphysSessionLoader attribute) (SessionLoader attribute) TrialsTable (class in ibllib.io.extractors.training_trials) TrialsTableBiased (class in ibllib.io.extractors.biased_trials) TrialsTableEphys (class in ibllib.io.extractors.biased_trials) TrialType (class in ibllib.io.extractors.training_trials) type (CameraQC property)

U

uncycle_pgts() (in module ibllib.time) uninhibit() (WindowsInhibitor method) unit_stability() (in module brainbox.metrics.single_units) update() (QC method) update_experimenter_evaluation() (AlignmentQC method) update_extended_qc() (QC method) upload_channels() (AlignmentQC method) uploadData() (DataHandler method) (RemoteAwsDataHandler method) (RemoteGlobusDataHandler method) (RemoteHttpDataHandler method) (SDSCDataHandler method) (ServerDataHandler method) (ServerGlobusDataHandler method)

url (SpikeSortingLoader property) url_from_eid() (in module ibllib.io.video)

V

V_THRESHOLD (in module ibllib.io.extractors.fibrephotometry), [1] validate_ttl_test() (in module ibllib.ephys.ephysqc) var_name (TrialType attribute) var_names (CameraTimestampsBpod attribute) (Choice attribute) (ContrastLR attribute), [1] (ErrorCueTriggerTimes attribute) (FeedbackTimes attribute) (FeedbackType attribute) (FibrePhotometry attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (HabituationTrials attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (ItiInTimes attribute) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (PhasePosQuiescence attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimFreezeTriggerTimes attribute) (StimOffTriggerTimes attribute) (StimOnOffFreezeTimes attribute) (StimOnTimes_deprecated attribute) (StimOnTriggerTimes attribute) (TrialsTable attribute) (TrialsTableBiased attribute) (TrialsTableEphys attribute) (Wheel attribute) (Widefield attribute)

vector (Trajectory attribute) velocity_smoothed() (in module brainbox.behavior.wheel) version (Task attribute) (Task00 attribute) version3A() (in module ibllib.ephys.sync_probes) version3B() (in module ibllib.ephys.sync_probes) vertical_lines() (in module ibllib.plots.misc) video_meta (CameraQC attribute) VideoCompress (class in ibllib.pipes.video_tasks) VideoConvert (class in ibllib.pipes.video_tasks) VideoRegisterRaw (class in ibllib.pipes.video_tasks) VideoStreamer (class in ibllib.io.video) (class in ibllib.oneibl.stream) VideoSyncQcBpod (class in ibllib.pipes.video_tasks) VideoSyncQcCamlog (class in ibllib.pipes.video_tasks) VideoSyncQcNidq (class in ibllib.pipes.video_tasks) VideoTask (class in ibllib.pipes.base_tasks)

W

weibull() (in module brainbox.behavior.pyschofit) weibull50() (in module brainbox.behavior.pyschofit) welchogram() (in module ibllib.io.extractors.training_audio) wf_comp() (in module brainbox.plot) wf_similarity() (in module brainbox.metrics.single_units) Wheel (class in ibllib.io.extractors.training_wheel) wheel (EphysSessionLoader attribute) (SessionLoader attribute) wheel_radius_cm (TestExtractedWheelUnits attribute) wheelMoves_fixture() (in module ibllib.tests.extractors.test_extractors) Widefield (class in ibllib.io.extractors.widefield)

WidefieldCompress (class in ibllib.pipes.widefield_tasks) WidefieldFOV (class in ibllib.pipes.widefield_tasks) WidefieldPreprocess (class in ibllib.pipes.widefield_tasks) WidefieldRegisterRaw (class in ibllib.pipes.widefield_tasks) WidefieldSync (class in ibllib.pipes.widefield_tasks) WidefieldTask (class in ibllib.pipes.base_tasks) WidefieldWiringException wiggle() (in module ibllib.plots.misc) WindowsInhibitor (class in ibllib.pipes.misc) write_flag_file() (in module ibllib.io.flags) write_params() (in module ibllib.io.session_params) write_yaml() (in module ibllib.io.session_params)

X

x (Insertion attribute) x2i() (BrainCoordinates method) xcorr() (in module brainbox.population.decode) xlim (BrainCoordinates property)

xscale (BrainCoordinates property) xyz (Insertion property) xyz2ccf() (AllenAtlas method) xyz2i() (BrainCoordinates method)

Y

y (Insertion attribute) y2i() (BrainCoordinates method)

ylim (BrainCoordinates property) yscale (BrainCoordinates property)

Z

z (Insertion attribute) z2i() (BrainCoordinates method)

zlim (BrainCoordinates property) zscale (BrainCoordinates property)