Index

_

_last_sent (EchoProtocol attribute)

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) add_lines() (DefaultPlot method) (in module brainbox.plot_base) add_spacer_states() (Spacer method) 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) alf_path (BaseBpodTrialsExtractor property) align_all_trials() (MotionAlignment method) align_motion() (MotionAlignment method) align_with_gpio() (in module ibllib.io.extractors.camera) AlignmentQC (class in ibllib.qc.alignment_qc) alignments (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestUploadToFlatIron attribute) AlignmentSignOffNote (class in ibllib.qc.critical_reasons) all_default_labels() (in module ibllib.io.extractors.default_channel_maps) ALLEN_CCF_LANDMARKS_MLAPDV_UM (in module iblatlas.atlas), [1] AllenAtlas (class in iblatlas.atlas) ALYX (ExpMessage attribute) alyx() (EchoProtocol method) (Service method) (Services method) amp_heatmap() (in module brainbox.plot) annotate_swanson() (in module iblatlas.plots)

any() (ExpMessage class method) append() (in module iblutil.io.jsonable) 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_dict() (in module iblutil.io.params) assert_expected() (Task method) assert_expected_inputs() (Task method) assert_expected_outputs() (Task method) (VideoRegisterRaw method) assert_valid_label() (in module ibllib.io.video) assign_callback() (Communicator method) (Services method) assign_task() (in module ibllib.pipes) asyncSetUp() (TestServices method) (TestUDP method) (TestWebSockets method) atlas (SpikeSortingLoader attribute) atlas_rel_path (AllenAtlas attribute) (FranklinPaxinosAtlas attribute) attribute_times() (in module ibllib.io.extractors.camera) audio (BaseBpodTrialsExtractor attribute) 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) await_all() (Services method) awaiting_response() (EchoProtocol method)

B

backend (TestCameraQC attribute) BadChannelsAp (class in ibllib.plots.figures) BaseBpodTrialsExtractor (class in ibllib.io.extractors.base) BaseExtractor (class in ibllib.io.extractors.base) bbox (DlcQC attribute) BehaviourPlots (class in ibllib.plots.figures) BehaviourTask (class in ibllib.pipes.base_tasks) beta (Insertion attribute) between_sorted() (in module iblutil.numerical) BiasedTrials (class in ibllib.io.extractors.biased_trials) bin_per_plane() (MesoscopePreprocess method) 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 iblutil.numerical) blake2b() (in module iblutil.io.hashfile) bpod (FpgaTrials attribute) bpod_fields (FpgaTrials attribute) (FpgaTrialsHabituation attribute) BPOD_FPGA_DRIFT_THRESHOLD_PPM (in module ibllib.io.extractors.ephys_fpga), [1] bpod_rsync_fields (FpgaTrials attribute) (FpgaTrialsHabituation attribute) bpod_trials (BaseBpodTrialsExtractor attribute) BrainAtlas (class in iblatlas.atlas) brainbox module brainbox.behavior module brainbox.behavior.dlc 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.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.singlecell 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 iblatlas.atlas) BrainRegions (class in iblatlas.regions) build_trials() (FpgaTrials method) (FpgaTrialsHabituation method) (TimelineTrials method) Bunch (class in iblutil.util)

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 iblatlas.atlas) ccf2xyz() (AllenAtlas method) CellQCMixin (class in ibllib.pipes.ephys_tasks) changeFilter() (GraphWindow 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_datasets() (S3Patcher method) 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) check_trace_all_nan() (DlcQC method) 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) CHMAPS (in module ibllib.io.extractors.ephys_fpga), [1] ChoiceWorldTrialsBpod (class in ibllib.pipes.behavior_tasks) ChoiceWorldTrialsNidq (class in ibllib.pipes.behavior_tasks) ChoiceWorldTrialsTimeline (class in ibllib.pipes.behavior_tasks) circles() (in module iblatlas.flatmaps) classify() (in module brainbox.population.decode) clean_shifts() (MotionAlignmentFullSession method) cleanUp() (DataHandler method) cleanup() (EchoProtocol method) cleanUp() (PopeyeDataHandler method) (RemoteAwsDataHandler method) (SDSCDataHandler method) (ServerDataHandler method) (ServerGlobusDataHandler method) cleanup() (Service method) (Services method) cleanUp() (Task method) clear_callbacks() (Communicator method) (Services method) client() (EchoProtocol static method) close() (Communicator method) (EchoProtocol method) (Services method) closeEvent() (GraphWindow method) cm_to_deg() (in module brainbox.behavior.wheel) cm_to_rad() (in module brainbox.behavior.wheel) collection (SpikeSortingLoader attribute) collections (SpikeSortingLoader attribute) color_cycle() (in module ibllib.plots.misc) Communicator (class in iblutil.io.net.base) 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_cell_qc() (CellQCMixin static method) compute_cluster_average() (in module brainbox.processing) compute_comparison_statistics() (in module brainbox.task.closed_loop) compute_dataset_qc_status() (TaskQC static method) 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_motion_energy() (MotionAlignmentFullSession 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_regions_volume() (AllenAtlas method) compute_session_duration_delay_location() (in module ibllib.pipes.training_status) compute_session_status() (TaskQC method) compute_session_status_from_dict() (in module ibllib.qc.task_metrics) compute_shifts() (MotionAlignmentFullSession 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 iblatlas.plots) concatenate_trials() (in module brainbox.behavior.training) confirmed_send() (EchoProtocol method) CONNECTED (ExpStatus attribute) connection_lost() (EchoProtocol method) connection_made() (EchoProtocol method) contamination() (in module brainbox.metrics.single_units) contamination_alt() (in module brainbox.metrics.single_units) contextMenu() (GraphWindow method) convert2dict() (DefaultPlot method) convert_pgts() (in module ibllib.time) coords_for_poly_hole() (in module iblatlas.plots) copy() (Bunch method) (TimeSeries method) correct_counter_discontinuities() (in module ibllib.io.raw_daq_loaders) coverage() (in module ibllib.pipes.histology) coverage_grid() (in module ibllib.pipes.histology) cpu (AudioCompress attribute) (AudioSync attribute) (DLC attribute) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysPulses attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (MesoscopePreprocess attribute) (RawEphysQC attribute) (SyncMtscomp attribute) (SyncPulses attribute) (Task attribute) create_alyx_probe_insertions() (in module ibllib.pipes.misc) create_alyx_tasks() (Pipeline method) create_app() (in module ibllib.misc.qt) create_audio_flags() (in module ibllib.io.flags) 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_dataset() (FTPPatcher method) create_dlc_flags() (in module ibllib.io.flags) 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_plots() (QcFrame method) create_register_flags() (in module ibllib.io.flags) create_tasks_list_from_pipeline() (Pipeline method) create_trajectory_dict() (in module ibllib.pipes.histology) create_transfer_flags() (in module ibllib.io.flags) criteria (TaskQC attribute) criteria_recording() (in module brainbox.behavior.training) 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) CriticalInsertionNote (class in ibllib.qc.critical_reasons) CriticalNote (class in ibllib.qc.critical_reasons) CriticalSessionNote (class in ibllib.qc.critical_reasons)

D

data_for_keys() (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.qc.camera) data_info (SessionLoader attribute) data_received() (EchoProtocol method) datagram_received() (EchoProtocol method) DataHandler (class in ibllib.oneibl.data_handlers) dataset_from_name() (in module ibllib.oneibl.data_handlers) datasets (SpikeSortingLoader attribute) date2isostr() (in module ibllib.time) decode() (Communicator static method) default_descriptions (CriticalInsertionNote property) (Note property) default_echo_timeout (EchoProtocol attribute), [1] default_path (BaseExtractor attribute) DefaultPlot (class in brainbox.plot_base) delete_dataset() (IBLGlobusPatcher method) delete_empty_folders() (in module ibllib.io.misc) delete_flags() (in module ibllib.io.flags) delete_note_prompt() (CriticalNote method) Density (class in ibllib.plots.misc) depth (Insertion attribute) describe() (Note method) descriptions (AlignmentSignOffNote attribute) (CriticalInsertionNote attribute) (CriticalSessionNote attribute) (Note attribute) (PassiveSignOffNote attribute) (RawEphysSignOffNote attribute) (SpikeSortingSignOffNote attribute) (TaskSignOffNote attribute) (VideoSignOffNote attribute)

descriptions_gui (CriticalInsertionNote attribute) 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) dir_size() (in module iblutil.util) display_info() (in module ibllib.pipes.training_status) display_status() (in module brainbox.behavior.training) DLC (class in ibllib.pipes.video_tasks) dlc_qc_plot() (in module ibllib.plots.figures) dlcenv (DLC attribute) DlcQC (class in ibllib.qc.dlc) download_raw_electrophysiology() (SpikeSortingLoader method) download_raw_waveforms() (SpikeSortingLoader method) 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

EchoProtocol (class in iblutil.io.net.app) eid (SessionLoader attribute) (SpikeSortingLoader attribute) (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestQC attribute) (TestRegisterRawDataTask attribute) encode() (Communicator static method) (EchoProtocol static method) ensure_list() (in module iblutil.util) entry (Insertion property) env (LightningPose attribute) (MesoscopePreprocess attribute) (SpikeSorting attribute) (Task attribute) eof_received() (EchoProtocol method) ephys_bad_channels() (in module ibllib.plots.figures) EphysAlignment (class in ibllib.pipes.ephys_alignment) EphysCompressNP1 (class in ibllib.pipes.ephys_tasks) EphysCompressNP21 (class in ibllib.pipes.ephys_tasks) EphysCompressNP24 (class in ibllib.pipes.ephys_tasks) EphysPostDLC (class in ibllib.pipes.video_tasks) EphysPulses (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.io.extractors.biased_trials) error_received() (EchoProtocol method) ES_CONTINUOUS (WindowsInhibitor attribute) ES_SYSTEM_REQUIRED (WindowsInhibitor attribute) ESTIMATE (Provenance 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) EXPCLEANUP (ExpMessage attribute) ExpectedDataset (class in ibllib.oneibl.data_handlers) EXPEND (ExpMessage attribute) ExperimentDescriptionRegisterRaw (class in ibllib.pipes.base_tasks) EXPINFO (ExpMessage attribute) EXPINIT (ExpMessage attribute)

EXPINTERRUPT (ExpMessage attribute) explanation (IblError attribute) (Neuropixel3BSyncFrontsNonMatching attribute) (NvidiaDriverNotReady attribute) (SyncBpodFpgaException attribute) (SyncBpodWheelException attribute) (WidefieldWiringException attribute) ExpMessage (class in iblutil.io.net.base) EXPSTART (ExpMessage attribute) ExpStatus (class in iblutil.io.net.base) EXPSTATUS (ExpMessage attribute) extent() (BrainAtlas method) extent_flmap() (FlatMap method) external_ip() (in module iblutil.io.net.base) extra_prompt (CriticalInsertionNote property) (CriticalSessionNote property) (Note property) (SignOffNote property) extract() (BaseBpodTrialsExtractor method) (BaseExtractor method) extract_behaviour() (BehaviourTask method) (ChoiceWorldTrialsBpod method) (ChoiceWorldTrialsNidq method) (ChoiceWorldTrialsTimeline method) (HabituationTrialsBpod method) (HabituationTrialsNidq method) extract_camera() (VideoSyncQcBpod method) (VideoSyncQcCamlog method) (VideoSyncQcNidq method) (VideoTask method) extract_camera_sync() (in module ibllib.io.extractors.camera) 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_sync_timeline() (in module ibllib.io.raw_daq_loaders) extract_task_replay() (in module ibllib.io.extractors.ephys_passive) extract_times() (MotionAlignmentFullSession 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) (TimelineTrials method) extractor (BehaviourTask attribute) (ChoiceWorldTrialsBpod attribute) (TaskQC attribute)

F

FAILED (TrainingStatus attribute) feat_vars() (in module brainbox.plot) feature2track() (EphysAlignment static method) feature2track_lin() (EphysAlignment static method) FibrePhotometrySync (class in ibllib.pipes.neurophotometrics) FileLock (class in iblutil.io.params) files (SpikeSortingLoader attribute) filter() (ExpectedDataset method) (OptionalDataset method) 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_contaminated_frames() (MotionAlignmentFullSession method) find_earliest_recompute_date() (in module ibllib.pipes.training_status) find_face() (CameraQC method) find_files() (ExpectedDataset method) (IBLRegistrationClient method) (OptionalDataset method) find_nearest() (in module ibllib.io.extractors.video_motion) find_pairs() (in module ibllib.pipes.scan_fix_passive_files) find_spacers() (Spacer method) find_spacers_from_fronts() (Spacer method) find_trial_ids() (in module brainbox.task.trials) find_triangle() (in module ibllib.pipes.mesoscope_tasks) 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 iblatlas.flatmaps) flatten() (in module iblutil.util) force (DLC attribute) (EphysPostDLC attribute) (LightningPose attribute) (SpikeSorting attribute) (Task attribute) format_existing_note() (SignOffNote method) format_note() (CriticalNote method) (Note method) (SignOffNote method) FpgaTrials (class in ibllib.io.extractors.ephys_fpga) FpgaTrialsHabituation (class in ibllib.io.extractors.ephys_fpga) frame (QcFrame attribute) frame2ttl (BaseBpodTrialsExtractor attribute) frame_diff() (in module brainbox.video) frame_diffs() (in module brainbox.video) FranklinPaxinosAtlas (class in iblatlas.atlas) FranklinPaxinosRegions (class in iblatlas.regions) from_dict() (in module iblutil.io.params) (Insertion static method) from_track() (Insertion static method) FTPPatcher (class in ibllib.oneibl.patcher) FUNCTIONAL (Provenance attribute)

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) generate_template() (Spacer method) 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_audio_event_times() (FpgaTrials method) get_bc_10() (in module iblatlas.plots) get_bout_edges() (MesoscopeSyncTimeline method) get_bpod_event_times() (FpgaTrials method) (FpgaTrialsHabituation method) (TimelineTrials method) get_bpod_extractor() (in module ibllib.io.extractors.bpod_trials) get_bpod_extractor_class() (in module ibllib.io.extractors.base) get_bpod_trials_task() (in module ibllib.qc.task_qc_viewer.task_qc) get_bpodqc_metrics_frame() (TaskQC method) 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_content_type() (Note method) get_correlations() (in module brainbox.population.cca) get_data_collection() (in module ibllib.pipes.training_status) get_data_handler() (Task method) get_datetime_key() (SignOffNote method) get_default_tau() (MesoscopePreprocess method) get_device_collection() (DynamicTask method) 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_frame() (VideoStreamer method) 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_insertion_track() (EphysAlignment method) get_lab() (in module ibllib.oneibl.registration) 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.registration) get_mac() (in module iblutil.util) get_main_probe_sync() (in module ibllib.io.extractors.ephys_fpga) get_main_window() (in module ibllib.misc.qt) get_micro_manipulator_data() (in module ibllib.pipes.histology) get_mock_session_settings() (in module ibllib.tests.test_oneibl) get_movement_onset() (in module brainbox.behavior.wheel) 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_pname() (EphysTask method) get_port_events() (in module ibllib.io.raw_data_loaders) get_probe_signature() (ApPlots method) (BadChannelsAp method) (HistologySlices method) (LfpPlots method) (ReportSnapshotProbe method) (SpikeSorting method) get_protocol() (BehaviourTask method) (DynamicTask method) get_protocol_number() (BehaviourTask method) get_protocol_period() (in module ibllib.io.extractors.ephys_fpga) get_provenance() (MesoscopeFOV static 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_roi_mask() (MotionAlignmentFullSession method) get_scale_factor() (EphysAlignment method) get_sess_dict() (in module ibllib.pipes.training_status) get_sessions() (in module brainbox.behavior.training) get_signatures() (MesoscopeTask method) (SpikeSorting method) (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_stimulus_update_times() (FpgaTrials 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_label() (in module ibllib.io.session_params) get_sync_namespace() (DynamicTask method) (in module ibllib.io.session_params) get_sync_values() (in module ibllib.io.session_params) get_task_collection() (BehaviourTask method) (DynamicTask method) (in module ibllib.io.session_params) (in module ibllib.qc.camera) get_task_protocol() (in module ibllib.io.extractors.base) (in module ibllib.io.session_params) get_task_protocol_number() (in module ibllib.io.session_params) get_timeshifts() (MesoscopeSyncTimeline static method) 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_training_table_from_aws() (in module ibllib.pipes.training_status) get_trial_start_times() (in module ibllib.io.extractors.training_wheel) get_trials_tasks() (in module ibllib.pipes.dynamic_pipeline) get_units_bunch() (in module brainbox.processing) get_valve_open_times() (TimelineTrials method) get_version() (SpikeSortingLoader method) get_video_collection() (in module ibllib.qc.camera) 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_data() (QcFrame method) get_wheel_position() (in module ibllib.io.extractors.training_wheel) get_wheel_positions() (FpgaTrials method) (in module ibllib.io.extractors.ephys_fpga) (TimelineTrials method) getData() (DataHandler method) getfile() (in module iblutil.io.params) getOutputFiles() (DataHandler method) glob_pattern (ExpectedDataset property) globus_path_from_dataset() (in module ibllib.oneibl.patcher) globus_sdk_mock (TestGlobusPatcher attribute) GlobusPatcher (class in ibllib.oneibl.patcher) gpu (DLC attribute) (GpuTask attribute) (LightningPose attribute) (SpikeSorting attribute) (Task attribute) (TaskGpuLock attribute) GpuTask (class in ibllib.tests.test_tasks) GraphWindow (class in ibllib.qc.task_qc_viewer.ViewEphysQC) 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) HabituationTrialsNidq (class in ibllib.pipes.behavior_tasks) hash_uuids() (in module iblutil.numerical)

HashUUIDs (class in iblutil.tests.test_numerical) HISTOLOGY (Provenance attribute) histology (SpikeSortingLoader attribute) HistologySlices (class in ibllib.plots.figures) hostname (Communicator property) hostname2ip() (in module iblutil.io.net.base)

I

i2x() (BrainCoordinates method) i2xyz() (BrainCoordinates method) i2y() (BrainCoordinates method) i2z() (BrainCoordinates method) iblatlas module iblatlas.atlas module iblatlas.flatmaps module iblatlas.genomics module iblatlas.genomics.agea module iblatlas.genomics.merfish module iblatlas.plots module iblatlas.regions module IblError IBLGlobusPatcher (class in ibllib.oneibl.patcher) ibllib module ibllib.ephys module ibllib.ephys.ephysqc module ibllib.ephys.spikes module ibllib.ephys.sync_probes module ibllib.exceptions 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.habituation_trials module ibllib.io.extractors.mesoscope module ibllib.io.extractors.opto_trials module ibllib.io.extractors.passive_plotting 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.misc 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.misc.qt module ibllib.oneibl module ibllib.oneibl.data_handlers module ibllib.oneibl.patcher module ibllib.oneibl.registration 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_tasks module ibllib.pipes.histology module ibllib.pipes.local_server module ibllib.pipes.mesoscope_tasks module ibllib.pipes.misc module ibllib.pipes.neurophotometrics module ibllib.pipes.scan_fix_passive_files module ibllib.pipes.sync_tasks module ibllib.pipes.tasks module ibllib.pipes.training_status 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.task_extractors module ibllib.qc.task_metrics module ibllib.qc.task_qc_viewer module

ibllib.qc.task_qc_viewer.task_qc module ibllib.qc.task_qc_viewer.ViewEphysQC 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_extractors module ibllib.tests.extractors.test_extractors_base module ibllib.tests.extractors.test_mesoscope 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.qc.test_task_qc_viewer module ibllib.tests.test_base_tasks 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_mesoscope 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 IBLRegistrationClient (class in ibllib.oneibl.registration) iblrig_video_compression() (in module ibllib.io.ffmpeg) iblutil module iblutil.io module iblutil.io.hashfile module iblutil.io.jsonable module iblutil.io.net module iblutil.io.net.app module iblutil.io.net.base module iblutil.io.params module iblutil.io.parquet module iblutil.numerical module iblutil.spacer module iblutil.tests module iblutil.tests.test_io module iblutil.tests.test_net module iblutil.tests.test_numerical module iblutil.tests.test_spacers module iblutil.tests.test_util module iblutil.util module identifiers (ExpectedDataset property) image (AllenAtlas attribute) (BrainAtlas 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_motion_registration() (MesoscopePreprocess method) image_raw_data() (in module brainbox.ephys_plots) image_rms_plot() (in module brainbox.ephys_plots) ImagePlot (class in brainbox.plot_base) import_mock() (TestExtractorMaps method) imshow() (CameraQC static method) IN_TRAINING (TrainingStatus attribute) in_triangle() (in module ibllib.pipes.mesoscope_tasks) infer_wheel_units() (in module ibllib.io.extractors.training_wheel) info() (EchoProtocol method) (Service method) (Services method) inhibit() (WindowsInhibitor static method) init() (EchoProtocol method) (Service method) (Services method) INITIALIZED (ExpStatus attribute) Input (class in ibllib.oneibl.data_handlers) input() (ExpectedDataset static method) insert_idx() (in module brainbox.behavior.dlc) Insertion (class in iblatlas.atlas) int2rgb() (in module iblatlas.genomics.merfish) interpolate_along_track() (in module ibllib.pipes.histology) interpolate_position() (in module brainbox.behavior.wheel) intersect2d() (in module iblutil.numerical) inverted (ExpectedDataset attribute) io_charge (DLC attribute) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysPostDLC attribute) (EphysPulses attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (LightningPose attribute) (RawEphysQC attribute) (SpikeSorting attribute) (SyncMtscomp attribute) (SyncPulses attribute) (Task attribute) is_active_trials_task() (in module ibllib.pipes.dynamic_pipeline) is_connected (Communicator property) (EchoProtocol property) (Services property) is_locked() (Task method) is_np_id() (in module iblutil.io.parquet) is_success() (in module iblutil.io.net.base) is_valid_ip() (in module iblutil.io.net.base) ismember() (in module iblutil.numerical) ismember2d() (in module iblutil.numerical) isostr2date() (in module ibllib.time)

J

job_creator() (in module ibllib.pipes.local_server) job_size (AudioCompress attribute) (AudioSync attribute) (ChoiceWorldTrialsBpod attribute) (ChoiceWorldTrialsNidq attribute) (DLC attribute) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysPulses attribute) (EphysRegisterRaw attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (FibrePhotometrySync attribute) (HabituationRegisterRaw attribute) (HabituationTrialsBpod attribute) (HabituationTrialsNidq attribute) (LightningPose attribute) (MesoscopeCompress attribute) (MesoscopeFOV attribute) (MesoscopePreprocess attribute) (MesoscopeRegisterSnapshots attribute) (MesoscopeSync attribute) (PassiveRegisterRaw attribute) (PassiveTaskNidq attribute) (PassiveTaskTimeline attribute) (RawEphysQC attribute) (RegisterRawDataTask attribute) (SpikeSorting attribute) (SyncMtscomp attribute) (SyncPulses attribute) (SyncRegisterRaw attribute) (Task attribute) (TrainingStatus 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)

K

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

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

L

label (AllenAtlas attribute) (BrainAtlas attribute) (Insertion attribute) label_from_path() (in module ibllib.io.video) LANDMARK (Provenance attribute) LaserBool (class in ibllib.io.extractors.opto_trials) launch_transfers() (GlobusPatcher method) launch_transfers_secondary() (GlobusPatcher method) lda_project() (in module brainbox.population.decode) level (DLC attribute) (EphysPostDLC attribute) (LightningPose attribute) (Task attribute) (Task10 attribute) (Task11 attribute) LfpPlots (class in ibllib.plots.figures) LightningPose (class in ibllib.pipes.video_tasks) 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) Listable() (in module iblutil.util) load() (Bunch static method) (in module iblatlas.genomics.agea) (in module iblatlas.genomics.merfish) (in module iblutil.io.parquet) 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) (MotionAlignmentFullSession method) (QC 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_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_iti() (in module brainbox.io.one) load_lfp() (in module brainbox.io.one) load_licks() (SessionLoader method) load_meta_files() (MesoscopePreprocess method) load_mic() (in module ibllib.io.raw_data_loaders) load_motion_energy() (SessionLoader method) 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_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_slice_files() (in module iblatlas.plots) load_spike_sorting() (EphysSessionLoader method) (in module brainbox.io.one) (SpikeSortingLoader method) load_spike_sorting_fast() (in module brainbox.io.one) load_spike_sorting_object() (SpikeSortingLoader method) load_spike_sorting_with_channel() (in module brainbox.io.one) load_stim_position_screen() (in module ibllib.io.raw_data_loaders) load_sync() (FpgaTrials method) (in module ibllib.io.extractors.ephys_fpga) (MesoscopeTask method) (TimelineTrials method) load_sync_tdms() (in module ibllib.io.raw_daq_loaders) load_task_jsonable() (in module iblutil.io.jsonable) load_timeline_sync_and_chmap() (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_triangulation() (MesoscopeFOV method) load_video_data() (CameraQC method) load_wheel() (SessionLoader method) load_wheel_reaction_times() (in module brainbox.io.one) load_widefield_mmap() (in module ibllib.io.raw_data_loaders) loadFile() (GraphWindow method) LocalDataHandler (class in ibllib.oneibl.data_handlers) lockfile (FileLock property) log (Task attribute) log_name (TestLogger attribute) log_to_file() (in module iblutil.util) logger (Communicator attribute) (EchoProtocol attribute) lpenv (LightningPose attribute)

M

main() (in module ibllib.qc.critical_reasons) (in module iblutil.io.net.app) 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) mask() (BrainAtlas method) md5() (in module iblutil.io.hashfile) merge_clusters() (SpikeSortingLoader static method) merge_clusters_channels() (in module brainbox.io.one) merge_params() (in module ibllib.io.session_params) MesoscopeCompress (class in ibllib.pipes.mesoscope_tasks) MesoscopeFOV (class in ibllib.pipes.mesoscope_tasks) MesoscopePreprocess (class in ibllib.pipes.mesoscope_tasks) MesoscopeRegisterSnapshots (class in ibllib.pipes.mesoscope_tasks) MesoscopeSync (class in ibllib.pipes.mesoscope_tasks) MesoscopeSyncTimeline (class in ibllib.io.extractors.mesoscope) MesoscopeTask (class in ibllib.pipes.base_tasks) mgrid (BrainCoordinates property) mindist() (Trajectory method) missed_spikes_est() (in module brainbox.metrics.single_units) (in module brainbox.plot) mktree() (FTPPatcher method) mock_input() (in module ibllib.tests.qc.test_critical_reasons) (TestFTPPatcher static method) MOCK_QT (in module ibllib.tests.qc.test_task_qc_viewer), [1] MockExtracor (class in ibllib.tests.extractors.test_extractors) module brainbox brainbox.behavior brainbox.behavior.dlc brainbox.behavior.training brainbox.behavior.wheel brainbox.core brainbox.ephys_plots brainbox.io brainbox.io.one brainbox.io.spikeglx 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.singlecell 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 iblatlas iblatlas.atlas iblatlas.flatmaps iblatlas.genomics iblatlas.genomics.agea iblatlas.genomics.merfish iblatlas.plots iblatlas.regions ibllib ibllib.ephys ibllib.ephys.ephysqc ibllib.ephys.spikes ibllib.ephys.sync_probes ibllib.exceptions 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.habituation_trials ibllib.io.extractors.mesoscope ibllib.io.extractors.opto_trials ibllib.io.extractors.passive_plotting 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.misc ibllib.io.raw_daq_loaders ibllib.io.raw_data_loaders ibllib.io.session_params ibllib.io.video ibllib.misc ibllib.misc.misc ibllib.misc.qt ibllib.oneibl ibllib.oneibl.data_handlers ibllib.oneibl.patcher ibllib.oneibl.registration 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_tasks ibllib.pipes.histology ibllib.pipes.local_server ibllib.pipes.mesoscope_tasks ibllib.pipes.misc ibllib.pipes.neurophotometrics ibllib.pipes.scan_fix_passive_files ibllib.pipes.sync_tasks ibllib.pipes.tasks ibllib.pipes.training_status 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.task_extractors ibllib.qc.task_metrics ibllib.qc.task_qc_viewer ibllib.qc.task_qc_viewer.task_qc ibllib.qc.task_qc_viewer.ViewEphysQC ibllib.tests ibllib.tests.extractors ibllib.tests.extractors.test_ephys_fpga ibllib.tests.extractors.test_ephys_passive ibllib.tests.extractors.test_extractors ibllib.tests.extractors.test_extractors_base ibllib.tests.extractors.test_mesoscope 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.qc.test_task_qc_viewer ibllib.tests.test_base_tasks ibllib.tests.test_dynamic_pipeline ibllib.tests.test_ephys ibllib.tests.test_histology ibllib.tests.test_io ibllib.tests.test_mesoscope 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 iblutil iblutil.io iblutil.io.hashfile iblutil.io.jsonable iblutil.io.net iblutil.io.net.app iblutil.io.net.base iblutil.io.params iblutil.io.parquet iblutil.numerical iblutil.spacer iblutil.tests iblutil.tests.test_io iblutil.tests.test_net iblutil.tests.test_numerical iblutil.tests.test_spacers iblutil.tests.test_util iblutil.util

motion_energy (SessionLoader attribute) motion_energy() (in module brainbox.video) MotionAlignment (class in ibllib.io.extractors.video_motion) MotionAlignmentFullSession (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 iblatlas.atlas) multiple_spike_trains() (in module brainbox.tests.test_metrics)

N

n_description (Note property) n_trials (QcFrame property) name (Communicator attribute), [1] (EchoProtocol attribute) (Pipeline property) (Service attribute) (Task property) NeedlesAtlas() (in module iblatlas.atlas) Neuropixel3BSyncFrontsNonMatching noise_cutoff() (in module brainbox.metrics.single_units)

Note (class in ibllib.qc.critical_reasons) note_title (CriticalInsertionNote property) (CriticalSessionNote property) (Note property) (SignOffNote property) np2str() (in module iblutil.io.parquet) np2uuid() (in module iblutil.io.parquet) numbered_descriptions() (Note method) NvidiaDriverNotReady nxyz (BrainCoordinates property)

O

on_error (Task attribute) on_event() (Communicator method) on_key_press() (Density method) (Traces method) one (Pipeline attribute) (SessionLoader attribute) (SpikeSortingLoader attribute) (Task attribute) (TestRegisterRawDataTask attribute) (TestRegistration attribute)

OptionalDataset (class in ibllib.oneibl.data_handlers) OptionalInput (class in ibllib.oneibl.data_handlers) OptionalOutput (class in ibllib.oneibl.data_handlers) other_reason_prompt() (Note method) outcome (QC property) Output (class in ibllib.oneibl.data_handlers) output() (ExpectedDataset static method) outputs (Task attribute) overall_outcome() (QC static method)

P

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) PassiveSignOffNote (class in ibllib.qc.critical_reasons) PassiveTaskNidq (class in ibllib.pipes.behavior_tasks) PassiveTaskTimeline (class in ibllib.pipes.behavior_tasks) patch_dataset() (Patcher method) (S3Patcher method) patch_datasets() (GlobusPatcher method) (Patcher method) (SDSCPatcher method) patch_imaging_meta() (in module ibllib.io.extractors.mesoscope) patch_settings() (in module ibllib.io.raw_data_loaders) Patcher (class in ibllib.oneibl.patcher) path2eid() (Task method) PAXINOS_CCF_LANDMARKS_MLAPDV_UM (in module iblatlas.atlas), [1] peri_event_time_histogram() (in module brainbox.plot) phi (Insertion attribute) phy_model_from_ks2_path() (in module ibllib.ephys.ephysqc) pid (SpikeSortingLoader attribute) pid2ref (SpikeSortingLoader property) pid_label (ReportSnapshotProbe property) pinColumn() (GraphWindow method) 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_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_points_on_slice() (in module iblatlas.plots) plot_polygon() (in module iblatlas.plots) plot_polygon_with_hole() (in module iblatlas.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_rawdata_snippet() (SpikeSortingLoader method) plot_reaction_time() (in module brainbox.behavior.training) plot_reaction_time_over_trials() (in module brainbox.behavior.training) plot_rfmapping() (in module ibllib.io.extractors.passive_plotting) plot_scalar_on_barplot() (in module iblatlas.plots) plot_scalar_on_flatmap() (in module iblatlas.plots) plot_scalar_on_slice() (in module iblatlas.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 iblatlas.plots) plot_swanson_vector() (in module iblatlas.plots) plot_sync_channels() (in module ibllib.io.extractors.passive_plotting) plot_tilted_slice() (BrainAtlas method) plot_timeline() (in module ibllib.io.extractors.mesoscope) 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 iblatlas.plots) plot_wheel_position() (in module brainbox.behavior.dlc) plot_with_behavior() (MotionAlignmentFullSession method) plot_without_behavior() (MotionAlignmentFullSession method)

PlotCanvas (class in ibllib.qc.task_qc_viewer.ViewEphysQC) PlotWindow (class in ibllib.qc.task_qc_viewer.ViewEphysQC) plt_window() (in module brainbox.behavior.dlc) pname (SpikeSortingLoader attribute) point (Trajectory attribute) PopeyeDataHandler (class in ibllib.oneibl.data_handlers) populate_raw_spikeglx() (in module ibllib.tests.fixtures.utils) populate_task_settings() (in module ibllib.tests.fixtures.utils) port (Communicator property) pose (SessionLoader attribute) prepare_lr_data() (in module iblatlas.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) (EphysCompressNP1 attribute) (EphysCompressNP21 attribute) (EphysCompressNP24 attribute) (EphysPulses attribute) (EphysRegisterRaw attribute) (EphysSyncPulses attribute) (EphysSyncRegisterRaw attribute) (FibrePhotometrySync attribute) (HabituationRegisterRaw attribute) (HabituationTrialsBpod attribute) (HabituationTrialsNidq attribute) (MesoscopeCompress attribute) (MesoscopeFOV attribute) (MesoscopePreprocess attribute) (MesoscopeRegisterSnapshots attribute) (MesoscopeSync attribute) (PassiveRegisterRaw attribute) (PassiveTaskNidq attribute) (PassiveTaskTimeline attribute) (RawEphysQC attribute) (RegisterRawDataTask attribute) (SpikeSorting attribute) (SyncMtscomp attribute) (SyncPulses attribute) (SyncRegisterRaw attribute) (Task attribute) (TrainingStatus 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) 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) process() (MotionAlignmentFullSession method) project() (Trajectory method) project_mlapdv() (MesoscopeFOV method) propagate_down() (BrainRegions method) protocol (Communicator property) protocol2extractor() (in module ibllib.io.extractors.base) Provenance (class in ibllib.pipes.mesoscope_tasks) ptp_over_noise() (in module brainbox.metrics.single_units) pupil (SessionLoader attribute)

Q

QC (class in ibllib.qc.base) qc (QcFrame attribute) qc_fpga_task() (in module ibllib.ephys.ephysqc) qc_gui_cli() (in module ibllib.qc.task_qc_viewer.task_qc)

qc_shifts() (MotionAlignmentFullSession method) QcFrame (class in ibllib.qc.task_qc_viewer.task_qc) query_criterion() (in module brainbox.behavior.training) quick_unit_metrics() (in module brainbox.metrics.single_units)

R

ram (Task attribute) range_str() (in module iblutil.util) raster() (SpikeSortingLoader method) raw_data_files (SpikeSortingLoader attribute) raw_destripe() (in module ibllib.plots.figures) raw_electrophysiology() (SpikeSortingLoader method) raw_names (Widefield attribute) raw_qc_session() (in module ibllib.ephys.ephysqc) raw_waveforms() (SpikeSortingLoader method) RawEphysQC (class in ibllib.pipes.ephys_tasks) RawEphysSignOffNote (class in ibllib.qc.critical_reasons) rawImagingData (MesoscopeSyncTimeline attribute) rcoeff() (in module iblutil.numerical) read() (in module iblutil.io.jsonable) (in module iblutil.io.params) (Streamer method) read_flag_file() (in module ibllib.io.flags) read_params() (in module ibllib.io.session_params) read_params_file() (DynamicTask method) READY (TrainingStatus attribute) READY4DELAY (TrainingStatus attribute) READY4EPHYSRIG (TrainingStatus attribute) READY4RECORDING (TrainingStatus attribute) reasons_prompt() (Note method) regions_from_allen_csv() (in module iblatlas.regions) register (ExpectedDataset property) register_aligned_track() (in module ibllib.pipes.histology) register_chronic_track() (in module ibllib.pipes.histology) register_chronic_track_files() (in module ibllib.pipes.histology) register_dataset() (in module ibllib.oneibl.registration) (Patcher method) register_datasets() (Patcher method) (Task method) register_fov() (MesoscopeFOV method) register_image() (Snapshot method) register_images() (ReportSnapshot method) (ReportSnapshotProbe method) (Snapshot method) (Task method) register_new_session() (in module ibllib.tests.fixtures.utils) register_session() (IBLRegistrationClient method) register_session_raw_data() (in module ibllib.oneibl.registration) register_snapshots() (RegisterRawDataTask method) register_track() (in module ibllib.pipes.histology) register_track_files() (in module ibllib.pipes.histology) RegisterRawDataTask (class in ibllib.pipes.base_tasks) regress() (in module brainbox.population.decode) remap() (BrainRegions method) RemoteAwsDataHandler (class in ibllib.oneibl.data_handlers) RemoteEC2DataHandler (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_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) reorder_data() (in module iblatlas.plots) report_health() (in module ibllib.pipes.local_server) ReportSnapshot (class in ibllib.plots.snapshot) ReportSnapshotProbe (class in ibllib.plots.snapshot) require_qt() (in module ibllib.misc.qt) rerun() (Pipeline method) (Task method) rerun_failed() (Pipeline method) reset_params() (TestFTPPatcher method) resolve_manual() (AlignmentQC method) responsive_units() (in module brainbox.task.closed_loop) revision (SessionLoader 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) roi_detection() (MesoscopePreprocess method) roi_mlapdv() (MesoscopeFOV method) role (EchoProtocol attribute) (EchoProtocol property) rrmdir() (in module iblutil.util) 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_app() (in module ibllib.misc.qt) run_count (Task02_error attribute) run_extractor_classes() (in module ibllib.io.extractors.base) run_qc() (BehaviourTask method) (ChoiceWorldTrialsBpod method) (ChoiceWorldTrialsNidq method) (HabituationTrialsBpod method) (HabituationTrialsNidq method) (VideoSyncQcBpod method) (VideoSyncQcCamlog method) (VideoSyncQcNidq method) (VideoTask method) RUNNING (ExpStatus attribute)

S

S3_BUCKET_IBL (in module iblatlas.atlas), [1] S3Patcher (class in ibllib.oneibl.patcher) samples2times() (SpikeSortingLoader method) samples_to_cm() (in module brainbox.behavior.wheel) save() (Bunch method) (in module iblutil.io.parquet) save_dataframe() (in module ibllib.pipes.training_status) save_names (BaseExtractor attribute) (BiasedTrials attribute) (CameraTimestampsBpod attribute) (EphysTrials attribute) (FpgaTrials attribute) (FpgaTrialsHabituation attribute) (LaserBool attribute) (MesoscopeSyncTimeline attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (TrainingTrials 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) scratch_folder_run (SpikeSorting property) scripts (DLC attribute) (LightningPose 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) send() (Communicator method) (EchoProtocol method) Server (EchoProtocol attribute), [1] server (Services attribute) server() (EchoProtocol static method) server_uri (Communicator attribute), [1] (EchoProtocol attribute) ServerDataHandler (class in ibllib.oneibl.data_handlers) ServerGlobusDataHandler (class in ibllib.oneibl.data_handlers) Service (class in iblutil.io.net.base) Services (class in iblutil.io.net.app) session_path (BaseExtractor attribute) (SessionLoader attribute) (SpikeSortingLoader attribute) (TestRegisterRawDataTask 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_hidden() (in module iblutil.io.params) 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) setUp() (MesoscopeCompress method) (MesoscopePreprocess method) (RemoteAwsDataHandler method) (RemoteEC2DataHandler method) (RemoteGlobusDataHandler method) (RemoteHttpDataHandler method) (SDSCDataHandler method) (ServerGlobusDataHandler method) (Task method) (TaskGpuLock method) (TestArrangeChannels2Bank method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestDynamicTask method) (TestEphysQC method) (TestExpectedDataset method) (TestExperimentDescriptionRegisterRaw method) (TestExtractedWheelUnits method) (TestExtractorMaps method) (TestExtractTrialData method) (TestFileLock method) (TestFTPPatcher method) (TestGetTrialsTasks method) (TestGlobusPatcher method) (TestHabituationQC method) (TestHistology method) (TestIBLChannelMaps method) (TestIO_ALF method) (TestLocalServer method) (TestMesoscopePreprocess method) (TestMesoscopeSyncTimeline method) (TestPipelineAlyx method) (TestPipesMisc method) (TestPlotBase method) (TestPopulation method) (TestQC method) (TestRawDaqLoaders method) (TestRegisterFOV method) (TestRegisterRawDataTask method) (TestRegistration method) (TestScanFixPassiveFiles method) (TestScatterXYC method) (TestSDSCDataHandler method) (TestsEphysAlignment method) (TestsEphysReconstruction method) (TestSessionParams method) (TestsFolderStructure method) (TestSignOffNote method) (TestsJsonable method) (TestsMisc method) (TestSpacersFromFronts method) (TestsParams method) (TestsPassiveExtractor method) (TestsRawDataLoaders method) (TestSyncExtraction method) (TestTask method), [1] (TestTaskMetrics method) (TestTaskQC method) (TestTraining method) (TestTrials method) (TestUserPmtSess method) (TestVideo method), [1] (TestWheel method) (TestWheelExtraction method) (TestWheelLoaders method) (TestWheelMovesExtraction method) (TestWidefieldExtractor method) (TestWidefieldRegister method)

setup_logger() (in module iblutil.util) setUpClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestCameraQC class method) (TestChronicTracingQC class method) (TestDlcQC class method) (TestDlcQcPlot class method) (TestEphysQC class method) (TestFileLock class method) (TestQC class method) (TestRegisterRawDataTask class method) (TestRegistration class method) (TestSnapshot class method) (TestTracingQc class method) (TestUploadToFlatIron method) (TestVideo class method) sha1() (in module iblutil.io.hashfile) SHELL_SCRIPT (SpikeSorting attribute) show_session_task_qc() (in module ibllib.qc.task_qc_viewer.task_qc) showEvent() (GraphWindow method) shuffle_analysis() (in module brainbox.population.cca) sign_off() (SignOffNote method) sign_off_categories (ExperimentDescriptionRegisterRaw attribute) sign_off_dict() (in module ibllib.qc.base) signature (AudioCompress property) (AudioSync property) (BehaviourPlots property) (ChoiceWorldTrialsBpod property) (ChoiceWorldTrialsNidq property) (ChoiceWorldTrialsTimeline property) (DLC property) (EphysCompressNP1 property) (EphysCompressNP21 property) (EphysCompressNP24 property) (EphysPostDLC property) (EphysPulses property) (EphysRegisterRaw property) (EphysSyncPulses property) (EphysSyncRegisterRaw property) (ExperimentDescriptionRegisterRaw property) (FibrePhotometrySync property) (HabituationRegisterRaw property) (HabituationTrialsBpod property) (HabituationTrialsNidq property) (LightningPose property) (MesoscopeCompress property) (MesoscopeFOV property) (MesoscopePreprocess property) (MesoscopeRegisterSnapshots property) (MesoscopeSync property) (PassiveRegisterRaw property) (PassiveTaskNidq property) (PassiveTaskTimeline property) (RawEphysQC property) (ReportSnapshotProbe attribute) (SpikeSorting property) (SyncMtscomp property) (SyncPulses property) (SyncRegisterRaw property) (Task property) (TrainingStatus property) (TrialRegisterRaw property) (VideoCompress property) (VideoConvert property) (VideoRegisterRaw property) (VideoSyncQcBpod property) (VideoSyncQcCamlog property) (VideoSyncQcNidq property) (WidefieldCompress property) (WidefieldFOV property) (WidefieldPreprocess property) (WidefieldRegisterRaw property) (WidefieldSync property) SignOffNote (class in ibllib.qc.critical_reasons) sigtest_linshift() (in module brainbox.population.decode) sigtest_pseudosessions() (in module brainbox.population.decode) single_cluster_raster() (MotionAlignmentFullSession static method) skip_task_replay() (in module ibllib.io.extractors.ephys_passive) sleepless() (in module ibllib.pipes.misc) slice() (BrainAtlas method) slidingRP_viol() (in module brainbox.metrics.single_units) Snapshot (class in ibllib.plots.snapshot) SomePipeline (class in ibllib.tests.test_tasks) SORTER_REPOSITORY (SpikeSorting attribute) Spacer (class in iblutil.spacer) spectrum() (in module ibllib.plots.misc) sph2cart() (in module iblatlas.atlas) spike_sorter (SpikeSortingLoader attribute) SPIKE_SORTER_NAME (SpikeSorting attribute) spike_sorting_metrics() (in module brainbox.metrics.single_units) spike_sorting_metrics_ks2() (in module ibllib.ephys.ephysqc) spike_sorting_path (SpikeSortingLoader attribute) SpikeSorting (class in ibllib.pipes.ephys_tasks) (class in ibllib.plots.figures) SpikeSortingLoader (class in brainbox.io.one) SpikeSortingSignOffNote (class in ibllib.qc.critical_reasons) 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) starplot() (in module ibllib.plots.misc) start() (EchoProtocol method) (Service method) (Services method) status() (EchoProtocol method) (Service method) (Services method) stop() (EchoProtocol method) (Service method) (Services method) STOPPED (ExpStatus attribute) str2class() (in module ibllib.pipes.tasks) str2np() (in module iblutil.io.parquet) Streamer (class in brainbox.io.spikeglx) structarr() (in module ibllib.misc.misc) subject (TestRegistration attribute) surface_normal() (in module ibllib.pipes.mesoscope_tasks) swanson() (in module iblatlas.flatmaps) swanson_json() (in module iblatlas.flatmaps) sync() (in module brainbox.processing) (in module ibllib.ephys.sync_probes) SYNC_BATCH_SIZE_SECS (in module ibllib.io.extractors.ephys_fpga), [1] sync_bpod_clock() (FpgaTrials static method) sync_field (FpgaTrials attribute) (FpgaTrialsHabituation attribute) (TimelineTrials attribute) sync_gen() (TestSyncExtraction method) 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_collection (BaseBpodTrialsExtractor attribute) task_queue() (in module ibllib.pipes.local_server) 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) TaskSignOffNote (class in ibllib.qc.critical_reasons) tearDown() (MesoscopeCompress method) (MesoscopePreprocess method) (Task method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestEphysQC method) (TestExtractTrialData method) (TestIO_ALF method) (TestLogger method) (TestMesoscopePreprocess method) (TestPipelineAlyx method) (TestPipesMisc method) (TestRegisterFOV method) (TestRegistration method) (TestScanFixPassiveFiles method) (TestServices method) (TestsFolderStructure method) (TestSignOffNote method) (TestsJsonable method) (TestsMisc method) (TestsParams method) (TestsPassiveExtractor method) (TestsRawDataLoaders method) (TestUDP method) (TestUserPmtSess method) (TestWebSockets method) (TestWidefieldExtractor method) (TestWidefieldRegister method) (WidefieldPreprocess method) tearDownClass() (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestCameraQC class method) (TestChronicTracingQC class method) (TestDlcQC class method) (TestDlcQcPlot class method) (TestEphysQC class method) (TestQC class method) (TestRegisterRawDataTask class method) (TestRegistration 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_aggregate() (TestSessionParams method) test_align_to_trial() (TestTTLsExtraction method) test_alignments() (TestAlignmentQcExisting method) (TestAlignmentQcManual method) test_alyx() (TestUDP method) test_and() (TestExpectedDataset method) test_assert_trials_data() (TestBehaviourTask method) test_assert_valid_label() (TestVideo method) test_assign() (TestServices method) test_attribute_times() (TestCameraExtractors method) test_audio_ttl_start_up_down() (TestTTLsExtraction method) test_audio_ttl_wiring_camera() (TestTTLsExtraction method) test_awaiting_response() (TestUDP method) test_between_sorted_multiple_times() (TestBetweeenSorted method) test_between_sorted_out_of_range() (TestBetweeenSorted method) test_between_sorted_single_time() (TestBetweeenSorted method) test_bincount_2d() (TestBincount2D method) test_bpod_trace_extraction() (TestTTLsExtraction method) test_bunch_io() (TestBunch method) test_callback_error() (TestUDP 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_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_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_close() (TestServices method) (TestUDP method) test_clusters_metrics() (in module brainbox.tests.test_metrics) test_communicator() (TestUDP method) test_compute() (TestHabituationQC method) test_compute_cluster_averag() (TestProcessing method) test_compute_dateset_qc_status() (TestAggregateOutcome method) test_compute_outcome_from_extended_qc() (TestQC method) test_concatenate_and_computations() (TestTraining method) test_confirmed_send_validation() (TestUDP method) test_connection_made_validation() (TestUDP method) (TestWebSockets method) test_consolidate_exptQC() (TestMesoscopePreprocess method) test_copy() (TestBunch method) test_create_alyx_probe_insertions() (TestPipesMisc method) test_create_sessions() (TestRegistration method) test_custom_spacer_extract() (TestSpacersFromFronts method) test_data_content() (TestUploadToFlatIron method) test_dataset_from_name() (TestDataHandlers method) test_date2isostr() (TestUtils method) test_decode() (TestBase method) test_decorator_argument_passing() (TestSleeplessDecorator method) test_default() (TestPlotBase method) test_delete_empty_folders() (TestsMisc method) test_differentiate_units() (TestTask method) test_dir_size() (TestDirSize method) test_direction_changes() (TestWheel method) test_drift_estimate() (in module brainbox.tests.test_metrics) test_dsets_2_path() (TestAlyx2Path method) test_empty() (TestSpacersFromFronts method) test_encode() (TestBase 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() (TestDlcQC method) (TestEphysQC method) test_ensure_list() (TestEnsureList method) test_experiment_description_registration() (TestExperimentDescriptionRegisterRaw method) test_ExpMessage() (TestBase method) test_extended_qc() (TestQC method) test_external_ip() (TestBase method) test_extract_first_movement_times() (TestWheelMovesExtraction method) test_extract_spacers() (TestSpacersFromFronts method) test_extract_sync_timeline() (TestRawDaqLoaders method) test_extract_wheel_moves() (TestExtractedWheelUnits method) (TestWheelMovesExtraction method) test_file_handler_log_input() (TestLogger method) test_file_handler_setup() (TestLogger method) test_file_handler_stand_alone() (TestLogger method) test_file_lock_async() (TestFileLock method) test_file_lock_sync() (TestFileLock method) test_filename_parser() (TestHistology method) test_filter() (TestExpectedDataset method) test_find_pairs() (TestScanFixPassiveFiles method) test_find_spacers() (TestSpacer method) test_find_trial_ids() (TestTrials method) test_find_triangle() (TestMesoscopeFOV method) test_firing_rate() (in module brainbox.tests.test_singlecell) test_flatten() (TestFlatten method) test_frame2ttl_flickers() (TestTTLsExtraction 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_active_wheel_period() (TestCameraQC method) test_get_bpod_custom_extractor() (TestGetBpodExtractor method) test_get_bpod_extractor() (TestGetBpodExtractor method) test_get_bpod_extractor_class() (TestExtractorMaps method) test_get_bpod_trials_task() (TestTaskQC method) test_get_brain_exit_entry() (TestHistology method) test_get_choice() (TestExtractTrialData method) test_get_collections() (TestSessionParams method) test_get_collections_repeat_protocols() (TestSessionParams method) test_get_contrastLR() (TestExtractTrialData method) test_get_default_tau() (TestMesoscopePreprocess method) test_get_device_collection() (TestDynamicTask 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_lab() (TestUtils method) test_get_mac() (TestGetMac method) test_get_movement_onset() (TestWheel method) test_get_new_filename() (TestPipesMisc method) test_get_pause_duration() (TestExtractTrialData method) test_get_plane_paths() (TestMesoscopePreprocess method) test_get_probabilityLeft() (TestExtractTrialData method) test_get_protocol() (TestBehaviourTask method) test_get_protocol_number() (TestBehaviourTask method) (TestSessionParams method) test_get_provenance() (TestMesoscopeFOV 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_stimOnTrigger_times() (TestExtractTrialData method) test_get_task_collection() (TestBehaviourTask method) (TestCameraQC method) test_get_task_extractor_map() (TestExtractorMaps method) test_get_timeshifts_multidepth() (TestMesoscopeSyncTimeline method) test_get_trials_tasks() (TestGetTrialsTasks method) test_getData() (TestDataHandlers method) test_gpu_lock_and_local_data_handler() (TestLocks method) test_groom_pin_state() (TestCameraExtractors method) test_guiinput_ins() (TestUserPmtSess method) test_handler() (TestSDSCDataHandler method) test_hash_uuids() (HashUUIDs method) test_histology_get_brain_regions() (TestHistology method) test_histology_insertion_from_track() (TestHistology method) test_ibl_sync_maps() (TestIBLChannelMaps method) test_identifiers() (TestExpectedDataset method) test_image() (TestPlotBase method) test_image_motion_registration() (TestMesoscopePreprocess method) test_image_scaling() (TestSnapshot method) test_impeccable_dataset() (TestFpgaTask method) test_in_training() (TestTraining method) test_init() (TestServices method) test_input_files_to_register() (TestTask method) test_interpolate_rf_mapping_stimulus() (TestsPassiveExtractor method) test_is_success() (TestBase method) test_is_trials_object_attribute() (TestFpgaTrials method) test_ismember() (TestIsmember method) test_ismember2d() (TestIsmember method) test_ismember2d_uuids() (TestIsmember 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_line() (TestPlotBase method) test_linear_scaling() (TestsEphysAlignment method) test_listable() (TestListable 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_iti() (TestIO_ONE method) test_load_passive_stim_meta() (TestsPassiveExtractor method) test_load_settings() (TestsRawDataLoaders method) test_load_task_jsonable() (TestLoadTaskData method) test_load_task_jsonable_partial() (TestLoadTaskData method) test_merge_params() (TestSessionParams method) test_meta() (TestMesoscopePreprocess method) test_move_rename_pairs() (TestScanFixPassiveFiles method) test_movement_log() (TestWheelMovesExtraction method) test_movements() (TestWheel method) test_movements_FPGA() (TestWheel method) test_nearest_neighbour_1d() (TestMesoscopeFOV method) test_new_default_param() (TestsParams method) test_no_duplicates() (TestLogger method)

test_no_pad() (TestArrangeChannels2Bank method) test_no_scaling() (TestsEphysAlignment method) test_noise() (TestSpacersFromFronts method) test_noise_cut_off() (in module brainbox.tests.test_metrics) test_note_already_existing() (TestUserPmtSess method) test_note_probe_ins() (TestUserPmtSess method) test_offset() (TestsEphysAlignment method) test_on_error_received() (TestUDP method) test_on_event() (TestUDP method) test_or() (TestExpectedDataset 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_uri() (TestBase method) test_patch_data() (TestSessionParams method) test_patch_datasets() (TestGlobusPatcher method) test_patch_imaging_meta() (TestImagingMeta method) test_peths_synthetic() (TestPeths method) test_pipeline_alyx() (TestPipelineAlyx method) test_plotting() (TestBunch method) test_probe() (TestPlotBase method) test_probe_names_from_session_path() (TestPipesMisc method) test_protocol2extractor() (TestExtractorMaps method) test_psychometric_insufficient_data() (TestTraining method) test_query_criterion() (TestTraining method) test_range_str() (TestRangeStr method) test_rcoeff() (TestRcoeff method) test_read_yaml() (TestSessionParams method) test_ready4delay() (TestTraining method) test_ready4ephys() (TestTraining method) test_ready4recording() (TestTraining method) test_receive_validation() (TestUDP method) test_register_chained_session() (TestRegistration method) test_register_fov() (TestRegisterFOV method) test_register_multiple() (TestSnapshot method) test_register_snapshots() (TestRegisterRawDataTask method) test_registration_datasets() (TestRegistration method) test_registration_session() (TestRegistration method) test_registration_session_passive() (TestRegistration method) test_regress() (TestPopulation method) test_remove_files() (TestWidefieldExtractor method) test_rename_and_move() (TestPipesMisc method) test_rename_files() (TestRegisterRawDataTask method), [1] (TestWidefieldRegister method) test_responsive_units() (TestTask method) test_rf_map() (TestPassive method) test_RGB_conversion() (TestScatterXYC method) test_RGB_conversion_with_clim() (TestScatterXYC method) test_roc_between_two_events() (TestTask method) test_roc_single_event() (TestTask method) test_roi_detection() (TestMesoscopePreprocess method) test_rrmdir() (TestRrmdir method) test_save_files() (TestWidefieldExtractor method) test_saving_method() (TestBaseExtractorSavingMethods method) test_scan_fix() (TestScanFixPassiveFiles method) test_scatter() (TestPlotBase method) test_send_validation() (TestWebSockets method) test_sequential_signal() (TestServices method) test_server_upload_data() (TestDataHandlers method) test_service_methods() (TestServices method) test_set_hidden() (TestParams method) test_setup() (TestFTPPatcher method) test_setup_compressed() (TestMesoscopePreprocess method) test_setup_uncompressed() (TestMesoscopePreprocess method) test_show_session_task_qc() (TestTaskQC method) test_sign_off() (TestSignOffNote method) test_sigtest_linshift() (TestPopulation method) test_sigtest_pseudosessions() (TestPopulation method) test_size_outputs() (TestExtractTrialData method) test_snapshot_default() (TestSnapshot method) test_spacer() (TestSpacer method) test_spacer_support() (TestBehaviourTask method) test_spike_detection() (TestDetectSpikes method) test_star_plot() (TestMiscPlot method) test_start() (TestUDP method) (TestWebSockets method) test_stim_aligned() (TestPassive method) test_stimOnOffFreeze_times() (TestExtractTrialData method) test_str2class() (TestMisc method) test_surface_normal() (TestMesoscopeFOV method) test_sync() (TestBunch method) (TestProcessing method) test_sync_3A() (TestSyncExtraction method) test_sync_3B() (TestSyncExtraction method) test_sync_bpod_bonsai_poor_quality_timestamps() (TestSyncWheelBpod method) test_sync_label() (TestMisc method) test_sync_nidq() (TestSyncExtraction method) test_task_queue() (TestLocalServer method) test_time_fields() (TestFpgaTrials method) test_timeline_meta2chmap() (TestRawDaqLoaders method) test_timeline_meta2wiring() (TestRawDaqLoaders method) test_timestamp_saving() (TestWidefieldExtractor method) test_traces_by_trial() (TestWheel method) test_tracing_exists() (TestChronicTracingQC method) (TestTracingQc method) test_tracing_not_exists() (TestChronicTracingQC method) (TestTracingQc method) test_trained_1a() (TestTraining method) test_trained_1b() (TestTraining method) test_training_to_bias() (TestTraining method) test_ttl_bpod_gaelle_writes_protocols_but_guido_doesnt_read_them() (TestTTLsExtraction method) test_type() (TestServices method) test_uniform_scaling() (TestsEphysAlignment method) test_update() (TestQC method) test_update_collections() (TestDataHandlers method) test_update_dataset_qc() (TestDatasetQC method) test_update_surgery_json() (TestMesoscopeFOV method) test_upload_existing_note() (TestSignOffNote method) test_upload_note_prompt() (TestSignOffNote method) test_upload_to_flatiron() (TestUploadToFlatIron method) test_url_from_eid() (TestVideo method) test_userinput_ins() (TestUserPmtSess method) test_userinput_sess() (TestUserPmtSess method) test_uuids_conversions() (TestParquet method) test_uuids_intersections() (TestParquet method) test_velocity_filtered() (TestWheel method) test_wheel_folders() (TestExtractTrialData method) test_wheel_trace_from_sync() (TestWheelExtraction method) test_wiggle() (TestMiscPlot method) test_with_depth() (TestArrangeChannels2Bank method) test_within_ranges() (TestWithinRanges 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) test_xor() (TestExpectedDataset 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) TestBase (class in iblutil.tests.test_net) TestBaseExtractorSavingMethods (class in ibllib.tests.extractors.test_extractors) TestBehaviourTask (class in ibllib.tests.test_base_tasks) TestBetweeenSorted (class in iblutil.tests.test_numerical) TestBincount2D (class in iblutil.tests.test_numerical) TestBunch (class in brainbox.tests.test_cca) (class in iblutil.tests.test_util) TestCameraExtractors (class in ibllib.tests.extractors.test_extractors) TestCameraQC (class in ibllib.tests.qc.test_camera_qc) TestChronicTracingQC (class in ibllib.tests.qc.test_alignment_qc) TestCreateLegacyAcqusitionDescriptions (class in ibllib.tests.test_dynamic_pipeline) TestDataHandlers (class in ibllib.tests.test_oneibl) TestDatasetQC (class in ibllib.tests.qc.test_task_metrics) TestDetectBadChannels (class in ibllib.tests.test_ephys) TestDetectSpikes (class in ibllib.tests.test_ephys) TestDirSize (class in iblutil.tests.test_util) TestDlcQC (class in ibllib.tests.qc.test_dlc_qc) TestDlcQcPlot (class in ibllib.tests.test_plots) TestDynamicTask (class in ibllib.tests.test_tasks) TestEnsureList (class in iblutil.tests.test_util) TestEphysQC (class in ibllib.tests.test_ephys) TestExpectedDataset (class in ibllib.tests.test_oneibl) TestExperimentDescriptionRegisterRaw (class in ibllib.tests.test_tasks) TestExtractedWheelUnits (class in ibllib.tests.extractors.test_ephys_fpga) TestExtractorMaps (class in ibllib.tests.extractors.test_extractors_base) TestExtractTrialData (class in ibllib.tests.extractors.test_extractors) TestFileLock (class in iblutil.tests.test_io) testFlagFileRead() (TestsRawDataLoaders method) TestFlatten (class in iblutil.tests.test_util) TestFpgaTask (class in ibllib.tests.test_ephys) TestFpgaTrials (class in ibllib.tests.extractors.test_ephys_fpga) TestFTPPatcher (class in ibllib.tests.test_oneibl) TestGetBpodExtractor (class in ibllib.tests.extractors.test_extractors) TestGetMac (class in iblutil.tests.test_util) TestGetTrialsTasks (class in ibllib.tests.test_dynamic_pipeline) TestGlobusPatcher (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) TestImagingMeta (class in ibllib.tests.test_mesoscope) TestIO_ALF (class in brainbox.tests.test_io) TestIO_ONE (class in brainbox.tests.test_io) TestIsmember (class in iblutil.tests.test_numerical) TestListable (class in iblutil.tests.test_util) TestLoadTaskData (class in iblutil.tests.test_io) TestLocalServer (class in ibllib.tests.test_pipes) TestLocks (class in ibllib.tests.test_tasks) TestLogger (class in iblutil.tests.test_util) TestMesoscopeFOV (class in ibllib.tests.test_mesoscope) TestMesoscopePreprocess (class in ibllib.tests.test_mesoscope) TestMesoscopeSyncTimeline (class in ibllib.tests.extractors.test_mesoscope) TestMisc (class in ibllib.tests.test_dynamic_pipeline) (class in ibllib.tests.test_tasks) TestMiscPlot (class in ibllib.tests.test_plots) TestNeuropixel (class in ibllib.tests.test_ephys) TestParams (class in iblutil.tests.test_io) TestParquet (class in iblutil.tests.test_io) 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) TestRangeStr (class in iblutil.tests.test_util) TestRawDaqLoaders (class in ibllib.tests.test_io) TestRcoeff (class in iblutil.tests.test_numerical) testReadWrite() (TestsJsonable method) TestRegisterFOV (class in ibllib.tests.test_mesoscope) TestRegisterRawDataTask (class in ibllib.tests.test_base_tasks) (class in ibllib.tests.test_pipes) TestRegistration (class in ibllib.tests.test_oneibl) TestRrmdir (class in iblutil.tests.test_util) tests_headers() (TestNeuropixel method) TestScanFixPassiveFiles (class in ibllib.tests.test_pipes) TestScatterXYC (class in brainbox.tests.test_plot_base) TestSDSCDataHandler (class in ibllib.tests.test_oneibl) TestsEphysAlignment (class in ibllib.tests.test_histology) TestsEphysReconstruction (class in ibllib.tests.test_histology) TestServices (class in iblutil.tests.test_net) TestSessionParams (class in ibllib.tests.test_io) TestsFolderStructure (class in ibllib.tests.extractors.test_ephys_fpga) TestSignOffNote (class in ibllib.tests.qc.test_critical_reasons) TestsJsonable (class in iblutil.tests.test_io) TestSleeplessDecorator (class in ibllib.tests.test_pipes) TestsMisc (class in ibllib.tests.test_io) TestSnapshot (class in ibllib.tests.test_plots) TestSpacer (class in iblutil.tests.test_spacers) TestSpacersFromFronts (class in iblutil.tests.test_spacers) TestsParams (class in ibllib.tests.test_io) TestsPassiveExtractor (class in ibllib.tests.extractors.test_ephys_passive) TestsRawDataLoaders (class in ibllib.tests.test_io) TestSyncExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestSyncWheelBpod (class in ibllib.tests.extractors.test_extractors) TestTask (class in brainbox.tests.test_task) (class in ibllib.tests.test_tasks) TestTaskMetrics (class in ibllib.tests.qc.test_task_metrics) TestTaskQC (class in ibllib.tests.qc.test_task_qc_viewer) TestTracingQc (class in ibllib.tests.qc.test_alignment_qc) TestTraining (class in brainbox.tests.test_behavior) TestTrials (class in brainbox.tests.test_trials) TestTTLsExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestUDP (class in iblutil.tests.test_net) TestUploadToFlatIron (class in ibllib.tests.qc.test_alignment_qc) TestUserPmtSess (class in ibllib.tests.qc.test_critical_reasons) TestUtils (class in ibllib.tests.test_oneibl) (class in ibllib.tests.test_time) TestVideo (class in brainbox.tests.test_video) (class in ibllib.tests.test_io) TestWebSockets (class in iblutil.tests.test_net) 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) TestWithinRanges (class in iblutil.tests.test_numerical) theta (Insertion attribute) thresholding() (TaskQC static method) tilted_slice() (BrainAtlas method) time_elapsed_secs (Task attribute) time_out_secs (Task attribute) timeline (TimelineTrials attribute) timeline_get_channel() (in module ibllib.io.raw_daq_loaders) timeline_meta2chmap() (in module ibllib.io.raw_daq_loaders) timeline_meta2wiring() (in module ibllib.io.raw_daq_loaders) TimelineTrials (class in ibllib.io.extractors.mesoscope) timeout (Services attribute) times (Spacer property) TimeSeries (class in brainbox.core) timesprobe2times() (SpikeSortingLoader method) tip (Insertion property) tmp (TestFileLock attribute) tmpdir (TestRegisterRawDataTask attribute) to_fronts() (TestSpacersFromFronts static method) Traces (class in ibllib.plots.misc) traces_by_trial() (in module brainbox.behavior.wheel) track2feature() (EphysAlignment static method) TRAINED (TrainingStatus attribute) TRAINED_1A (TrainingStatus attribute) TRAINED_1B (TrainingStatus attribute) TrainingStatus (class in brainbox.behavior.training) (class in ibllib.pipes.behavior_tasks) TrainingTrials (class in ibllib.io.extractors.training_trials) Trajectory (class in iblatlas.atlas) trajectory (Insertion property) (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestUploadToFlatIron attribute) trial_times_to_times() (in module ibllib.io.raw_data_loaders) TrialRegisterRaw (class in ibllib.pipes.behavior_tasks) trials (SessionLoader attribute) TRIALS_KEYS (in module brainbox.behavior.training), [1] tv_double_clicked() (GraphWindow method) type (CameraQC property)

U

UNBIASABLE (TrainingStatus attribute) uncycle_pgts() (in module ibllib.time) uninhibit() (WindowsInhibitor static method) unit_stability() (in module brainbox.metrics.single_units) UNTRAINABLE (TrainingStatus attribute) update() (QC method) update_collections() (in module ibllib.oneibl.data_handlers) update_dataset_qc() (in module ibllib.qc.task_metrics) update_existing_note() (CriticalNote method) (Note method) (SignOffNote method) update_experimenter_evaluation() (AlignmentQC method) update_extended_qc() (QC method) update_surgery_json() (MesoscopeFOV method) updateDataframe() (GraphWindow method)

upload_channels() (AlignmentQC method) upload_note() (Note method) (SignOffNote method) upload_training_table_to_aws() (in module ibllib.pipes.training_status) uploadData() (DataHandler method) (PopeyeDataHandler method) (RemoteAwsDataHandler method) (RemoteEC2DataHandler method) (RemoteGlobusDataHandler method) (RemoteHttpDataHandler method) (SDSCDataHandler method) (ServerDataHandler method) (ServerGlobusDataHandler method) url (SpikeSortingLoader property) url_from_eid() (in module ibllib.io.video) uuid2np() (in module iblutil.io.parquet)

V

validate() (ExpMessage static method) validate_ttl_test() (in module ibllib.ephys.ephysqc) validate_uri() (in module iblutil.io.net.base) var_names (BaseExtractor attribute) (BiasedTrials attribute) (CameraTimestampsBpod attribute) (EphysTrials attribute) (FpgaTrials attribute) (FpgaTrialsHabituation attribute) (HabituationTrials attribute) (LaserBool attribute) (MesoscopeSyncTimeline attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (TrainingTrials attribute) (Wheel attribute) (Widefield attribute) vector (Trajectory attribute)

velocity_filtered() (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) VideoSignOffNote (class in ibllib.qc.critical_reasons) VideoStreamer (class in ibllib.io.video) 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) viewqc() (in module ibllib.qc.task_qc_viewer.ViewEphysQC) volumes (BrainAtlas attribute)

W

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 (SessionLoader attribute) WHEEL_RADIUS_CM (in module ibllib.io.extractors.ephys_fpga), [1] wheel_radius_cm (TestExtractedWheelUnits attribute) WHEEL_TICKS (in module ibllib.io.extractors.ephys_fpga), [1] 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) within_ranges() (in module iblutil.numerical) write() (in module iblutil.io.jsonable) (in module iblutil.io.params) 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) x0 (BrainCoordinates attribute) x2i() (BrainCoordinates method) xcorr() (in module brainbox.population.decode) xlim (BrainCoordinates property) xscale (BrainCoordinates property)

xyz (Insertion property) xyz0 (BrainCoordinates attribute) xyz2ccf() (AllenAtlas method) xyz2i() (BrainCoordinates method) xyz_picks (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestUploadToFlatIron attribute)

Y

y (Insertion attribute) y0 (BrainCoordinates attribute)

y2i() (BrainCoordinates method) ylim (BrainCoordinates property) yscale (BrainCoordinates property)

Z

z (Insertion attribute) z0 (BrainCoordinates attribute)

z2i() (BrainCoordinates method) zlim (BrainCoordinates property) zscale (BrainCoordinates property)