Index

A

acorr() (in module brainbox.singlecell.singlecell) acronym (BrainRegions attribute) add_covariate() (NeuralGLM method) add_covariate_boxcar() (NeuralGLM method) add_covariate_raw() (NeuralGLM method) add_covariate_timing() (NeuralGLM method) add_default_handler() (in module oneibl.onelight) add_repo() (in module oneibl.onelight) add_uuid_string() (in module alf.io) adjust_extremes_linear() (EphysAlignment method) adjust_extremes_uniform() (EphysAlignment static method) alf module alf.files module alf.folders module alf.io module

alf_parts() (in module alf.files) AlfBunch (class in alf.io) ALFMultipleCollectionsFound ALFMultipleObjectsFound ALFObjectNotFound AlignmentQC (class in ibllib.qc.alignment_qc) AllenAtlas (class in ibllib.atlas.atlas) alyx() (OneAlyx property) AlyxClient (class in oneibl.webclient) AlyxSubjectNotFound amp_heatmap() (in module brainbox.plot.plot) ancestors() (BrainRegions method) append() (AlfBunch method) (in module ibllib.io.jsonable) (SessionDataInfo method) apply_sync() (in module ibllib.ephys.sync_probes) arrange_into_regions() (EphysAlignment static method) as_dict() (in module ibllib.io.params) authenticate() (AlyxClient method)

B

BaseBpodTrialsExtractor (class in ibllib.io.extractors.base) BaseExtractor (class in ibllib.io.extractors.base) bc (BrainAtlas attribute) behavior_exists() (in module ibllib.pipes.misc) beta (Insertion attribute) bin_spike_trains() (NeuralGLM method) bin_spikes() (in module brainbox.processing.processing) bin_spikes_trials() (in module brainbox.population.cca) bincount2D() (in module brainbox.processing.processing) binf() (NeuralGLM method) bp() (in module ibllib.dsp.fourier) bpod_fpga_sync() (in module ibllib.io.extractors.ephys_fpga) bpod_trials (BaseBpodTrialsExtractor attribute) BrainAtlas (class in ibllib.atlas.atlas) brainbox module brainbox.behavior module brainbox.behavior.behavior module brainbox.behavior.pyschofit module brainbox.behavior.training module brainbox.behavior.wheel module brainbox.core module brainbox.core.core module brainbox.experimental module brainbox.experimental.experimental module brainbox.io module brainbox.io.io module brainbox.io.one module brainbox.io.parquet module brainbox.lfp module brainbox.lfp.lfp module brainbox.metrics module brainbox.metrics.electrode_drift module brainbox.metrics.metrics module brainbox.modeling module brainbox.modeling.dataset module brainbox.modeling.fitting_method module brainbox.modeling.glm module brainbox.modeling.parameter module brainbox.plot module brainbox.plot.plot module

brainbox.population module brainbox.population.cca module brainbox.population.population module brainbox.processing module brainbox.processing.processing module brainbox.quality module brainbox.quality.lfp_qc module brainbox.quality.permutation_test module brainbox.quality.quality module brainbox.simulation module brainbox.simulation.simulation module brainbox.singlecell module brainbox.singlecell.singlecell module brainbox.spike_features module brainbox.spike_features.spike_features module brainbox.task module brainbox.task.task module brainbox.tests module brainbox.tests.test_behavior module brainbox.tests.test_brainbox_io module brainbox.tests.test_cca module brainbox.tests.test_core module brainbox.tests.test_io module brainbox.tests.test_metrics module brainbox.tests.test_modeling module brainbox.tests.test_plot module brainbox.tests.test_population module brainbox.tests.test_processing module brainbox.tests.test_singlecell module brainbox.tests.test_task module BrainCoordinates (class in ibllib.atlas.atlas) BrainRegions (class in ibllib.atlas.atlas) Bunch (class in brainbox.core.core) (class in oneibl.onelight) butter_filter() (in module brainbox.lfp.lfp)

C

calculate_peths() (in module brainbox.singlecell.singlecell) CameraTimestamps (class in ibllib.io.extractors.ephys_fpga) (class in ibllib.io.extractors.training_trials) cart2sph() (in module ibllib.atlas.atlas) ccf2xyz() (AllenAtlas method) check_audio_pre_trial() (in module ibllib.qc.task_metrics) check_correct_trial_event_sequence() (in module ibllib.qc.task_metrics) check_create_raw_session_flag() (in module ibllib.pipes.misc) check_detected_wheel_moves() (in module ibllib.qc.task_metrics) check_dimensions() (AlfBunch property) (in module alf.io) check_error_trial_event_sequence() (in module ibllib.qc.task_metrics) check_errorCue_delays() (in module ibllib.qc.task_metrics) check_goCue_delays() (in module ibllib.qc.task_metrics) check_iti_delays() (in module ibllib.qc.task_metrics) check_n_trial_events() (in module ibllib.qc.task_metrics) check_n_ttl_between() (in module ibllib.io.extractors.passive) check_negative_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) check_polarity() (in module ibllib.io.extractors.passive) check_positive_feedback_stimOff_delays() (in module ibllib.qc.task_metrics) 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_transfer() (in module ibllib.pipes.misc) check_trial_length() (in module ibllib.qc.task_metrics) 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) Choice (class in ibllib.io.extractors.training_trials) clean_publish() (FigshareUploader method) cli_ask_default() (in module ibllib.pipes.misc) cli_ask_options() (in module ibllib.pipes.misc) cm_to_deg() (in module brainbox.behavior.wheel) cm_to_rad() (in module brainbox.behavior.wheel) coherence() (in module brainbox.lfp.lfp) color_cycle() (in module ibllib.plots) combine_weights() (NeuralGLM method) compile_design_matrix() (NeuralGLM method) compress() (in module ibllib.io.ffmpeg) compress_file() (Reader method) compute() (AlignmentQC method) (HabituationQC method) (ONEQC method) (TaskQC method) compute_alignment_status() (AlignmentQC method) compute_bias_info() (in module brainbox.behavior.training) compute_median_reaction_time() (in module brainbox.behavior.training) compute_n_trials() (in module brainbox.behavior.training) compute_performance_easy() (in module brainbox.behavior.training)

compute_psychometric() (in module brainbox.behavior.training) compute_session_status() (TaskQC method) compute_similarity_matrix() (AlignmentQC method) compute_training_info() (in module brainbox.behavior.training) concatenate_trials() (in module brainbox.behavior.training) config_dir() (in module oneibl.onelight) config_file() (in module oneibl.onelight) confirm_ephys_remote_folder() (in module ibllib.pipes.misc) confirm_video_remote_folder() (in module ibllib.pipes.misc) connect() (FtpUploader method) contamination_est() (in module brainbox.metrics.metrics) contamination_est2() (in module brainbox.metrics.metrics) ContrastLR (class in ibllib.io.extractors.biased_trials) (class in ibllib.io.extractors.training_trials) convbasis() (in module brainbox.modeling.glm) convert_pgts() (in module ibllib.time) convolve() (in module ibllib.dsp.fourier) copy() (Bunch method), [1] (TimeSeries method) copy_wiring_files() (in module ibllib.pipes.misc) coverage() (in module ibllib.pipes.histology) cpu (EphysAudio attribute) (EphysDLC attribute) (EphysPulses attribute) (RawEphysQC attribute) (Task attribute) (TrainingAudio attribute) (TrainingDLC attribute) create_alyx_probe_insertions() (in module ibllib.pipes.misc) create_alyx_tasks() (Pipeline method) 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_custom_ephys_wirings() (in module ibllib.pipes.misc) create_dataset() (FTPPatcher method) (Patcher method) create_dlc_flags() (in module ibllib.io.flags) create_ephys_flags() (in module ibllib.pipes.misc) create_ephys_transfer_done_flag() (in module ibllib.pipes.misc) create_ephyspc_params() (in module ibllib.pipes.misc) create_extract_flags() (in module ibllib.io.flags) create_flags() (in module ibllib.io.flags) create_other_flags() (in module ibllib.io.flags) create_register_flags() (in module ibllib.io.flags) create_session() (RegistrationClient method) create_sessions() (RegistrationClient method) create_trajectory_dict() (in module ibllib.pipes.histology) create_transfer_flags() (in module ibllib.io.flags) create_video_transfer_done_flag() (in module ibllib.pipes.misc) create_videopc_params() (in module ibllib.pipes.misc) criteria (TaskQC attribute) criterion_1a() (in module brainbox.behavior.training) criterion_1b() (in module brainbox.behavior.training) criterion_delay() (in module brainbox.behavior.training) criterion_ephys() (in module brainbox.behavior.training) csv_as_list() (in module ibllib.io.ascii) cum_drift() (in module brainbox.metrics.metrics)

D

d_neglog() (in module brainbox.modeling.glm) data (SessionDataInfo attribute) dataframe() (in module alf.io) DataSet (class in brainbox.modeling.dataset) dataset_id (SessionDataInfo attribute) dataset_record_to_url() (in module oneibl.webclient) dataset_type (SessionDataInfo attribute) date2isostr() (in module ibllib.time) dd_neglog() (in module brainbox.modeling.glm) decode() (in module brainbox.population.population) decompress_file() (Reader method) default() (in module oneibl.params) default_config() (in module oneibl.onelight) default_download_dir() (in module oneibl.onelight) default_path (BaseExtractor attribute) delete() (AlyxClient method) delete_dataset() (Patcher method) delete_empty_folders() (in module ibllib.io.misc) delete_flags() (in module ibllib.io.flags) delete_session_datasets() (Patcher method)

dense_layout() (in module ibllib.ephys.neuropixel) denseconv() (in module brainbox.modeling.glm) Density (class in ibllib.plots) dephas() (in module ibllib.dsp.fourier) depth (Insertion attribute) depth() (in module brainbox.spike_features.spike_features) descendants() (BrainRegions method) detect_missing_histology_tracks() (in module ibllib.pipes.histology) dft() (in module ibllib.dsp.fourier) dft2() (in module ibllib.dsp.fourier) differentiate_units() (in module brainbox.task.task) display_status() (in module brainbox.behavior.training) download_dataset() (OneAlyx method) download_datasets() (OneAlyx method) download_dir() (in module oneibl.onelight) download_file() (in module oneibl.onelight) download_raw_partial() (OneAlyx method) download_taskqc_raw_data() (in module ibllib.qc.oneutils) driftmap() (in module brainbox.plot.plot) driftmap_color() (in module brainbox.plot.plot) dxyz() (BrainCoordinates property)

E

eid (SessionDataInfo attribute) eid2path() (in module ibllib.misc.exp_ref) eid2ref() (in module ibllib.misc.exp_ref) eid_from_path() (OneAlyx method) entry() (Insertion property) EphysAlignment (class in ibllib.pipes.ephys_alignment) EphysAudio (class in ibllib.pipes.ephys_preprocessing) ephysCW_end() (in module ibllib.io.extractors.passive) EphysDLC (class in ibllib.pipes.ephys_preprocessing) EphysExtractionPipeline (class in ibllib.pipes.ephys_preprocessing) EphysMtscomp (class in ibllib.pipes.ephys_preprocessing) EphysPulses (class in ibllib.pipes.ephys_preprocessing) EphysSyncSpikeSorting (class in ibllib.pipes.ephys_preprocessing) EphysTrials (class in ibllib.pipes.ephys_preprocessing) EphysVideoCompress (class in ibllib.pipes.ephys_preprocessing) eq() (in module ibllib.misc.version) erf_psycho() (in module brainbox.behavior.pyschofit) erf_psycho_2gammas() (in module brainbox.behavior.pyschofit) ErrorCueTriggerTimes (class in ibllib.io.extractors.training_trials) 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) exists() (in module alf.io) exit_points() (Trajectory method)

explanation (ALFMultipleCollectionsFound attribute) (ALFMultipleObjectsFound attribute) (ALFObjectNotFound attribute) (AlyxSubjectNotFound attribute) (IblError attribute) (Neuropixel3BSyncFrontsNonMatching attribute) (SyncBpodFpgaException attribute) (SyncBpodWheelException attribute) export_to_alf() (in module ibllib.io.certification_protocol) extract() (BaseBpodTrialsExtractor method) (BaseExtractor method) extract_all() (in module ibllib.io.extractors.biased_trials) (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.io.extractors.habituation_trials) (in module ibllib.io.extractors.training_trials) (in module ibllib.io.extractors.training_wheel) extract_behaviour_sync() (in module ibllib.io.extractors.ephys_fpga) extract_camera_sync() (in module ibllib.io.extractors.ephys_fpga) extract_data() (TaskQCExtractor method) extract_first_movement_times() (in module ibllib.io.extractors.training_wheel) extract_rmsmap() (in module ibllib.ephys.ephysqc) extract_sound() (in module ibllib.io.extractors.training_audio) extract_stimulus_info_to_alf() (in module ibllib.io.certification_protocol) extract_sync() (in module ibllib.io.extractors.ephys_fpga) extract_training() (in module ibllib.pipes.training_preprocessing) extract_waveforms() (in module brainbox.io.io) extract_wheel_moves() (in module ibllib.io.extractors.training_wheel) extract_wheel_sync() (in module ibllib.io.extractors.ephys_fpga)

F

falls() (in module ibllib.dsp.utils) fcn_cosine() (in module ibllib.dsp.utils) feat_vars() (in module brainbox.plot.plot) feature2track() (EphysAlignment static method) feature2track_lin() (EphysAlignment static method) FeedbackTimes (class in ibllib.io.extractors.training_trials) FeedbackType (class in ibllib.io.extractors.training_trials) fexpand() (in module ibllib.dsp.fourier) figshare_request() (in module oneibl.onelight) FigshareOne (class in oneibl.onelight) FigshareUploader (class in oneibl.onelight) file_record_to_url() (in module oneibl.webclient) file_size (SessionDataInfo attribute) fill_dataframe() (TrialData method) filter_by() (in module alf.files) filter_units() (in module brainbox.processing.processing) find_between() (in module ibllib.io.extractors.passive) find_first_2d() (in module brainbox.io.parquet) find_mouse_sessions() (in module alf.folders) find_pairs() (in module ibllib.pipes.scan_fix_passive_files) find_session_dirs() (in module oneibl.onelight) find_session_files() (in module oneibl.onelight) find_sessions() (in module alf.folders) find_subject_folders() (in module alf.folders) find_subject_names() (in module alf.folders) firing_rate() (in module brainbox.plot.plot) (in module brainbox.singlecell.singlecell)

firing_rate_cv() (in module brainbox.metrics.metrics) firing_rate_fano_factor() (in module brainbox.metrics.metrics) firstlast() (WindowGenerator property) fit() (FittingMethod method) (MaximumLikelihoodEstimation method) (NeuralGLM method) (Trajectory static method) fit_cca() (in module brainbox.population.cca) fit_phase() (in module ibllib.dsp.fourier) FittingMethod (class in brainbox.modeling.fitting_method) flatten() (in module ibllib.misc.flatten) format_date_range() (in module ibllib.time) format_download_dir() (in module oneibl.onelight) FpgaTrials (class in ibllib.io.extractors.ephys_fpga) freduce() (in module ibllib.dsp.fourier) from_datasets() (SessionDataInfo static method) from_dict() (in module ibllib.io.params) (Insertion static method) from_pandas() (SessionDataInfo static method) from_session_details() (SessionDataInfo static method) from_track() (Insertion static method) fronts() (in module ibllib.dsp.utils) fs() (Reader property) fscale() (in module ibllib.dsp.fourier) FTPPatcher (class in oneibl.patcher) FtpUploader (class in oneibl.onelight) full_rcos() (in module brainbox.modeling.glm)

G

ge() (in module ibllib.misc.version) get() (AlyxClient method) (BrainRegions method) (in module oneibl.params) get_bpodqc_metrics_frame() (in module ibllib.qc.task_metrics) get_brain_entry() (Insertion static method) get_brain_exit() (Insertion static method) get_brain_locations() (EphysAlignment method) get_brain_regions() (in module ibllib.pipes.histology) get_cca_projection() (in module brainbox.population.cca) get_channel_locations() (EphysAlignment method) get_config() (in module oneibl.onelight) get_contrast_reversal_stimulus() (in module ibllib.io.certification_protocol) get_correlations() (in module brainbox.population.cca) get_details() (OneAlyx method) get_event_bin_indexes() (in module brainbox.population.cca) get_expected_ttl_pulses() (in module ibllib.io.certification_protocol) get_feedback_times_ge5() (FeedbackTimes static method) get_feedback_times_lt5() (FeedbackTimes static method) get_hardware_config() (in module ibllib.io.spikeglx) get_histology_regions() (EphysAlignment static method) get_ibl_sync_map() (in module ibllib.io.extractors.ephys_fpga) get_iblscripts_folder() (in module ibllib.pipes.misc) get_id_raisefall_from_analogttl() (in module ibllib.io.extractors.passive) get_included_trials_ge5() (IncludedTrials static method) get_included_trials_lt5() (IncludedTrials static method) get_insertion_track() (EphysAlignment method) get_lab_training_status() (in module brainbox.behavior.training) get_labels() (BrainAtlas method) get_micro_manipulator_data() (in module ibllib.pipes.histology) get_nearest_boundary() (EphysAlignment static method) get_neuropixel_version_from_files() (in module ibllib.io.spikeglx) get_neuropixel_version_from_folder() (in module ibllib.io.spikeglx) get_new_filename() (in module ibllib.pipes.misc) get_one() (in module oneibl.onelight) get_perp_vector() (EphysAlignment method)

get_picked_tracks() (in module ibllib.pipes.histology) get_port_events() (in module ibllib.io.raw_data_loaders) get_repo() (in module oneibl.onelight) get_rf_ttl_pulses() (in module ibllib.io.certification_protocol) get_scale_factor() (EphysAlignment method) get_session_extractor_type() (in module ibllib.io.raw_data_loaders) get_session_path() (in module alf.io) (in module ibllib.io.certification_protocol) get_sessions() (in module brainbox.behavior.training) get_signed_contrast() (in module brainbox.behavior.training) get_spacer_times() (in module ibllib.io.certification_protocol) (in module ibllib.io.extractors.passive) get_stim_num_from_name() (in module ibllib.io.certification_protocol) get_stimOn_times_ge5() (StimOnTimes static method) get_stimOn_times_lt5() (StimOnTimes static method) get_subject_training_status() (in module brainbox.behavior.training) get_sync_map() (in module ibllib.io.spikeglx) get_task_extractor_type() (in module ibllib.io.raw_data_loaders) get_task_stimulus() (in module ibllib.io.certification_protocol) get_times_between() (in module ibllib.io.extractors.passive) get_track_and_feature() (EphysAlignment method) get_training_status() (in module brainbox.behavior.training) get_trial_start_times() (in module ibllib.io.extractors.training_wheel) get_units_bunch() (in module brainbox.processing.processing) get_wheel_position() (in module ibllib.io.extractors.training_wheel) getfile() (in module ibllib.io.params) gflatten() (in module ibllib.misc.flatten) glob_ephys_files() (in module ibllib.io.spikeglx) GlobusPatcher (class in oneibl.patcher) GoCueTimes (class in ibllib.io.extractors.training_trials) GoCueTriggerTimes (class in ibllib.io.extractors.training_trials) gpu (EphysDLC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (TrainingDLC attribute) gt() (in module ibllib.misc.version)

H

HabituationQC (class in ibllib.qc.task_metrics) HabituationTrials (class in ibllib.io.extractors.habituation_trials) hash (SessionDataInfo attribute) help() (OneAlyx method)

hp() (in module ibllib.dsp.fourier) http_download_file() (in module oneibl.webclient) http_download_file_list() (in module oneibl.webclient) HttpOne (class in oneibl.onelight)

I

i2x() (BrainCoordinates method) i2xyz() (BrainCoordinates method) i2y() (BrainCoordinates method) i2z() (BrainCoordinates method) IblError ibllib module ibllib() (in module ibllib.misc.version) ibllib.atlas module ibllib.atlas.atlas module ibllib.dsp module ibllib.dsp.fourier module ibllib.dsp.savitzky_golay module ibllib.dsp.smooth module ibllib.dsp.utils module ibllib.ephys module ibllib.ephys.ephysqc module ibllib.ephys.neuropixel module ibllib.ephys.spikes module ibllib.ephys.sync_probes module ibllib.exceptions module ibllib.graphic module ibllib.io module ibllib.io.ascii module ibllib.io.certification_protocol module ibllib.io.extractors module ibllib.io.extractors.base module ibllib.io.extractors.biased_trials module ibllib.io.extractors.ephys_fpga module ibllib.io.extractors.habituation_trials module ibllib.io.extractors.passive module ibllib.io.extractors.training_audio module ibllib.io.extractors.training_trials module ibllib.io.extractors.training_wheel module ibllib.io.ffmpeg module ibllib.io.flags module ibllib.io.globus module ibllib.io.hashfile module ibllib.io.jsonable module ibllib.io.misc module ibllib.io.npy_header module ibllib.io.params module ibllib.io.raw_data_loaders module ibllib.io.spikeglx module ibllib.misc module ibllib.misc.exp_ref module ibllib.misc.flatten module

ibllib.misc.misc module ibllib.misc.timing module ibllib.misc.version module ibllib.pipes module ibllib.pipes.ephys_alignment module ibllib.pipes.ephys_preprocessing module ibllib.pipes.histology module ibllib.pipes.local_server module ibllib.pipes.misc module ibllib.pipes.purge_rig_data module ibllib.pipes.scan_fix_passive_files module ibllib.pipes.tasks module ibllib.pipes.training_preprocessing module ibllib.pipes.transfer_rig_data module ibllib.plots module ibllib.qc module ibllib.qc.alignment_qc module ibllib.qc.base module ibllib.qc.oneqc_metrics module ibllib.qc.oneutils module ibllib.qc.qcplots module ibllib.qc.task_extractors module ibllib.qc.task_metrics module ibllib.time module iblrig_video_compression() (in module ibllib.io.ffmpeg) id (BrainRegions attribute) iflatten() (in module ibllib.misc.flatten) IncludedTrials (class in ibllib.io.extractors.training_trials) infer_wheel_units() (in module ibllib.io.extractors.training_wheel) Insertion (class in ibllib.atlas.atlas) interpolate_along_track() (in module ibllib.pipes.histology) interpolate_position() (in module brainbox.behavior.wheel) interpolate_rf_mapping_stimulus() (in module ibllib.io.certification_protocol) (in module ibllib.io.extractors.passive) intersect2d() (in module brainbox.core.core) Intervals (class in ibllib.io.extractors.training_trials) io_charge (EphysDLC attribute) (EphysPulses attribute) (RawEphysQC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (TrainingDLC attribute) is_details_dict() (in module alf.io) is_documented_by() (in module oneibl.onelight) is_exp_ref() (in module ibllib.misc.exp_ref) is_file_in_session_dir() (in module oneibl.onelight) is_mtscomp() (Reader property) is_session_dir() (in module oneibl.onelight) is_session_path() (in module alf.io) is_uuid() (in module alf.io) is_uuid_string() (in module alf.io) is_valid() (in module alf.files) isi_viol() (in module brainbox.metrics.metrics) ismember() (in module brainbox.core.core) ismember2d() (in module brainbox.core.core) isostr2date() (in module ibllib.time) iter_files() (FigshareUploader method) ItiDuration (class in ibllib.io.extractors.training_trials) ItiInTimes (class in ibllib.io.extractors.habituation_trials) (class in ibllib.io.extractors.training_trials)

J

job_creator() (in module ibllib.pipes.local_server) job_runner() (in module ibllib.pipes.local_server) json_field_delete() (AlyxClient method)

json_field_remove_key() (AlyxClient method) json_field_update() (AlyxClient method) json_field_write() (AlyxClient method)

K

key_value_search() (in module ibllib.io.extractors.passive) key_vis_stim() (in module ibllib.io.extractors.passive)

keywords() (OneAlyx static method) ks2_to_alf() (in module ibllib.ephys.spikes)

L

label (EphysExtractionPipeline attribute) (Insertion attribute) (TrainingExtractionPipeline attribute) last_movement_onset() (in module brainbox.behavior.wheel) launch_transfers() (GlobusPatcher method) lda_project() (in module brainbox.population.population) le() (in module ibllib.misc.version) leaves() (BrainRegions method) level (BrainRegions attribute) (EphysAudio attribute) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPulses attribute) (EphysSyncSpikeSorting attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (RawEphysQC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (TrainingAudio attribute) (TrainingDLC attribute) (TrainingTrials attribute) lim() (BrainCoordinates method) list() (HttpOne method) (ONE method) (OneAbstract method) (OneAlyx method) (OneOffline method) Listable() (in module oneibl.one) load() (Bunch static method) (in module brainbox.io.parquet) (OneAbstract method) (OneAlyx method) (OneOffline method) load_ambient_sensor() (in module ibllib.io.raw_data_loaders) load_array() (in module oneibl.onelight) load_bpod() (in module ibllib.io.raw_data_loaders) load_bpod_fronts() (in module ibllib.io.raw_data_loaders) load_channel_locations() (in module brainbox.io.one) load_data() (AlignmentQC method) (in module ibllib.io.raw_data_loaders) (QC method) (TaskQC method)

load_dataset() (HttpOne method) (ONE method) (OneAlyx method) load_dstype_qc_metrics() (ONEQC method) load_encoder_events() (in module ibllib.io.raw_data_loaders) load_encoder_positions() (in module ibllib.io.raw_data_loaders) load_encoder_trial_info() (in module ibllib.io.raw_data_loaders) load_ephys_session() (in module brainbox.io.one) load_ephyspc_params() (in module ibllib.pipes.misc) load_file_content() (in module alf.io) load_lfp() (in module brainbox.io.one) load_mic() (in module ibllib.io.raw_data_loaders) load_nDatasetTypes() (ONEQC method) load_object() (HttpOne method) (in module alf.io) (ONE method) (OneAlyx method) load_params_dict() (in module ibllib.pipes.misc) load_raw_data() (TaskQCExtractor method) load_rf_mapping_stimulus() (in module ibllib.io.certification_protocol) load_session_metadata() (in module ibllib.io.certification_protocol) load_settings() (in module ibllib.io.raw_data_loaders) load_settings_file() (in module ibllib.pipes.scan_fix_passive_files) load_spike_sorting() (in module brainbox.io.one) load_spike_sorting_with_channel() (in module brainbox.io.one) load_stim_position_screen() (in module ibllib.io.raw_data_loaders) load_track_csv() (in module ibllib.pipes.histology) load_ttl_pulses() (in module ibllib.io.certification_protocol) load_videopc_params() (in module ibllib.pipes.misc) load_wheel_reaction_times() (in module brainbox.io.one) local_path (SessionDataInfo attribute) LocalOne (class in oneibl.onelight) log (Task attribute) logger_config() (in module ibllib.misc.misc) login() (in module ibllib.graphic) (in module ibllib.io.globus) login_auto() (in module ibllib.io.globus) lp() (in module ibllib.dsp.fourier) (in module ibllib.dsp.smooth) lt() (in module ibllib.misc.version)

M

main() (in module ibllib.pipes.transfer_rig_data) make_graph() (Pipeline method) make_http_root_file() (in module oneibl.onelight) max_drift() (in module brainbox.metrics.metrics) MaximumLikelihoodEstimation (class in brainbox.modeling.fitting_method) md5() (in module ibllib.io.hashfile) merge_clusters_channels() (in module brainbox.io.one) mgrid() (BrainCoordinates property) mindist() (Trajectory method) missed_spikes_est() (in module brainbox.metrics.metrics) (in module brainbox.plot.plot) mktree() (FTPPatcher method) mle_fit_psycho() (in module brainbox.behavior.pyschofit) module alf alf.files alf.folders alf.io brainbox brainbox.behavior brainbox.behavior.behavior brainbox.behavior.pyschofit brainbox.behavior.training brainbox.behavior.wheel brainbox.core brainbox.core.core brainbox.experimental brainbox.experimental.experimental brainbox.io brainbox.io.io brainbox.io.one brainbox.io.parquet brainbox.lfp brainbox.lfp.lfp brainbox.metrics brainbox.metrics.electrode_drift brainbox.metrics.metrics brainbox.modeling brainbox.modeling.dataset brainbox.modeling.fitting_method brainbox.modeling.glm brainbox.modeling.parameter brainbox.plot brainbox.plot.plot brainbox.population brainbox.population.cca brainbox.population.population brainbox.processing brainbox.processing.processing brainbox.quality brainbox.quality.lfp_qc brainbox.quality.permutation_test brainbox.quality.quality brainbox.simulation brainbox.simulation.simulation brainbox.singlecell brainbox.singlecell.singlecell brainbox.spike_features brainbox.spike_features.spike_features brainbox.task brainbox.task.task brainbox.tests brainbox.tests.test_behavior brainbox.tests.test_brainbox_io brainbox.tests.test_cca brainbox.tests.test_core brainbox.tests.test_io brainbox.tests.test_metrics brainbox.tests.test_modeling brainbox.tests.test_plot brainbox.tests.test_population brainbox.tests.test_processing brainbox.tests.test_singlecell brainbox.tests.test_task ibllib ibllib.atlas ibllib.atlas.atlas ibllib.dsp ibllib.dsp.fourier ibllib.dsp.savitzky_golay ibllib.dsp.smooth ibllib.dsp.utils ibllib.ephys ibllib.ephys.ephysqc ibllib.ephys.neuropixel ibllib.ephys.spikes ibllib.ephys.sync_probes ibllib.exceptions ibllib.graphic ibllib.io ibllib.io.ascii ibllib.io.certification_protocol ibllib.io.extractors ibllib.io.extractors.base ibllib.io.extractors.biased_trials ibllib.io.extractors.ephys_fpga ibllib.io.extractors.habituation_trials ibllib.io.extractors.passive ibllib.io.extractors.training_audio ibllib.io.extractors.training_trials ibllib.io.extractors.training_wheel ibllib.io.ffmpeg ibllib.io.flags ibllib.io.globus ibllib.io.hashfile ibllib.io.jsonable ibllib.io.misc ibllib.io.npy_header ibllib.io.params ibllib.io.raw_data_loaders ibllib.io.spikeglx ibllib.misc ibllib.misc.exp_ref ibllib.misc.flatten ibllib.misc.misc ibllib.misc.timing ibllib.misc.version ibllib.pipes ibllib.pipes.ephys_alignment ibllib.pipes.ephys_preprocessing ibllib.pipes.histology ibllib.pipes.local_server ibllib.pipes.misc ibllib.pipes.purge_rig_data ibllib.pipes.scan_fix_passive_files ibllib.pipes.tasks ibllib.pipes.training_preprocessing ibllib.pipes.transfer_rig_data ibllib.plots ibllib.qc ibllib.qc.alignment_qc ibllib.qc.base ibllib.qc.oneqc_metrics ibllib.qc.oneutils ibllib.qc.qcplots ibllib.qc.task_extractors ibllib.qc.task_metrics ibllib.time oneibl oneibl.dataclass oneibl.one oneibl.onelight oneibl.params oneibl.patcher oneibl.registration oneibl.webclient

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) multi_input() (in module ibllib.graphic)

N

name (BrainRegions attribute) name() (Pipeline property) (Task property) nc() (Reader property) NeedlesAtlas() (in module ibllib.atlas.atlas) neg_likelihood() (in module brainbox.behavior.pyschofit) neglog() (in module brainbox.modeling.glm) NeuralGLM (class in brainbox.modeling.glm)

Neuropixel3BSyncFrontsNonMatching next_num_folder() (in module alf.folders) np2str() (in module brainbox.io.parquet) np2uuid() (in module brainbox.io.parquet) ns() (Reader property) ns_optim_fft() (in module ibllib.dsp.fourier) numinput() (in module ibllib.graphic) nxyz() (BrainCoordinates property)

O

on_key_press() (Density method) (Traces method) ONE (class in oneibl.onelight) one (Pipeline attribute) (Task attribute) ONE() (in module oneibl.one) OneAbstract (class in oneibl.one) OneAlyx (class in oneibl.one) oneibl module oneibl.dataclass module oneibl.one module

oneibl.onelight module oneibl.params module oneibl.patcher module oneibl.registration module oneibl.webclient module OneOffline (class in oneibl.one) ONEQC (class in ibllib.qc.oneqc_metrics) outputs (Task attribute)

P

Parameter (class in brainbox.modeling.parameter) parent (BrainRegions attribute) parse_id() (in module oneibl.one) patch() (AlyxClient method) patch_dataset() (Patcher method) Patcher (class in oneibl.patcher) path2ref() (in module ibllib.misc.exp_ref) path_from_eid() (OneAlyx method) peri_event_time_histogram() (in module brainbox.plot.plot) permut_test() (in module brainbox.quality.permutation_test) phi (Insertion attribute) phy_model_from_ks2_path() (in module ibllib.ephys.ephysqc) Pipeline (class in ibllib.pipes.tasks) plot() (MaximumLikelihoodEstimation method) plot2d_all() (in module ibllib.pipes.histology) plot3d_all() (in module ibllib.pipes.histology) plot_correlations() (in module brainbox.population.cca) plot_cslice() (BrainAtlas method) plot_hslice() (BrainAtlas method) plot_pairwise_correlations() (in module brainbox.population.cca) plot_pairwise_correlations_mult() (in module brainbox.population.cca) plot_permut_test() (in module brainbox.quality.permutation_test) plot_results() (in module ibllib.qc.qcplots) plot_sslice() (BrainAtlas method) plot_tilted_slice() (BrainAtlas method) plot_top() (BrainAtlas method) point (Trajectory attribute) popup() (in module ibllib.graphic)

post() (AlyxClient method) power_spectrum() (in module brainbox.lfp.lfp) pprint() (in module ibllib.misc.misc) preprocess() (in module brainbox.population.cca) pres_ratio() (in module brainbox.metrics.metrics) (in module brainbox.plot.plot) print_progress() (in module ibllib.misc.misc) (WindowGenerator method) priority (EphysAudio attribute) (EphysMtscomp attribute) (EphysPulses attribute) (EphysSyncSpikeSorting attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (RawEphysQC attribute) (SpikeSorting_KS2_Matlab attribute) (Task attribute) (TrainingAudio attribute) (TrainingRegisterRaw attribute) (TrainingTrials attribute) ProbabilityLeft (class in ibllib.io.extractors.training_trials) ProbaContrasts (class in ibllib.io.extractors.ephys_fpga) probes_description() (in module ibllib.ephys.spikes) project() (Trajectory method) PsychofitTest (class in brainbox.tests.test_behavior) ptp_over_noise() (in module brainbox.metrics.metrics) purge_local_data() (in module ibllib.pipes.purge_rig_data) put() (AlyxClient method)

Q

QC (class in ibllib.qc.base)

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

R

r2ix() (BrainCoordinates method) r2iy() (BrainCoordinates method) r2iz() (BrainCoordinates method) raised_cosine() (in module brainbox.modeling.glm) ram (Task attribute) raw_qc_session() (in module ibllib.ephys.ephysqc) RawEphysQC (class in ibllib.pipes.ephys_preprocessing) rc2xy() (in module ibllib.ephys.neuropixel) read() (in module ibllib.io.jsonable) (in module ibllib.io.npy_header) (in module ibllib.io.params) (in module ibllib.io.spikeglx) (Reader method) read_flag_file() (in module ibllib.io.flags) read_meta_data() (in module ibllib.io.spikeglx) read_root_file() (in module oneibl.onelight) read_samples() (Reader method) read_sync() (Reader method) read_sync_analog() (Reader method) read_sync_digital() (Reader method) read_ts() (in module alf.io) Reader (class in ibllib.io.spikeglx) rec2col() (in module brainbox.io.parquet) ref2dict() (in module ibllib.misc.exp_ref) ref2dj() (in module ibllib.misc.exp_ref) ref2eid() (in module ibllib.misc.exp_ref) ref2path() (in module ibllib.misc.exp_ref) regions_from_allen_csv() (in module ibllib.atlas.atlas) register_aligned_track() (in module ibllib.pipes.histology) register_dataset() (in module oneibl.registration) (Patcher method) register_datasets() (Task method) register_session() (RegistrationClient method) register_session_raw_data() (in module oneibl.registration) register_sync() (RegistrationClient method) register_track() (in module ibllib.pipes.histology)

register_track_files() (in module ibllib.pipes.histology) RegistrationClient (class in oneibl.registration) remove_empty_folders() (in module alf.folders) remove_uuid_file() (in module alf.io) remove_uuid_recursive() (in module alf.io) rename_data() (TaskQCExtractor static method) rename_ephys_files() (in module ibllib.pipes.misc) rename_files_compatibility() (in module oneibl.registration) rename_session() (in module ibllib.pipes.misc) RepNum (class in ibllib.io.extractors.training_trials) repo_dir() (in module oneibl.onelight) report_health() (in module ibllib.pipes.local_server) repository() (in module oneibl.onelight) rerun() (Pipeline method) (Task method) rerun_failed() (Pipeline method) reshape_RF() (in module ibllib.io.extractors.passive) resolve_manual() (AlignmentQC method) ResponseTimes (class in ibllib.io.extractors.training_trials) responsive_units() (in module brainbox.task.task) rest() (AlyxClient method) RewardVolume (class in ibllib.io.extractors.training_trials) rgb (BrainRegions attribute) rises() (in module ibllib.dsp.utils) rms() (in module ibllib.dsp.utils) rmsmap() (in module ibllib.ephys.ephysqc) roc_between_two_events() (in module brainbox.task.task) roc_single_event() (in module brainbox.task.task) rolling_window() (in module ibllib.dsp.smooth) run() (AlignmentQC method) (Pipeline method) (QC method) (Task method) (TaskQC method) run_alyx_task() (in module ibllib.pipes.tasks) run_extractor_classes() (in module ibllib.io.extractors.base)

S

samples_to_cm() (in module brainbox.behavior.wheel) save() (Bunch method) (in module brainbox.io.parquet) save_bool() (in module ibllib.io.raw_data_loaders) save_metadata() (in module alf.io) save_names (BaseExtractor attribute) (CameraTimestamps attribute), [1] (Choice attribute) (ContrastLR attribute), [1] (ErrorCueTriggerTimes attribute) (FeedbackTimes attribute) (FeedbackType attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (ItiInTimes attribute), [1] (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimCenterTimes attribute) (StimCenterTriggerTimes attribute) (StimFreezeTriggerTimes attribute) (StimOffTriggerTimes attribute), [1] (StimOnOffFreezeTimes attribute) (StimOnTimes attribute) (StimOnTriggerTimes attribute) (TrialType attribute) (Wheel attribute) save_object_npy() (in module alf.io) savitzky_golay() (in module ibllib.dsp.savitzky_golay) scale_histology_regions() (EphysAlignment method) score() (NeuralGLM method) search() (HttpOne method) (in module alf.folders) (ONE method) (OneAbstract method) (OneAlyx method) (OneOffline method) search_terms() (ONE method) (OneAlyx static method) session_name() (in module alf.folders) session_path (BaseExtractor attribute) session_path() (in module alf.folders) SessionDataInfo (class in oneibl.dataclass) set_config() (in module oneibl.onelight) set_download_dir() (ONE method) set_figshare_url() (in module oneibl.onelight) (ONE method)

set_local_dir() (ONE method) set_repo() (in module oneibl.onelight) settings (BaseBpodTrialsExtractor attribute) setup() (in module ibllib.io.globus) (in module oneibl.params) (OneAlyx static method) setUp() (PsychofitTest method) (Task method) (TestIO_ALF method) (TestModels method) (TestTask method) (TestTraining method) (TestWheel method) setup_alyx_params() (in module oneibl.params) setup_silent() (in module oneibl.params) sha1() (in module ibllib.io.hashfile) shape() (Reader property) shift() (in module ibllib.dsp.fourier) shuffle_analysis() (in module brainbox.population.cca) slice() (BrainAtlas method) (WindowGenerator property) slice_array() (WindowGenerator method) smooth_demo() (in module ibllib.dsp.smooth) spectrum() (in module ibllib.plots) sph2cart() (in module ibllib.atlas.atlas) SpikeSorting_KS2_Matlab (class in ibllib.pipes.ephys_preprocessing) split_by_area() (in module brainbox.population.cca) split_sync() (in module ibllib.io.spikeglx) split_timepoints() (in module brainbox.population.cca) split_trials() (in module brainbox.population.cca) squares() (in module ibllib.plots) SSHPatcher (class in oneibl.patcher) StimCenterTimes (class in ibllib.io.extractors.habituation_trials) StimCenterTriggerTimes (class in ibllib.io.extractors.habituation_trials) StimFreezeTriggerTimes (class in ibllib.io.extractors.training_trials) StimOffTriggerTimes (class in ibllib.io.extractors.habituation_trials) (class in ibllib.io.extractors.training_trials) StimOnOffFreezeTimes (class in ibllib.io.extractors.training_trials) StimOnTimes (class in ibllib.io.extractors.training_trials) StimOnTriggerTimes (class in ibllib.io.extractors.training_trials) str2np() (in module brainbox.io.parquet) strinput() (in module ibllib.graphic) structarr() (in module ibllib.misc.misc) subjects_data_folder() (in module alf.folders) sync() (in module brainbox.processing.processing) (in module ibllib.ephys.sync_probes) sync_probe_front_times() (in module ibllib.ephys.sync_probes) sync_rotary_encoder() (in module ibllib.io.extractors.training_wheel) sync_spike_sortings() (in module ibllib.ephys.spikes) sync_trials_robust() (in module ibllib.io.raw_data_loaders) SyncBpodFpgaException SyncBpodWheelException

T

Task (class in ibllib.pipes.tasks) TaskQC (class in ibllib.qc.task_metrics) TaskQCExtractor (class in ibllib.qc.task_extractors) tasks (Pipeline attribute) tasks_runner() (in module ibllib.pipes.local_server) tearDown() (PsychofitTest method) (Task method) (TestIO_ALF method) test_acorr_0() (TestPopulation method) test_acorr_1() (TestPopulation method) test_amp_heatmap() (in module brainbox.tests.test_plot) test_bincount_2d() (TestProcessing method) test_bunch_io() (TestBunch method) test_concatenate_and_computations() (TestTraining method) test_derivative() (TestWheel method) test_differentiate_units() (TestTask method) test_direction_changes() (TestWheel method) test_erf_psycho() (PsychofitTest method) test_erf_psycho_2gammas() (PsychofitTest method) test_feat_cutoff() (in module brainbox.tests.test_metrics) (in module brainbox.tests.test_plot) test_feat_vars() (in module brainbox.tests.test_plot) test_firing_rate() (in module brainbox.tests.test_plot) (in module brainbox.tests.test_singlecell) test_firing_rate_coeff_var() (in module brainbox.tests.test_metrics) test_get_spike_counts_in_bins() (TestTask method) test_get_unit_bunches() (in module brainbox.tests.test_processing) test_GLM_timingkernel() (TestModels method) test_in_training() (TestTraining method) test_interpolate_rf_mapping_stimulus() (in module ibllib.io.extractors.passive) test_ismember() (TestIsmember method) test_key_value_search() (in module ibllib.io.extractors.passive) test_key_vis_stim() (in module ibllib.io.extractors.passive) test_load_ephys() (TestIO_ALF method) test_mle_fit_psycho() (PsychofitTest method) test_movements() (TestWheel method) test_movements_FPGA() (TestWheel method) test_neg_likelihood() (PsychofitTest method) test_peths_synthetic() (TestPeths method) test_plotting() (TestBunch method) test_ready4delay() (TestTraining method) test_ready4ephys() (TestTraining method) test_ready4recording() (TestTraining method) test_rec2col() (TestParquet method) test_responsive_units() (TestTask method) test_roc_between_two_events() (TestTask method) test_roc_single_event() (TestTask method) test_single_unit_wf_comp() (in module brainbox.tests.test_plot) test_sync() (TestBunch method) (TestProcessing method) test_traces_by_trial() (TestWheel method) test_trained_1a() (TestTraining method)

test_trained_1b() (TestTraining method) test_training_to_bias() (TestTraining method) test_unit_stability() (in module brainbox.tests.test_metrics) test_uuids_conversions() (TestParquet method) test_uuids_intersections() (TestParquet method) test_weibull() (PsychofitTest method) test_weibull50() (PsychofitTest method) test_wf_similarity() (in module brainbox.tests.test_metrics) test_xcorr_0() (TestPopulation method) test_xcorr_1() (TestPopulation method) test_xcorr_2() (TestPopulation method) TestBunch (class in brainbox.tests.test_cca) (class in brainbox.tests.test_core) TestIO_ALF (class in brainbox.tests.test_brainbox_io) TestIsmember (class in brainbox.tests.test_core) TestModels (class in brainbox.tests.test_modeling) TestParquet (class in brainbox.tests.test_io) TestPeths (class in brainbox.tests.test_singlecell) TestPopulation (class in brainbox.tests.test_population) (class in brainbox.tests.test_singlecell) TestProcessing (class in brainbox.tests.test_processing) TestTask (class in brainbox.tests.test_task) TestTraining (class in brainbox.tests.test_behavior) TestWheel (class in brainbox.tests.test_behavior) theta (Insertion attribute) tilted_slice() (BrainAtlas method) time_elapsed_secs (Task attribute) time_out_secs (Task attribute) TimeSeries (class in brainbox.core.core) timing() (in module ibllib.misc.timing) tip() (Insertion property) to_alf() (in module alf.files) to_df() (AlfBunch method) (Bunch method) to_eid() (OneAlyx method) Traces (class in ibllib.plots) traces_by_trial() (in module brainbox.behavior.wheel) track2feature() (EphysAlignment static method) TrainingAudio (class in ibllib.pipes.training_preprocessing) TrainingDLC (class in ibllib.pipes.training_preprocessing) TrainingExtractionPipeline (class in ibllib.pipes.training_preprocessing) TrainingRegisterRaw (class in ibllib.pipes.training_preprocessing) TrainingTrials (class in ibllib.pipes.training_preprocessing) TrainingVideoCompress (class in ibllib.pipes.training_preprocessing) Trajectory (class in ibllib.atlas.atlas) trajectory() (Insertion property) transfer_folder() (in module ibllib.pipes.misc) trial_times_to_times() (in module ibllib.io.raw_data_loaders) TrialData (class in brainbox.modeling.dataset) TrialType (class in ibllib.io.extractors.training_trials) truncate_ttl_signal() (in module ibllib.io.extractors.passive) tscale() (WindowGenerator method) type() (Reader property)

U

uncycle_pgts() (in module ibllib.time) UniqueSingletons (class in oneibl.webclient) unit_metrics_ks2() (in module ibllib.ephys.ephysqc) unit_stability() (in module brainbox.metrics.metrics) update() (QC method) update_extended_qc() (QC method)

update_repo() (in module oneibl.onelight) upload() (FtpUploader method) upload_channels() (AlignmentQC method) upload_dir() (FigshareUploader method) url (SessionDataInfo attribute) uuid2np() (in module brainbox.io.parquet)

V

validate_ttl_test() (in module ibllib.ephys.ephysqc) var_name (TrialType attribute) var_names (CameraTimestamps attribute), [1] (Choice attribute) (ContrastLR attribute), [1] (ErrorCueTriggerTimes attribute) (FeedbackTimes attribute) (FeedbackType attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (HabituationTrials attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (ItiInTimes attribute), [1] (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimCenterTimes attribute) (StimCenterTriggerTimes attribute) (StimFreezeTriggerTimes attribute) (StimOffTriggerTimes attribute), [1] (StimOnOffFreezeTimes attribute) (StimOnTimes attribute) (StimOnTriggerTimes attribute) (Wheel attribute)

vector (Trajectory attribute) velocity_smoothed() (in module brainbox.behavior.wheel) verify_hash() (Reader method) version (Task attribute) version() (Reader property) version3A() (in module ibllib.ephys.sync_probes) version3B() (in module ibllib.ephys.sync_probes) vertical_lines() (in module ibllib.plots)

W

walk() (in module oneibl.onelight) weibull() (in module brainbox.behavior.pyschofit) weibull50() (in module brainbox.behavior.pyschofit) welchogram() (in module ibllib.io.extractors.training_audio) wf_comp() (in module brainbox.plot.plot) wf_similarity() (in module brainbox.metrics.metrics) Wheel (class in ibllib.io.extractors.training_wheel)

wiggle() (in module ibllib.plots) WindowGenerator (class in ibllib.dsp.utils) within_ranges() (in module brainbox.behavior.wheel) write() (in module ibllib.io.jsonable) (in module ibllib.io.params) write_flag_file() (in module ibllib.io.flags) write_root_file() (in module oneibl.onelight)

X

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

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

Y

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

ylim() (BrainCoordinates property) yscale() (BrainCoordinates property)

Z

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

zlim() (BrainCoordinates property) zscale() (BrainCoordinates property)