Index

A

acorr() (in module brainbox.singlecell) acronym (BrainRegions attribute) adc_shifts() (in module ibllib.ephys.neuropixel) add_atlas_dwi() (MouseBrainViewer method) add_atlas_segmentation() (MouseBrainViewer method) add_box_widget() (Viewer method) add_button() (Viewer method) (ViewerWindow method) add_callback() (in module iblviewer.utils) (Viewer method) add_camera_embed_ui() (Viewer method) add_caption_symbol() (in module iblviewer.utils) add_checkbox() (ViewerWindow method) add_combo() (ViewerWindow method) add_covariate() (DesignMatrix method) add_covariate_boxcar() (DesignMatrix method) add_covariate_raw() (DesignMatrix method) add_covariate_timing() (DesignMatrix method) add_data_embed_ui() (Viewer method) add_input() (ViewerWindow method) add_lines() (DefaultPlot method) (in module brainbox.plot_base) (MouseBrainViewer method) (Viewer method) add_many_points_test() (MouseBrainViewer method) add_mesh() (Viewer method) add_object_embed_ui() (Viewer method) add_origin() (MouseBrainViewer method) add_points() (MouseBrainViewer method) (Viewer method) add_probe() (Viewer method) (VolumeController method) add_scalar_bar() (in module iblviewer.utils) add_scalar_data() (Points method) add_scene_embed_ui() (Viewer method) add_segments() (MouseBrainViewer method) (Viewer method) add_slider() (Viewer method) (ViewerWindow method) add_spheres() (MouseBrainViewer method) (Viewer method) add_surface_mesh() (Viewer method) add_text() (Viewer method) add_uuid_string() (in module one.alf.files) add_video_export_embed_ui() (Viewer method) add_volume() (MouseBrainViewer method) (Viewer method) adjust_extremes_linear() (EphysAlignment method)

adjust_extremes_uniform() (EphysAlignment static method) agc() (in module ibllib.dsp.voltage) AlfBunch (class in one.alf.io) ALFError ALFMultipleCollectionsFound ALFMultipleObjectsFound ALFMultipleRevisionsFound ALFObjectNotFound align_all_trials() (MotionAlignment method) align_motion() (MotionAlignment method) align_to_axis() (SlicerModel method) align_with_audio() (in module ibllib.io.extractors.camera) AlignmentQC (class in ibllib.qc.alignment_qc) all_elements() (UIModel method) AllenAtlas (class in ibllib.atlas.atlas) AllenAtlasExt (class in iblviewer.mouse_brain) alpha_map (LUTModel attribute) alyx() (OneAlyx property) AlyxClient (class in one.webclient) AlyxSubjectNotFound amp_heatmap() (in module brainbox.plot) ancestors() (BrainRegions method) animation_callback() (Viewer method) animation_function (ViewerModel attribute) animation_playing (ViewerModel attribute) append() (AlfBunch method) apply_lut() (SlicerView method) apply_sync() (in module ibllib.ephys.sync_probes) arrange_channels2banks() (in module brainbox.plot_base) arrange_into_regions() (EphysAlignment static method) as_globus_path() (in module ibllib.io.globus) assert_eq() (TestVersionTags method) assert_g() (TestVersionTags method) assert_l() (TestVersionTags method) assert_read_glx() (TestsSpikeGLX_Meta method) assert_valid_label() (in module ibllib.io.video) assign_scalars() (Viewer method) atlas (IBLAtlasModel attribute) atlas_lut (IBLAtlasModel attribute) atlas_mapping_ids (IBLAtlasModel attribute) atlas_volume (IBLAtlasModel attribute) attribute_times() (in module ibllib.io.extractors.camera) authenticate() (AlyxClient method) autocomplete() (in module one.util) autofocus (CameraModel attribute) average_drift() (in module brainbox.metrics.single_units) axes (VolumeModel attribute) axis (SlicerModel attribute)

B

backend (TestCameraQC attribute) background_color (UIModel attribute) base_color_map (LUTModel attribute) (VolumeModel attribute) base_url (AlyxClient attribute) BaseBpodTrialsExtractor (class in ibllib.io.extractors.base) BaseExtractor (class in ibllib.io.extractors.base) bbox (DlcQC attribute) bc (BrainAtlas attribute) behavior_exists() (in module ibllib.pipes.misc) beta (Insertion attribute) between_sorted() (in module brainbox.numerical) bin_spikes() (in module brainbox.processing) bin_spikes_trials() (in module brainbox.population.cca) bincount2D() (in module brainbox.processing) binf() (DesignMatrix method) (NeuralModel method) blend_maps() (in module iblviewer.volume) bounds (SlicerModel attribute) box_widget() (in module iblviewer.utils) box_widget_update() (VolumeController method) bp() (in module ibllib.dsp.fourier) bpod_trials (BaseBpodTrialsExtractor attribute) BrainAtlas (class in ibllib.atlas.atlas) brainbox module brainbox.atlas module brainbox.behavior module brainbox.behavior.dlc module brainbox.behavior.pyschofit module brainbox.behavior.training module brainbox.behavior.wheel module brainbox.core module brainbox.ephys_plots module brainbox.io module brainbox.io.one module brainbox.io.spikeglx module brainbox.lfp module brainbox.metrics module brainbox.metrics.electrode_drift module brainbox.metrics.single_units module brainbox.modeling module brainbox.modeling.design_matrix module brainbox.modeling.linear module brainbox.modeling.neural_model module brainbox.modeling.poisson module brainbox.modeling.utils module

brainbox.numerical module brainbox.plot module brainbox.plot_base module brainbox.population module brainbox.population.cca module brainbox.population.decode module brainbox.processing module brainbox.quality module brainbox.quality.lfp_qc module brainbox.quality.permutation_test module brainbox.singlecell module brainbox.spike_features module brainbox.task module brainbox.task.closed_loop module brainbox.task.passive module brainbox.task.trials module brainbox.tests module brainbox.tests.test_behavior module brainbox.tests.test_cca module brainbox.tests.test_io module brainbox.tests.test_metrics module brainbox.tests.test_passive module brainbox.tests.test_plot_base module brainbox.tests.test_population module brainbox.tests.test_processing module brainbox.tests.test_singlecell module brainbox.tests.test_task module brainbox.tests.test_trials module brainbox.tests.test_video module brainbox.video module BrainCoordinates (class in ibllib.atlas.atlas) BrainRegions (class in ibllib.atlas.regions) build() (LUTModel method) build_actor() (VolumeController method) build_lut() (VolumeModel method) Bunch (class in brainbox.core) butter_filter() (in module brainbox.lfp) button_config (UIModel attribute)

C

cache_dir() (AlyxClient property) caches_int2str() (in module one.tests.util) calculate_peths() (in module brainbox.singlecell) camera (CameraModel attribute) CAMERA (UIModel attribute) camera_context() (Viewer method) CameraModel (class in iblviewer.application) CameraQC (class in ibllib.qc.camera) cameras (ViewerModel attribute) CameraTimestampsBpod (class in ibllib.io.extractors.camera) CameraTimestampsFPGA (class in ibllib.io.extractors.camera) cart2sph() (in module ibllib.atlas.atlas) ccf2xyz() (AllenAtlas method) center (VolumeModel attribute) change_file_name() (in module iblviewer.utils) check_audio_pre_trial() (in module ibllib.qc.task_metrics) check_brightness() (CameraQC method) check_camera_times() (CameraQC method) check_correct_trial_event_sequence() (in module ibllib.qc.task_metrics) check_create_raw_session_flag() (in module ibllib.pipes.misc) check_detected_wheel_moves() (in module ibllib.qc.task_metrics) check_dimensions() (AlfBunch property) (in module one.alf.io) 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_normal() (SlicerModel method) check_nvidia_driver() (in module ibllib.misc.misc) 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_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_transfer() (in module ibllib.pipes.misc) check_trial_length() (in module ibllib.qc.task_metrics) check_wheel_alignment() (CameraQC method) check_wheel_freeze_during_quiescence() (in module ibllib.qc.task_metrics) check_wheel_integrity() (in module ibllib.qc.task_metrics) check_wheel_move_before_feedback() (in module ibllib.qc.task_metrics) check_wheel_move_during_closed_loop() (in module ibllib.qc.task_metrics) check_wheel_move_during_closed_loop_bpod() (in module ibllib.qc.task_metrics) Choice (class in ibllib.io.extractors.training_trials) classify() (in module brainbox.population.decode) clear_box_widget() (Viewer method) clear_color_bar() (Viewer method) clear_depth_picking() (Viewer method) clear_line_widget() (Viewer method) clear_rest_cache() (AlyxClient method) cli_ask_default() (in module ibllib.pipes.misc) cli_ask_options() (in module ibllib.pipes.misc) clip_on_axis() (VolumeController method) clip_to_bounds() (Viewer method) (VolumeController method) clipping_planes (SlicerModel attribute) close() (Reader method) (Viewer method) cm_to_deg() (in module brainbox.behavior.wheel) cm_to_rad() (in module brainbox.behavior.wheel) code_to_outcome() (QC static method) coherence() (in module brainbox.lfp) Collection (class in iblviewer.collection) color (UIModel attribute) color_cycle() (in module ibllib.plots) color_map (LUTModel attribute) color_map_function (LUTModel attribute)

combine_weights() (NeuralModel method) compile_design_matrix() (DesignMatrix method) compress() (in module ibllib.io.ffmpeg) compress_file() (Reader method) compute() (AlignmentQC method) (HabituationQC method) (TaskQC method) compute_alignment_status() (AlignmentQC method) compute_bias_info() (in module brainbox.behavior.training) compute_cluster_average() (in module brainbox.processing) compute_labels() (in module brainbox.metrics.single_units) 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_range() (VolumeModel method) compute_session_status() (TaskQC method) compute_session_status_from_dict() (TaskQC static method) compute_similarity_matrix() (AlignmentQC method) compute_size() (VolumeModel method) compute_training_info() (in module brainbox.behavior.training) concatenate_trials() (in module brainbox.behavior.training) confirm_ephys_remote_folder() (in module ibllib.pipes.misc) confirm_video_remote_folder() (in module ibllib.pipes.misc) contamination() (in module brainbox.metrics.single_units) contamination_alt() (in module brainbox.metrics.single_units) context (UIModel attribute) context_changed (UIModel attribute) contexts (UIModel attribute) ContrastLR (class in ibllib.io.extractors.biased_trials) (class in ibllib.io.extractors.training_trials) convbasis() (in module brainbox.modeling.design_matrix) ConversionMixin (class in one.converters) convert2dict() (DefaultPlot method) convert_pgts() (in module ibllib.time) convolve() (in module ibllib.dsp.fourier) copy() (Bunch method) (TimeSeries method) copy_wiring_files() (in module ibllib.pipes.misc) coverage() (in module ibllib.pipes.histology) coverage_grid() (in module ibllib.pipes.histology) cpu (EphysAudio attribute) (EphysDLC attribute) (EphysPassive 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) create_dlc_flags() (in module ibllib.io.flags) create_ephys_flags() (in module ibllib.pipes.misc) create_ephys_transfer_done_flag() (in module ibllib.pipes.misc) create_ephyspc_params() (in module ibllib.pipes.misc) create_extract_flags() (in module ibllib.io.flags) create_fake_alf_folder_dlc_data() (in module ibllib.tests.fixtures.utils) create_fake_complete_ephys_session() (in module ibllib.tests.fixtures.utils) create_fake_ephys_recording_bad_passive_transfer_sessions() (in module ibllib.tests.fixtures.utils) create_fake_raw_behavior_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_ephys_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_raw_video_data_folder() (in module ibllib.tests.fixtures.utils) create_fake_session_folder() (in module ibllib.tests.fixtures.utils) create_file_tree() (in module one.tests.util) create_flags() (in module ibllib.io.flags) create_other_flags() (in module ibllib.io.flags) create_register_flags() (in module ibllib.io.flags) create_schema_cache() (in module one.tests.util) 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) Cross3D() (in module iblviewer.objects) current (Collection attribute) current_key_id (Collection attribute)

D

dark_mode (UIModel attribute) DATA (UIModel attribute) data (VolumeModel attribute) data_context() (Viewer method) data_for_keys() (in module ibllib.qc.camera) data_map_step (VolumeModel attribute) data_max (VolumeModel attribute) data_min (VolumeModel attribute) DATA_TYPE (VolumeModel attribute) data_type (VolumeModel attribute) dataframe() (in module one.alf.io) dataset2type() (OneAlyx method) dataset_record_to_url() (in module one.webclient) datasets2records() (in module one.util) date2isostr() (in module ibllib.time) decompress_destripe_cbin() (in module ibllib.dsp.voltage) decompress_file() (Reader method) DEFAULT (UIModel attribute) default() (in module one.params) default_path (BaseExtractor attribute) DefaultPlot (class in brainbox.plot_base) define_view_axis() (ViewerModel method) delete() (AlyxClient method) delete_empty_folders() (in module ibllib.io.misc) delete_flags() (in module ibllib.io.flags) denoise() (in module ibllib.dsp.cadzow) dense_layout() (in module ibllib.ephys.neuropixel) denseconv() (in module brainbox.modeling.design_matrix) Density (class in ibllib.plots) dephas() (in module ibllib.dsp.fourier) depth (Insertion attribute)

depth() (in module brainbox.spike_features) derank() (in module ibllib.dsp.cadzow) descendants() (BrainRegions method) describe() (in module one.alf.spec) describe_dataset() (OneAlyx method) describe_revision() (OneAlyx method) DesignMatrix (class in brainbox.modeling.design_matrix) destripe() (in module ibllib.dsp.voltage) detect_missing_histology_tracks() (in module ibllib.pipes.histology) dft() (in module ibllib.dsp.fourier) dft2() (in module ibllib.dsp.fourier) dict2ref() (ConversionMixin static method) differentiate_units() (in module brainbox.task.closed_loop) dimensions (VolumeModel attribute) disable_shading() (VolumeController method) display_status() (in module brainbox.behavior.training) distance_factor (CameraModel attribute) DlcQC (class in ibllib.qc.dlc) download_cache_tables() (AlyxClient method) download_file() (AlyxClient method) download_raw_partial() (in module ibllib.io.spikeglx) draw_axes() (Viewer method) draw_color_bar() (Viewer method) draw_outline() (Viewer method) driftmap() (in module brainbox.plot) driftmap_color() (in module brainbox.plot) dset (TestAlyx2Path attribute), [1] dstypes (CameraQC attribute) (DlcQC attribute) dstypes_fpga (CameraQC attribute) dwi_volume (IBLAtlasModel attribute) dxyz() (BrainCoordinates property)

E

edit_probe() (Viewer method) eid2path() (ConversionMixin method) (OneAlyx method) eid2ref() (ConversionMixin method) embed (UIModel attribute) embed_menu_x (UIModel attribute) embed_menu_y (UIModel attribute) embed_slider_width (UIModel attribute) embed_submenu_x (UIModel attribute) embed_submenu_y (UIModel attribute) enable_shading() (VolumeController method) ensure_list() (in module one.util) ensure_required_data() (CameraQC method) entry() (Insertion property) EphysAlignment (class in ibllib.pipes.ephys_alignment) EphysAudio (class in ibllib.pipes.ephys_preprocessing) EphysCellsQc (class in ibllib.pipes.ephys_preprocessing) EphysDLC (class in ibllib.pipes.ephys_preprocessing) EphysExtractionPipeline (class in ibllib.pipes.ephys_preprocessing) EphysMtscomp (class in ibllib.pipes.ephys_preprocessing) EphysPassive (class in ibllib.pipes.ephys_preprocessing) EphysPulses (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 one.alf.io) exit_interactive_mode() (Viewer method) exit_points() (Trajectory method) explanation (ALFError attribute) (ALFMultipleCollectionsFound attribute) (ALFMultipleObjectsFound attribute) (ALFMultipleRevisionsFound attribute) (ALFObjectNotFound attribute) (AlyxSubjectNotFound attribute) (IblError attribute) (Neuropixel3BSyncFrontsNonMatching attribute) (NvidiaDriverNotReady attribute) (SyncBpodFpgaException attribute) (SyncBpodWheelException attribute)

export_to_alf() (in module ibllib.io.certification_protocol) export_turntable_video() (Viewer method) extent() (BrainAtlas method) extract() (BaseBpodTrialsExtractor method) (BaseExtractor method) extract_all() (in module ibllib.io.extractors.biased_trials) (in module ibllib.io.extractors.bpod_trials) (in module ibllib.io.extractors.camera) (in module ibllib.io.extractors.ephys_fpga) (in module ibllib.io.extractors.habituation_trials) (in module ibllib.io.extractors.opto_trials) (in module ibllib.io.extractors.training_trials) (in module ibllib.io.extractors.training_wheel) extract_behaviour_sync() (in module ibllib.io.extractors.ephys_fpga) extract_camera_sync() (in module ibllib.io.extractors.camera) extract_data() (TaskQCExtractor method) extract_first_movement_times() (in module ibllib.io.extractors.training_wheel) extract_passive_periods() (in module ibllib.io.extractors.ephys_passive) extract_replay_debug() (in module ibllib.io.extractors.ephys_passive) extract_rfmapping() (in module ibllib.io.extractors.ephys_passive) extract_rmsmap() (in module ibllib.ephys.ephysqc) extract_sound() (in module ibllib.io.extractors.training_audio) extract_stimulus_info_to_alf() (in module ibllib.io.certification_protocol) extract_sync() (in module ibllib.io.extractors.ephys_fpga) extract_task_replay() (in module ibllib.io.extractors.ephys_passive) extract_waveforms() (in module brainbox.io.spikeglx) extract_wheel_moves() (in module ibllib.io.extractors.training_wheel) extract_wheel_sync() (in module ibllib.io.extractors.ephys_fpga)

F

falls() (in module ibllib.dsp.utils) fcn_cosine() (in module ibllib.dsp.utils) fcns_value2status (TaskQC attribute) feat_vars() (in module brainbox.plot) feature2track() (EphysAlignment static method) feature2track_lin() (EphysAlignment static method) FeedbackTimes (class in ibllib.io.extractors.training_trials) FeedbackType (class in ibllib.io.extractors.training_trials) fexpand() (in module ibllib.dsp.fourier) file_path (VolumeModel attribute) file_record_to_url() (in module one.webclient) filename_parts() (in module one.alf.files) filter_by() (in module one.alf.io) 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_datasets() (in module one.util) filter_left_right() (in module brainbox.task.trials) filter_revision_last_before() (in module one.util) filter_trials() (in module brainbox.task.trials) filter_units() (in module brainbox.processing) find_face() (CameraQC method) find_first_2d() (in module brainbox.numerical) find_keys() (Collection method) find_nearest() (in module ibllib.io.extractors.video_motion) find_pairs() (in module ibllib.pipes.scan_fix_passive_files) find_region() (MouseBrainViewer method) find_trial_ids() (in module brainbox.task.trials) firing_rate() (in module brainbox.plot) (in module brainbox.singlecell)

firing_rate_coeff_var() (in module brainbox.metrics.single_units) firing_rate_fano_factor() (in module brainbox.metrics.single_units) first_picked_position (ViewerModel attribute) firstlast() (WindowGenerator property) fit() (NeuralModel method) (SequentialSelector method) (Trajectory static method) fit_cca() (in module brainbox.population.cca) fit_phase() (in module ibllib.dsp.fourier) fk() (in module ibllib.dsp.voltage) flip_normal() (SlicerModel method) folder_parts() (in module one.alf.files) font (UIModel attribute) font_path (UIModel attribute) font_size (UIModel attribute) format_date_range() (in module ibllib.time) FpgaTrials (class in ibllib.io.extractors.ephys_fpga) frame_diff() (in module brainbox.video) frame_diffs() (in module brainbox.video) freduce() (in module ibllib.dsp.fourier) from_dict() (Insertion static method) from_track() (Insertion static method) fronts() (in module ibllib.dsp.utils) fs() (Reader property) fscale() (in module ibllib.dsp.fourier) fshift() (in module ibllib.dsp.fourier) FTPPatcher (class in ibllib.oneibl.patcher) full_rcos() (in module brainbox.modeling.utils)

G

ge() (in module ibllib.misc.version) generate_pseudo_blocks() (in module brainbox.task.closed_loop) generate_pseudo_session() (in module brainbox.task.closed_loop) generate_pseudo_stimuli() (in module brainbox.task.closed_loop) generate_spike_train() (in module brainbox.tests.test_metrics) get() (AlyxClient method) (BrainRegions method) (in module one.params) get_active_wheel_period() (CameraQC static method) get_actor_bounds() (in module iblviewer.utils) get_actor_center() (in module iblviewer.utils) get_actor_dimensions() (in module iblviewer.utils) get_actor_type() (Viewer method) (ViewerModel method) get_alf_path() (in module one.alf.files) get_allen_volume_file_name() (IBLAtlasModel method) get_allen_volume_url() (IBLAtlasModel method) get_atlas_model() (IBLAtlasModel method) get_axis_aligned_info() (SlicerModel method) get_bounding_planes() (in module iblviewer.utils) get_box_plane_id() (SlicerModel method) 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_button_state() (Viewer method) get_cache_dir() (in module one.params) get_cca_projection() (in module brainbox.population.cca) get_channel_locations() (EphysAlignment method) get_clipping_planes() (VolumeController method) get_contrast_reversal_stimulus() (in module ibllib.io.certification_protocol) get_correlations() (in module brainbox.population.cca) get_current_key() (Collection method) get_default_client() (in module one.params) get_details() (One method) (OneAlyx method) get_diameter() (DlcQC method) get_dlc_everything() (in module brainbox.behavior.dlc) get_dwi_model() (IBLAtlasModel method) get_element() (UIModel method) get_elements() (UIModel method) get_event_aligned_raster() (in module brainbox.task.trials) get_event_bin_indexes() (in module brainbox.population.cca) get_expected_ttl_pulses() (in module ibllib.io.certification_protocol) get_feature_event_times() (in module brainbox.behavior.dlc) get_feedback_times_ge5() (FeedbackTimes static method) get_feedback_times_lt5() (FeedbackTimes static method) get_file() (in module one.tests.util) get_file_name() (in module iblviewer.utils) get_frame() (VideoStreamer method), [1] 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_included_trials_ge5() (IncludedTrials static method) get_included_trials_lt5() (IncludedTrials static method) get_insertion_track() (EphysAlignment method) get_keys() (Collection method) get_lab_training_status() (in module brainbox.behavior.training) get_labels() (BrainAtlas method) get_licks() (in module brainbox.behavior.dlc) get_local_data_file_path() (in module iblviewer.utils) get_local_endpoint() (in module ibllib.io.globus) get_main_probe_sync() (in module ibllib.io.extractors.ephys_fpga) get_mapped_data() (IBLAtlasModel method) get_mapped_volume() (IBLAtlasModel method) get_micro_manipulator_data() (in module ibllib.pipes.histology) get_name() (Collection method) (IBLAtlasModel method) 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_new_name() (Collection method) get_num_regions() (IBLAtlasModel method) get_number_of_arrays() (Points method) get_object_names() (Viewer method) get_on_off_times_and_positions() (in module brainbox.task.passive) get_opacity() (VolumeController method) get_or_create() (Collection method)

get_params_dir() (in module one.params) get_perp_vector() (EphysAlignment method) get_picked_tracks() (in module ibllib.pipes.histology) get_pipeline() (in module ibllib.io.extractors.base) get_planes_bounds() (in module iblviewer.utils) get_port_events() (in module ibllib.io.raw_data_loaders) get_pregenerated_events() (ProbaContrasts static method) get_psth() (in module brainbox.task.trials) get_region_and_row_id() (IBLAtlasModel method) get_region_names() (MouseBrainViewer method) get_regions_mask() (IBLAtlasModel method) get_related_actors() (VolumeController method) get_relative_opacity_unit() (VolumeController method) get_rest_dir() (in module one.params) get_rf_map_over_depth() (in module brainbox.task.passive) get_rf_ttl_pulses() (in module ibllib.io.certification_protocol) get_scale_factor() (EphysAlignment method) get_selectable_key_by_id() (Viewer method) get_selection_info() (MouseBrainViewer method) (Viewer method) get_selection_opacity() (Viewer method) get_selection_slices_opacity() (Viewer method) get_session_extractor_type() (in module ibllib.io.extractors.base) get_session_path() (in module ibllib.io.certification_protocol) (in module one.alf.files) get_sessions() (in module brainbox.behavior.training) get_signed_contrast() (in module brainbox.behavior.training) get_slices_opacity() (VolumeController method) get_slider_bounds() (Viewer method) get_sniffs() (in module brainbox.behavior.dlc) get_sorted_scalars() (LUTModel method) get_spacer_times() (in module ibllib.io.certification_protocol) get_spacing() (VolumeController method) 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_stim_num_from_name() (in module ibllib.io.certification_protocol) get_stimOn_times_ge5() (StimOnTimes_deprecated static method) get_stimOn_times_lt5() (StimOnTimes_deprecated static method) get_subject_training_status() (in module brainbox.behavior.training) get_surface_mesh_path() (in module iblviewer.utils) get_svd_map() (in module brainbox.task.passive) get_sync_fronts() (in module ibllib.io.extractors.ephys_fpga) get_sync_map() (in module ibllib.io.spikeglx) get_task_extractor_type() (in module ibllib.io.extractors.base) get_task_stimulus() (in module ibllib.io.certification_protocol) get_time_series_info() (Viewer method) get_track_and_feature() (EphysAlignment method) get_training_status() (in module brainbox.behavior.training) get_transformation_matrix() (in module iblviewer.utils) get_trial_start_times() (in module ibllib.io.extractors.training_wheel) get_type() (in module iblviewer.utils) get_unique_name() (in module iblviewer.utils) get_unique_object_name() (Viewer method) get_units_bunch() (in module brainbox.processing) get_value_from_scalar_map() (IBLAtlasModel method) get_value_from_xyz() (VolumeController method) 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_view_objects() (Viewer method) get_view_objects_names() (Viewer method) get_wheel_position() (in module ibllib.io.extractors.training_wheel) get_window() (Viewer method) glob_ephys_files() (in module ibllib.io.spikeglx) global_slicer (ViewerModel attribute) globus_path_from_dataset() (in module ibllib.oneibl.patcher) GlobusPatcher (class in ibllib.oneibl.patcher) GoCueTimes (class in ibllib.io.extractors.training_trials) GoCueTriggerTimes (class in ibllib.io.extractors.training_trials) got_new_selection() (ViewerModel method) got_selection() (ViewerModel method) gpu (EphysDLC attribute) (SpikeSorting attribute) (Task attribute) (TrainingDLC attribute) groom_pin_state() (in module ibllib.io.extractors.camera) gt() (in module ibllib.misc.version) guess_volume_type() (VolumeModel method)

H

HabituationQC (class in ibllib.qc.task_metrics) HabituationTrials (class in ibllib.io.extractors.habituation_trials) handle_actor2d_click() (Viewer method) handle_drag_release() (Viewer method) handle_key_press() (Viewer method) handle_left_mouse_press() (Viewer method) handle_left_mouse_release() (Viewer method)

handle_lut_update() (Viewer method) handle_object_click() (Viewer method) handle_timer() (Viewer method) handle_void_click() (Viewer method) hp() (in module ibllib.dsp.fourier) http_download_file() (in module one.webclient) http_download_file_list() (in module one.webclient)

I

i2x() (BrainCoordinates method) i2xyz() (BrainCoordinates method) i2y() (BrainCoordinates method) i2z() (BrainCoordinates method) ibl_back_end (IBLAtlasModel attribute) IBL_TRANSPOSE (IBLAtlasModel attribute) IBLAtlasModel (class in iblviewer.mouse_brain) IblError ibllib module ibllib() (in module ibllib.misc.version) ibllib.atlas module ibllib.atlas.atlas module ibllib.atlas.regions module ibllib.dsp module ibllib.dsp.cadzow module ibllib.dsp.fourier module ibllib.dsp.savitzky_golay module ibllib.dsp.smooth module ibllib.dsp.utils module ibllib.dsp.voltage 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.certification_protocol 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.ephys_fpga module ibllib.io.extractors.ephys_passive module ibllib.io.extractors.habituation_trials 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.ffmpeg module ibllib.io.flags module ibllib.io.globus module ibllib.io.misc module ibllib.io.npy_header module ibllib.io.raw_data_loaders module ibllib.io.spikeglx module ibllib.io.video module ibllib.misc module ibllib.misc.misc module ibllib.misc.timing module ibllib.misc.version module ibllib.oneibl module ibllib.oneibl.patcher module ibllib.oneibl.registration module ibllib.oneibl.stream 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.remote_server 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.camera module ibllib.qc.critical_reasons module ibllib.qc.dlc module ibllib.qc.qcplots module

ibllib.qc.task_extractors module ibllib.qc.task_metrics module ibllib.tests module ibllib.tests.extractors module ibllib.tests.extractors.test_ephys_fpga module ibllib.tests.extractors.test_ephys_passive module ibllib.tests.extractors.test_ephys_trials module ibllib.tests.extractors.test_extractors module ibllib.tests.fixtures module ibllib.tests.fixtures.utils module ibllib.tests.qc module ibllib.tests.qc.test_alignment_qc module ibllib.tests.qc.test_base_qc module ibllib.tests.qc.test_camera_qc module ibllib.tests.qc.test_critical_reasons module ibllib.tests.qc.test_dlc_qc module ibllib.tests.qc.test_task_metrics module ibllib.tests.test_atlas module ibllib.tests.test_dsp module ibllib.tests.test_ephys module ibllib.tests.test_histology module ibllib.tests.test_io module ibllib.tests.test_misc module ibllib.tests.test_oneibl module ibllib.tests.test_pipes module ibllib.tests.test_spikeglx module ibllib.tests.test_tasks module ibllib.tests.test_time module ibllib.time module iblrig_video_compression() (in module ibllib.io.ffmpeg) iblviewer module IBLViewer (class in iblviewer.launcher) iblviewer.application module iblviewer.collection module iblviewer.launcher module iblviewer.mouse_brain module iblviewer.objects module iblviewer.qt_application module iblviewer.utils module iblviewer.volume module id (BrainRegions 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_rms_plot() (in module brainbox.ephys_plots) ImagePlot (class in brainbox.plot_base) imshow() (CameraQC static method) IncludedTrials (class in ibllib.io.extractors.training_trials) index_last_before() (in module one.util) infer_wheel_units() (in module ibllib.io.extractors.training_wheel) initialize() (IBLAtlasModel method) (MouseBrainViewer method) (SlicerView method) (Viewer method) (ViewerApp method) (ViewerModel method) (ViewerWindow method) (VolumeController method) initialize_clipping_planes() (VolumeController method) initialize_mapper() (SlicerView method) initialize_picker() (VolumeController method) initialize_selection_ui() (Viewer method) initialize_slicer_box() (VolumeController method) initialize_ui() (ViewerWindow method) initialize_vtk_ui() (Viewer method) initialize_window_interactions() (Viewer method) initialized() (Viewer method) Insertion (class in ibllib.atlas.atlas) interactive_subsampling (VolumeModel attribute) interactive_volume_subsampling (ViewerModel attribute) 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) intersect2d() (in module brainbox.numerical) Intervals (class in ibllib.io.extractors.training_trials) io_charge (EphysDLC attribute) (EphysPassive attribute) (EphysPulses attribute) (RawEphysQC attribute) (SpikeSorting attribute) (Task attribute) (TrainingDLC attribute) ipeak (TestParabolicMax attribute) is_camera_context() (UIModel method) is_data_context() (UIModel method) is_exp_ref() (ConversionMixin static method) is_logged_in() (AlyxClient method) is_mtscomp() (Reader property) is_object_context() (UIModel method) is_open() (Reader property) is_probe() (Viewer method) is_scene_context() (UIModel method) is_segmented() (VolumeModel method) is_selection_line() (ViewerModel method) is_selection_point() (ViewerModel method) is_selection_surface() (ViewerModel method) is_selection_volume() (ViewerModel method) is_session_path() (in module one.alf.spec) is_uuid() (in module one.alf.spec) is_uuid_string() (in module one.alf.spec) is_valid() (in module one.alf.spec) is_valid_context() (UIModel method) is_video_export_context() (UIModel method) is_volume() (Viewer method) ismember() (in module brainbox.numerical) ismember2d() (in module brainbox.numerical) isostr2date() (in module ibllib.time) isosurface() (Viewer method) (VolumeController method) isosurfaces (VolumeModel attribute) ItiDuration (class in ibllib.io.extractors.training_trials) ItiInTimes (class in ibllib.io.extractors.training_trials)

J

job_creator() (in module ibllib.pipes.local_server) job_run_ks2() (in module ibllib.pipes.remote_server) job_runner() (in module ibllib.pipes.local_server) job_transfer_ks2() (in module ibllib.pipes.remote_server)

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

K

kfilt() (in module ibllib.dsp.voltage)

ks2_to_alf() (in module ibllib.ephys.spikes) ks2_to_tar() (in module ibllib.ephys.spikes)

L

label (EphysExtractionPipeline attribute) (Insertion attribute) (TrainingExtractionPipeline attribute) label_from_path() (in module ibllib.io.video) LaserBool (class in ibllib.io.extractors.opto_trials) last_context (UIModel attribute) last_movement_onset() (in module brainbox.behavior.wheel) last_picked_position (ViewerModel attribute) lateralize() (AllenAtlasExt method) lateralized (VolumeModel attribute) launch() (IBLViewer method) launch_transfers() (GlobusPatcher method) launch_transfers_secondary() (GlobusPatcher method) LazyId (class in one.util) lda_project() (in module brainbox.population.decode) le() (in module ibllib.misc.version) leaves() (BrainRegions method) level (BrainRegions attribute) (EphysAudio attribute) (EphysCellsQc attribute) (EphysDLC attribute) (EphysMtscomp attribute) (EphysPassive attribute) (EphysPulses attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (RawEphysQC attribute) (SpikeSorting attribute) (Task attribute) (Task02_error attribute) (Task10 attribute) (Task11 attribute) (TrainingAudio attribute) (TrainingDLC attribute) (TrainingTrials attribute) likelihood_threshold() (in module brainbox.behavior.dlc) lim() (BrainCoordinates method) LINE (ViewerModel attribute) line_amp_plot() (in module brainbox.ephys_plots) line_fr_plot() (in module brainbox.ephys_plots) LinearGLM (class in brainbox.modeling.linear) LinePlot (class in brainbox.plot_base) Lines (class in iblviewer.objects) lines (ViewerModel attribute) list_collections() (One method) list_datasets() (One method) (OneAlyx method) list_endpoints() (AlyxClient method) list_revisions() (One method) list_subjects() (One method) Listable() (in module one.util) load() (Bunch static method) load_ambient_sensor() (in module ibllib.io.raw_data_loaders) load_bounding_mesh() (MouseBrainViewer method) 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_channels_from_insertion() (in module brainbox.io.one) load_collection() (OneAlyx method) load_data() (AlignmentQC method) (CameraQC method) (DlcQC method) (in module ibllib.io.raw_data_loaders) (MotionAlignment method) (QC method) (TaskQC method) load_dataset() (One method) load_dataset_from_id() (One method) load_datasets() (One method) load_embedded_frame_data() (in module ibllib.io.raw_data_loaders) load_encoder_events() (in module ibllib.io.raw_data_loaders) load_encoder_positions() (in module ibllib.io.raw_data_loaders) load_encoder_trial_info() (in module ibllib.io.raw_data_loaders) load_ephys_session() (in module brainbox.io.one) load_ephyspc_params() (in module ibllib.pipes.misc) load_fake_bpod_data() (TestHabituationQC static method) (TestTaskMetrics static method) load_fake_wheel_data() (TestTaskMetrics static method) load_file_content() (in module one.alf.io) load_gltf_mesh() (in module iblviewer.utils) load_lfp() (in module brainbox.io.one) load_mic() (in module ibllib.io.raw_data_loaders) load_object() (in module one.alf.io) (One method) load_params_dict() (in module ibllib.pipes.misc) load_passive_rfmap() (in module brainbox.io.one) load_raw_data() (TaskQCExtractor method) load_reference_frames() (CameraQC static 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_surface_mesh() (in module iblviewer.utils) load_track_csv() (in module ibllib.pipes.histology) load_trials_df() (in module brainbox.io.one) load_ttl_pulses() (in module ibllib.io.certification_protocol) load_video_data() (CameraQC method) load_videopc_params() (in module ibllib.pipes.misc) load_volume() (IBLAtlasModel method) (VolumeModel method) load_wheel_reaction_times() (in module brainbox.io.one) 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) logout() (AlyxClient method) lp() (in module ibllib.dsp.fourier) (in module ibllib.dsp.smooth) lt() (in module ibllib.misc.version) LUTModel (class in iblviewer.volume) luts (ViewerModel attribute) (VolumeModel attribute)

M

main() (in module ibllib.pipes.transfer_rig_data) (in module ibllib.qc.critical_reasons) (in module iblviewer.launcher) (in module iblviewer.qt_application) main_context (UIModel attribute) main_gui() (in module ibllib.qc.critical_reasons) make_graph() (Pipeline method) make_parquet_db() (in module one.alf.cache) mapped_lut (LUTModel attribute) mapping (VolumeModel attribute) mapping_name (VolumeModel attribute) maxi (TestParabolicMax attribute) merge_clusters_channels() (in module brainbox.io.one) mgrid() (BrainCoordinates property) MIN_SLAB_THICKNESS (SlicerModel attribute) mindist() (Trajectory method) mirror_volume() (VolumeController method) missed_spikes_est() (in module brainbox.metrics.single_units) (in module brainbox.plot) mktree() (FTPPatcher method) mle_fit_psycho() (in module brainbox.behavior.pyschofit) mock_input() (in module ibllib.tests.qc.test_critical_reasons) (TestFTPPatcher static method) MockExtracor (class in ibllib.tests.extractors.test_extractors) module brainbox brainbox.atlas brainbox.behavior brainbox.behavior.dlc brainbox.behavior.pyschofit brainbox.behavior.training brainbox.behavior.wheel brainbox.core brainbox.ephys_plots brainbox.io brainbox.io.one brainbox.io.spikeglx brainbox.lfp brainbox.metrics brainbox.metrics.electrode_drift brainbox.metrics.single_units brainbox.modeling brainbox.modeling.design_matrix brainbox.modeling.linear brainbox.modeling.neural_model brainbox.modeling.poisson brainbox.modeling.utils brainbox.numerical brainbox.plot brainbox.plot_base brainbox.population brainbox.population.cca brainbox.population.decode brainbox.processing brainbox.quality brainbox.quality.lfp_qc brainbox.quality.permutation_test brainbox.singlecell brainbox.spike_features brainbox.task brainbox.task.closed_loop brainbox.task.passive brainbox.task.trials brainbox.tests brainbox.tests.test_behavior brainbox.tests.test_cca brainbox.tests.test_io brainbox.tests.test_metrics brainbox.tests.test_passive brainbox.tests.test_plot_base brainbox.tests.test_population brainbox.tests.test_processing brainbox.tests.test_singlecell brainbox.tests.test_task brainbox.tests.test_trials brainbox.tests.test_video brainbox.video ibllib ibllib.atlas ibllib.atlas.atlas ibllib.atlas.regions ibllib.dsp ibllib.dsp.cadzow ibllib.dsp.fourier ibllib.dsp.savitzky_golay ibllib.dsp.smooth ibllib.dsp.utils ibllib.dsp.voltage ibllib.ephys ibllib.ephys.ephysqc ibllib.ephys.neuropixel ibllib.ephys.spikes ibllib.ephys.sync_probes ibllib.exceptions ibllib.graphic ibllib.io ibllib.io.certification_protocol ibllib.io.extractors ibllib.io.extractors.base ibllib.io.extractors.biased_trials ibllib.io.extractors.bpod_trials ibllib.io.extractors.camera ibllib.io.extractors.ephys_fpga ibllib.io.extractors.ephys_passive ibllib.io.extractors.habituation_trials 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.ffmpeg ibllib.io.flags ibllib.io.globus ibllib.io.misc ibllib.io.npy_header ibllib.io.raw_data_loaders ibllib.io.spikeglx ibllib.io.video ibllib.misc ibllib.misc.misc ibllib.misc.timing ibllib.misc.version ibllib.oneibl ibllib.oneibl.patcher ibllib.oneibl.registration ibllib.oneibl.stream 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.remote_server 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.camera ibllib.qc.critical_reasons ibllib.qc.dlc ibllib.qc.qcplots ibllib.qc.task_extractors ibllib.qc.task_metrics ibllib.tests ibllib.tests.extractors ibllib.tests.extractors.test_ephys_fpga ibllib.tests.extractors.test_ephys_passive ibllib.tests.extractors.test_ephys_trials ibllib.tests.extractors.test_extractors ibllib.tests.fixtures ibllib.tests.fixtures.utils ibllib.tests.qc ibllib.tests.qc.test_alignment_qc ibllib.tests.qc.test_base_qc ibllib.tests.qc.test_camera_qc ibllib.tests.qc.test_critical_reasons ibllib.tests.qc.test_dlc_qc ibllib.tests.qc.test_task_metrics ibllib.tests.test_atlas ibllib.tests.test_dsp ibllib.tests.test_ephys ibllib.tests.test_histology ibllib.tests.test_io ibllib.tests.test_misc ibllib.tests.test_oneibl ibllib.tests.test_pipes ibllib.tests.test_spikeglx ibllib.tests.test_tasks ibllib.tests.test_time ibllib.time iblviewer iblviewer.application iblviewer.collection iblviewer.launcher iblviewer.mouse_brain iblviewer.objects iblviewer.qt_application iblviewer.utils iblviewer.volume one one.alf one.alf.cache one.alf.exceptions one.alf.files one.alf.io one.alf.spec one.api one.converters one.params one.tests one.tests.alf one.tests.alf.test_alf_files one.tests.alf.test_alf_io one.tests.alf.test_alf_spec one.tests.alf.test_cache one.tests.test_alyxclient one.tests.test_alyxrest one.tests.test_converters one.tests.test_one one.tests.test_params one.tests.util one.util one.webclient

motion_energy() (in module brainbox.video) MotionAlignment (class in ibllib.io.extractors.video_motion) MouseBrainViewer (class in iblviewer.mouse_brain) move_camera_pivot() (Viewer method) 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) MplCanvas (class in iblviewer.qt_application) multi_input() (in module ibllib.graphic) multiple_spike_trains() (in module brainbox.tests.test_metrics)

N

name (BrainRegions attribute) (LUTModel attribute) (SlicerModel attribute) (VolumeModel 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.utils) NeuralModel (class in brainbox.modeling.neural_model) Neuropixel3BSyncFrontsNonMatching

next() (Collection method) next_num_folder() (in module one.alf.io) next_time_series() (Viewer method) noise_cutoff() (in module brainbox.metrics.single_units) normal (SlicerModel attribute) NORMALIZED_SUFFIX (VolumeModel attribute) ns() (Reader property) ns_optim_fft() (in module ibllib.dsp.fourier) numinput() (in module ibllib.graphic) numpy2vtk() (in module iblviewer.utils) NvidiaDriverNotReady nxyz() (BrainCoordinates property)

O

OBJECT (UIModel attribute) object_context() (Viewer method) objects_changed() (Viewer method) OBJECTS_TYPE (ViewerModel attribute) offline() (One property) offscreen (ViewerModel attribute) on_key_press() (Density method) (Traces method) onAnteriorCameraPreset() (ViewerWindow method) onChangeSelection() (ViewerWindow method) onClipToBounds() (ViewerWindow method) onClose() (ViewerWindow method) onDorsalCameraPreset() (ViewerWindow method) one module One (class in one.api) one (Pipeline attribute) (Task attribute) (TestOneAlyx attribute) (TestOneDownload attribute) ONE() (in module one.api) one.alf module one.alf.cache module one.alf.exceptions module one.alf.files module one.alf.io module one.alf.spec module one.api module one.converters module one.params module one.tests module one.tests.alf module one.tests.alf.test_alf_files module one.tests.alf.test_alf_io module one.tests.alf.test_alf_spec module one.tests.alf.test_cache module one.tests.test_alyxclient module one.tests.test_alyxrest module

one.tests.test_converters module one.tests.test_one module one.tests.test_params module one.tests.util module one.util module one.webclient module one_path_from_dataset() (in module one.converters) OneAlyx (class in one.api) onEditProbe() (ViewerWindow method) onExportImage() (ViewerWindow method) onExportVideo() (ViewerWindow method) onIsosurface() (ViewerWindow method) onLeftCameraPreset() (ViewerWindow method) onNewProbe() (ViewerWindow method) onObjectsChanged() (ViewerWindow method) onOpacityChange() (ViewerWindow method) onPosteriorCameraPreset() (ViewerWindow method) onRemoveObject() (ViewerWindow method) onRightCameraPreset() (ViewerWindow method) onSearch() (ViewerWindow method) onSelectionChanged() (ViewerWindow method) onSliceOpacityChange() (ViewerWindow method) onSlicerToggle() (ViewerWindow method) onTimeSeriesChange() (ViewerWindow method) onToggleAutofocus() (ViewerWindow method) onToggleColorBar() (ViewerWindow method) onToggleDarkBackground() (ViewerWindow method) onToggleHollow() (ViewerWindow method) onToggleInfoText() (ViewerWindow method) onToggleMarker() (ViewerWindow method) onToggleMarkerType() (ViewerWindow method) onToggleOrthoCamera() (ViewerWindow method) onToggleOutline() (ViewerWindow method) onToggleStatistics() (ViewerWindow method) onToggleVolumesLOD() (ViewerWindow method) onVentralCameraPreset() (ViewerWindow method) onViewerInitialized() (ViewerWindow method) onViewSelection() (ViewerWindow method) open() (Reader method) origin (IBLAtlasModel attribute) (SlicerModel attribute) (ViewerModel attribute) orthographic_scale_factor (CameraModel attribute) outcome() (QC property) outline_color (ViewerModel attribute) outline_opacity (ViewerModel attribute) outline_width (ViewerModel attribute) outputs (Task attribute) overall_outcome() (QC static method)

P

parabolic_max() (in module ibllib.dsp.utils) parent (BrainRegions attribute) parse_args() (IBLViewer method) parse_id() (in module one.util) parse_values() (in module one.converters) PassiveChoiceWorld (class in ibllib.io.extractors.ephys_passive) patch() (AlyxClient method) patch_dataset() (Patcher method) patch_datasets() (GlobusPatcher method) (Patcher method) Patcher (class in ibllib.oneibl.patcher) path2eid() (ConversionMixin method) (OneAlyx method) path2pid() (ConversionMixin method) path2record() (ConversionMixin method) path2ref() (ConversionMixin static method) path2url() (ConversionMixin method) (OneAlyx method) path_from_dataset() (in module one.converters) path_from_filerecord() (in module one.converters) path_parts() (in module one.alf.files) path_pattern() (in module one.alf.spec) peri_event_time_histogram() (in module brainbox.plot) permut_test() (in module brainbox.quality.permutation_test) phi (Insertion attribute) phy_model_from_ks2_path() (in module ibllib.ephys.ephysqc) pick() (VolumeController method) pick_object() (in module iblviewer.utils) pickings (ViewerModel attribute) pid2eid() (OneAlyx method) Pipeline (class in ibllib.pipes.tasks) play_time_series() (Viewer method) playback_speed (ViewerModel attribute) plot2d_all() (in module ibllib.pipes.histology) plot3d_all() (in module ibllib.pipes.histology) plot_alignment() (MotionAlignment method) plot_atlas() (in module brainbox.atlas) plot_audio_times() (in module ibllib.io.extractors.passive_plotting) plot_correlations() (in module brainbox.population.cca) plot_cslice() (BrainAtlas method) plot_gabor_times() (in module ibllib.io.extractors.passive_plotting) plot_hslice() (BrainAtlas method) plot_image() (in module brainbox.plot_base) plot_line() (in module brainbox.plot_base) 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_permut_test() (in module brainbox.quality.permutation_test) plot_probe() (in module brainbox.plot_base) plot_results() (in module ibllib.qc.qcplots) plot_rfmapping() (in module ibllib.io.extractors.passive_plotting) plot_scatter() (in module brainbox.plot_base) plot_sslice() (BrainAtlas method) plot_stims_times() (in module ibllib.io.extractors.passive_plotting) plot_sync_channels() (in module ibllib.io.extractors.passive_plotting) plot_tilted_slice() (BrainAtlas method)

plot_top() (BrainAtlas method) plot_valve_times() (in module ibllib.io.extractors.passive_plotting) point (Trajectory attribute) POINT (ViewerModel attribute) Points (class in iblviewer.objects) points (ViewerModel attribute) PoissonGLM (class in brainbox.modeling.poisson) populate_raw_spikeglx() (in module ibllib.tests.fixtures.utils) populate_task_settings() (in module ibllib.tests.fixtures.utils) popup() (in module ibllib.graphic) post() (AlyxClient method) power_spectrum() (in module brainbox.lfp) PREFIX (SlicerModel attribute) (VolumeModel attribute) preprocess() (in module brainbox.population.cca) pres_ratio() (in module brainbox.metrics.single_units) (in module brainbox.plot) prev_traj_id (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) previous() (Collection method) previous_time_series() (Viewer method) print_progress() (in module ibllib.misc.misc) (WindowGenerator method) priority (EphysAudio attribute) (EphysCellsQc attribute) (EphysMtscomp attribute) (EphysPulses attribute) (EphysTrials attribute) (EphysVideoCompress attribute) (RawEphysQC attribute) (SpikeSorting 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) probe() (in module iblviewer.utils) (VolumeController method) probe00_id (TestTracingQc attribute) probe01_id (TestTracingQc attribute) probe_id (TestAlignmentQcExisting attribute) (TestAlignmentQcManual attribute) (TestUploadToFlatIron attribute) probe_initial_point1 (ViewerModel attribute) probe_initial_point2 (ViewerModel attribute) probe_lfp_spectrum_plot() (in module brainbox.ephys_plots) probe_rms_plot() (in module brainbox.ephys_plots) ProbePlot (class in brainbox.plot_base) probes (ViewerModel attribute) probes_description() (in module ibllib.ephys.spikes) project() (Trajectory method) PsychofitTest (class in brainbox.tests.test_behavior) ptp_over_noise() (in module brainbox.metrics.single_units) purge_local_data() (in module ibllib.pipes.purge_rig_data) put() (AlyxClient method) PYKILOSORT_REPO (SpikeSorting attribute)

Q

QC (class in ibllib.qc.base)

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

R

r2ix() (BrainCoordinates method) r2iy() (BrainCoordinates method) r2iz() (BrainCoordinates method) raised_cosine() (in module brainbox.modeling.utils) ram (Task attribute) range_str() (in module ibllib.misc.misc) RAW (VolumeModel attribute) raw_qc_session() (in module ibllib.ephys.ephysqc) RawEphysQC (class in ibllib.pipes.ephys_preprocessing) raycast() (VolumeController method) rc2xy() (in module ibllib.ephys.neuropixel) read() (in module ibllib.io.npy_header) (in module ibllib.io.spikeglx) (Reader method) read_flag_file() (in module ibllib.io.flags) read_meta_data() (in module ibllib.io.spikeglx) read_samples() (Reader method) read_sync() (Reader method) read_sync_analog() (Reader method) read_sync_digital() (Reader method) read_ts() (in module one.alf.io) read_volume() (VolumeModel method) Reader (class in ibllib.io.spikeglx) recompute_normals() (in module iblviewer.utils) record2path() (ConversionMixin method) record2url() (ConversionMixin method) recurse() (in module one.converters) ref2dict() (ConversionMixin static method) ref2dj() (ConversionMixin method) ref2eid() (ConversionMixin method) ref2path() (ConversionMixin method) refresh() (in module one.util) refresh_cache() (One method) regex() (in module one.alf.spec) regions_from_allen_csv() (in module ibllib.atlas.regions) register() (UIModel method) register_aligned_track() (in module ibllib.pipes.histology) register_controller() (Viewer method) register_dataset() (in module ibllib.oneibl.registration) (Patcher method) register_datasets() (Patcher method) (Task method) register_object() (Viewer method) register_session() (RegistrationClient method) register_session_raw_data() (in module ibllib.oneibl.registration) register_sync() (RegistrationClient method) register_track() (in module ibllib.pipes.histology) register_track_files() (in module ibllib.pipes.histology) RegistrationClient (class in ibllib.oneibl.registration) regress() (in module brainbox.population.decode) reject_channels() (in module ibllib.dsp.voltage)

rel_path2url() (AlyxClient method) rel_path_parts() (in module one.alf.files) rel_ses_files (TestsONEParquet attribute) rel_ses_path (TestsONEParquet attribute) remap() (IBLAtlasModel method) remap_atlas() (AllenAtlasExt method) remap_slow() (VolumeModel method) remove_callback() (Viewer method) remove_empty_folders() (in module one.alf.io) remove_object() (Viewer method) remove_uuid_file() (in module one.alf.io) remove_uuid_recursive() (in module one.alf.io) rename_data() (TaskQCExtractor static method) rename_ephys_files() (in module ibllib.pipes.misc) rename_files_compatibility() (in module ibllib.oneibl.registration) rename_session() (in module ibllib.pipes.misc) render() (Viewer method) RepNum (class in ibllib.io.extractors.training_trials) report_health() (in module ibllib.pipes.local_server) rerun() (Pipeline method) (Task method) rerun_failed() (Pipeline method) reset_clipping_planes() (VolumeController method) reset_params() (TestFTPPatcher method) resolution (VolumeModel attribute) resolve_manual() (AlignmentQC method) ResponseTimes (class in ibllib.io.extractors.training_trials) responsive_units() (in module brainbox.task.closed_loop) rest() (AlyxClient method) rest_schemes() (AlyxClient property) revisions_datasets_table() (in module one.tests.util) 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.closed_loop) roc_single_event() (in module brainbox.task.closed_loop) roi (MotionAlignment attribute) rolling_window() (in module ibllib.dsp.smooth) run() (AlignmentQC method) (CameraQC method) (DlcQC 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_extractor_classes() (in module ibllib.io.extractors.base) runtime (ViewerModel attribute)

S

samples_to_cm() (in module brainbox.behavior.wheel) save() (Bunch method) (in module one.params) save_bool() (in module ibllib.io.raw_data_loaders) save_metadata() (in module one.alf.io) save_names (BaseExtractor attribute) (CameraTimestampsBpod attribute) (Choice attribute) (ContrastLR attribute), [1] (FeedbackTimes attribute) (FeedbackType attribute) (FpgaTrials attribute) (GoCueTimes attribute) (GoCueTriggerTimes attribute) (IncludedTrials attribute) (Intervals attribute) (ItiDuration attribute) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimOnOffFreezeTimes attribute) (StimOnTimes_deprecated attribute) (StimOnTriggerTimes attribute) (TrialType attribute) (Wheel attribute) save_object_npy() (in module one.alf.io) savitzky_golay() (in module ibllib.dsp.savitzky_golay) scalar_lut (LUTModel attribute) scalar_map (LUTModel attribute) scalar_max (LUTModel attribute) scalar_min (LUTModel attribute) scalars (VolumeModel attribute) 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) SCENE (UIModel attribute) scene_context() (Viewer method) score() (LinearGLM method) (PoissonGLM method) sdsc_globus_path_from_dataset() (in module ibllib.oneibl.patcher) sdsc_path_from_dataset() (in module ibllib.oneibl.patcher) search() (One method) (OneAlyx method) search_terms() (One method) (OneAlyx method) SEGMENTED (VolumeModel attribute) select() (Viewer method) select_next_object() (Viewer method) select_object_by_id() (Viewer method) select_object_by_name() (Viewer method) select_previous_object() (Viewer method) selection (ViewerModel attribute) selection_camera_position (ViewerModel attribute) selection_changed (ViewerModel attribute) selection_changed() (Viewer method) selection_color_bar_visible (ViewerModel attribute) selection_controller (ViewerModel attribute) selection_marker_visible (ViewerModel attribute) selection_outline_visible (ViewerModel attribute) selection_point (ViewerModel attribute) selection_point_changed (ViewerModel attribute) selection_related_name (ViewerModel attribute) selection_related_value (ViewerModel attribute) selection_relative_point (ViewerModel attribute) selection_text_visible (ViewerModel attribute) selection_type (ViewerModel attribute) selection_value (ViewerModel attribute) SequentialSelector (class in brainbox.modeling.utils) ses2eid() (LazyId static method) ses2records() (in module one.util) ses_info (TestsONEParquet attribute) session_name() (in module ibllib.pipes.purge_rig_data) session_path (BaseExtractor attribute) session_path_parts() (in module one.alf.files) set_alpha_map() (VolumeController method) set_anterior_view() (MouseBrainViewer method) (Viewer method) set_button_state() (Viewer method) set_camera() (Viewer method) set_clim() (DefaultPlot method) set_clipping_planes() (in module iblviewer.utils) (VolumeController method) set_color() (ScatterPlot method) set_color_bar_visibility() (Viewer method) set_color_map() (SlicerView method) (VolumeController method) set_context() (UIModel method) set_current() (Collection method) set_dark_mode() (UIModel method) (Viewer method) (ViewerWindow method) set_dorsal_view() (MouseBrainViewer method) (Viewer method) set_element_visibility() (Viewer method) set_info_text_visibility() (Viewer method) set_info_visibility() (Viewer method) set_interactive_subsampling() (VolumeController method) set_labels() (DefaultPlot method) set_left_view() (MouseBrainViewer method) (Viewer method) set_light_mode() (ViewerWindow 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_marker_visibility() (Viewer method) set_menu_context() (Viewer method) set_offset() (ImagePlot method) (ProbePlot method) set_opacity() (ScatterPlot method) (VolumeController method) set_opacity_unit() (VolumeController method) set_outline_visibility() (Viewer method) set_position() (VolumeController method) set_posterior_view() (MouseBrainViewer method) (Viewer method) set_probe_position() (Viewer method) set_renderer() (Viewer method) set_right_view() (MouseBrainViewer method) (Viewer method) set_roi() (MotionAlignment static method) set_scale() (ImagePlot method) (ProbePlot method) set_selection_marker() (Viewer method) set_slice_type() (SlicerView method) set_slices_opacity() (VolumeController method) set_slices_visibility() (VolumeController method) set_time_series() (Viewer method) set_ui_visibility() (Viewer method) set_up_env() (in module one.tests.util) set_ventral_view() (MouseBrainViewer method) (Viewer method) set_volume_clipping() (VolumeController method) set_volume_visibility() (VolumeController method) set_xlim() (DefaultPlot method)

set_ylim() (DefaultPlot method) set_zlim() (DefaultPlot method) settings (BaseBpodTrialsExtractor attribute) setup() (FTPPatcher static method) (in module ibllib.io.globus) (in module one.params) (One static method) (OneAlyx static method) setUp() (PsychofitTest method) (Task method) (TestArrangeChannels2Bank method) (TestAuthentication method) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestDownloadHTTP method) (TestEphysBehaviorExtraction method) (TestExtractedWheelUnits method) (TestExtractTrialData method) (TestFTPPatcher method) (TestHabituationQC method) (TestHistology method) (TestIblChannelMaps method) (TestIO_ALF method) (TestJsonFieldMethods method) (TestOneDownload method) (TestONEParamUtil method) (TestOneRemote method) (TestOneSetup method) (TestPipelineAlyx method) (TestPipesMisc method) (TestPlotBase method) (TestPopulation method) (TestQC method) (TestRegistration method) (TestRestCache method) (TestsAlf method) (TestsAlfPartsFilters method) (TestScanFixPassiveFiles method) (TestScatterXYC method) (TestsEphysAlignment method) (TestsEphysReconstruction method) (TestsFolderStructure method) (TestsGlobus method) (TestsLoadFile method) (TestsMisc method) (TestsONEParquet method) (TestsParams method) (TestsPassiveExtractor method) (TestSpikeGLX_glob_ephys method) (TestSpikeGLX_hardwareInfo method) (TestsRawDataLoaders method) (TestsSpikeGLX_compress method) (TestsSpikeGLX_Meta method) (TestSyncExtraction method) (TestTask method) (TestTaskMetrics method) (TestTraining method) (TestTrials method) (TestUserPmtSess method) (TestVideo method), [1] (TestWheel method) (TestWheelExtraction method) (TestWheelLoaders method) (TestWheelMovesExtraction method) setup_rest_cache() (in module one.tests.util) setup_test_params() (in module one.tests.util) setUpClass() (TestALFFolders class method) (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestAtlasSlicesConversion class method) (TestBrainRegions class method) (TestCameraQC class method) (TestConverters class method) (TestDlcQC class method) (TestOneAlyx class method) (TestONECache class method) (TestOnlineConverters class method) (TestTracingQc class method) (TestUploadToFlatIron method) (TestVideo class method) shape() (Reader property) SHELL_SCRIPT (SpikeSorting attribute) show() (Viewer method) show_viewer() (ViewerWindow method) shuffle_analysis() (in module brainbox.population.cca) sigtest_linshift() (in module brainbox.population.decode) sigtest_pseudosessions() (in module brainbox.population.decode) slice() (BrainAtlas method) (WindowGenerator property) slice_array() (WindowGenerator method) slice_on_axis() (SlicerView method) slice_on_normal() (SlicerView method) SlicerModel (class in iblviewer.volume) slicers (ViewerModel attribute) (VolumeModel attribute) SlicerView (class in iblviewer.volume) slices (SlicerView attribute) slices_visible (VolumeModel attribute) slider_config (UIModel attribute) slider_value() (Viewer method) slidingRP_viol() (in module brainbox.metrics.single_units) smooth_demo() (in module ibllib.dsp.smooth) SomePipeline (class in ibllib.tests.test_tasks) SPEC_DESCRIPTION (in module one.alf.spec), [1] spectrum() (in module ibllib.plots) sph2cart() (in module ibllib.atlas.atlas) Spheres (class in iblviewer.objects) spherical_degree_angles_to_xyz() (in module iblviewer.utils) SPIKE_SORTER_NAME (SpikeSorting attribute) spike_sorting_metrics() (in module brainbox.metrics.single_units) spike_sorting_metrics_ks2() (in module ibllib.ephys.ephysqc) SpikeSorting (class in ibllib.pipes.ephys_preprocessing) split_by_area() (in module brainbox.population.cca) split_path() (in module iblviewer.utils) 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 ibllib.oneibl.patcher) StimFreezeTriggerTimes (class in ibllib.io.extractors.training_trials) StimOffTriggerTimes (class in ibllib.io.extractors.training_trials) StimOnOffFreezeTimes (class in ibllib.io.extractors.training_trials) StimOnTimes_deprecated (class in ibllib.io.extractors.training_trials) StimOnTriggerTimes (class in ibllib.io.extractors.training_trials) store() (Collection method) str2bool() (in module iblviewer.launcher) strinput() (in module ibllib.graphic) structarr() (in module ibllib.misc.misc) sub_selection_changed() (Viewer method) subjects_data_folder() (in module ibllib.pipes.misc) SURFACE (ViewerModel attribute) surfaces (ViewerModel attribute) sync() (in module brainbox.processing) (in module ibllib.ephys.sync_probes) 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() (in module ibllib.dsp.utils) sync_trials_robust() (in module ibllib.io.raw_data_loaders) SyncBpodFpgaException SyncBpodWheelException

T

target (CameraModel attribute) targets (Collection attribute) 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) 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) (TestBaseExtractorSavingMethods method) (TestCameraQC method) (TestDlcQC method) (TestExtractTrialData method) (TestIO_ALF method) (TestJsonFieldMethods method) (TestONECache method) (TestOneDownload method) (TestPipelineAlyx method) (TestPipesMisc method) (TestRegistration method) (TestRestCache method) (TestsAlf method) (TestsAlfPartsFilters method) (TestScanFixPassiveFiles method) (TestsFolderStructure method) (TestsLoadFile method) (TestsMisc method) (TestsONEParquet method) (TestsParams method) (TestsPassiveExtractor method) (TestSpikeGLX_glob_ephys method) (TestsRawDataLoaders method) (TestsSpikeGLX_compress method) (TestUserPmtSess method) tearDownClass() (TestALFFolders class method) (TestAlignmentQcExisting class method) (TestAlignmentQcManual class method) (TestCameraQC class method) (TestDlcQC class method) (TestOneAlyx class method) (TestONECache class method) (TestTracingQc class method) (TestUploadToFlatIron class method) tempdir (TestALFFolders attribute) (TestConverters attribute) (TestOneAlyx attribute) (TestONECache attribute) (TestOneDownload attribute) test_1d() (TestParabolicMax method) test_2d() (TestParabolicMax method) test__set_eid_or_path() (TestQC method) test_acorr_0() (TestPopulation method) test_acorr_1() (TestPopulation method) test_add_uuid() (TestALFGet method) test_align_to_trial() (TestEphysSyncExtraction method) test_alignments() (TestAlignmentQcExisting method) (TestAlignmentQcManual method) test_allen_ba() (TestAtlasSlicesConversion method) test_ancestors_descendants() (TestBrainRegions method) test_append_list() (TestAlfBunch method) test_append_numpy() (TestAlfBunch method) test_as_globus_path() (TestsGlobus method) test_assert_valid_label() (TestVideo method) test_attribute_times() (TestCameraExtractors method) test_auth_methods() (TestAuthentication method) test_authentication() (TestAuthentication method) test_autocomplete() (TestOneMisc method) test_behavior_exists() (TestPipesMisc method) test_bincount_2d() (TestProcessing method) test_bpod_trace_extraction() (TestEphysSyncExtraction method) test_brain_coordinates() (TestsCoordinatesSimples method) test_cache_mode() (TestRestCache method) test_cache_returned_on_error() (TestRestCache method) test_caches_response() (TestRestCache method) test_ccf_xyz() (TestAtlasSlicesConversion method) test_channel_locations() (TestsEphysReconstruction method) test_channels() (Tests_REST method) test_check_audio_pre_trial() (TestTaskMetrics method) test_check_brightness() (TestCameraQC method) test_check_camera_times() (TestCameraQC method) test_check_correct_trial_event_sequence() (TestTaskMetrics method) test_check_create_raw_session_flag() (TestPipesMisc method) test_check_detected_wheel_moves() (TestTaskMetrics method) test_check_dimensions() (TestAlfBunch method) (TestsAlf method) test_check_dropped_frames() (TestCameraQC method) test_check_ephys_file() (TestsSpikeGLX_Meta method) test_check_error_trial_event_sequence() (TestTaskMetrics method) test_check_errorCue_delays() (TestTaskMetrics method) test_check_exists() (TestONECache 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_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_resolution() (TestCameraQC method) test_check_response_feedback_delays() (TestTaskMetrics method) test_check_response_stimFreeze_delays() (TestTaskMetrics method) test_check_reward_volume_set() (TestTaskMetrics method) test_check_reward_volumes() (TestTaskMetrics method) test_check_stimFreeze_delays() (TestTaskMetrics method) test_check_stimOff_delays() (TestTaskMetrics method) test_check_stimOff_itiIn_delays() (TestTaskMetrics method) test_check_stimOn_delays() (TestTaskMetrics method) test_check_stimOn_goCue_delays() (TestTaskMetrics method) test_check_stimulus_move_before_goCue() (TestTaskMetrics method) test_check_time_trace_length_match() (TestDlcQC method) test_check_timestamps() (TestCameraQC method) test_check_trace_all_nan() (TestDlcQC method) test_check_transfer() (TestPipesMisc method) test_check_trial_length() (TestTaskMetrics method) test_check_wheel_alignment() (TestCameraQC method) test_check_wheel_freeze_during_quiescence() (TestTaskMetrics method) test_check_wheel_integrity() (TestTaskMetrics method) test_check_wheel_move_before_feedback() (TestTaskMetrics method) test_check_wheel_move_during_closed_loop() (TestTaskMetrics method) test_classify() (TestPopulation method) test_clear_cache() (TestRestCache method) test_clusters_metrics() (in module brainbox.tests.test_metrics) test_code_to_outcome() (TestQC method) test_collection_spec() (TestOneMisc method) test_compare_version_tags() (TestVersionTags method) test_compress() (TestsSpikeGLX_compress method) test_compute() (TestHabituationQC method) test_compute_cluster_averag() (TestProcessing method) test_concatenate_and_computations() (TestTraining method) test_create_alyx_probe_insertions() (TestPipesMisc method) test_create_ephys_flags() (TestPipesMisc method) test_create_ephys_transfer_done_flag() (TestPipesMisc method) test_create_video_transfer_done_flag() (TestPipesMisc method) test_creation() (TestProbeInsertion method) test_data_content() (TestUploadToFlatIron method) test_datasets2records() (TestOneAlyx method) test_datasets_df() (TestsONEParquet method) test_date2isostr() (TestUtils method) test_default() (TestPlotBase method) test_default_values() (TestSpikeGLX_hardwareInfo method) test_delete_empty_folders() (TestsMisc method) test_derivative() (TestWheel method) test_describe() (TestALFSpec method) test_describe_dataset() (TestOneAlyx method) test_describe_revision() (TestOneAlyx method) test_dft() (TestFFT method) test_dict2ref() (TestConverters method) test_differentiate_units() (TestTask method) test_direction_changes() (TestWheel method) test_download_datasets() (TestDownloadHTTP method) (TestOneDownload method) test_download_datasets_with_api() (TestDownloadHTTP method) test_drift_estimate() (in module brainbox.tests.test_metrics) test_dromedary() (TestALFSpec method) test_dsets_2_path() (TestAlyx2Path method), [1] test_dsp_cosine_func() (TestDspMisc method) test_eid2path() (TestConverters method) test_empty() (TestJsonFieldMethods 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_endpoints_docs() (TestDownloadHTTP method) test_ensure_data() (TestCameraQC method) (TestDlcQC method) test_erf_psycho() (PsychofitTest method) test_erf_psycho_2gammas() (PsychofitTest method) test_error_cases() (TestParabolicMax method) test_eval_trajectory() (TestTrajectory method) test_exists() (TestsAlf method) test_exit_volume() (TestTrajectory method) test_expired_cache() (TestRestCache method) test_expiry_param() (TestRestCache method) test_extended_qc() (TestQC method) test_extract_all() (TestExtractTrialData method) test_extract_first_movement_times() (TestWheelMovesExtraction method) test_extract_wheel_moves() (TestExtractedWheelUnits method) (TestWheelMovesExtraction method) test_fexpand() (TestFFT method) test_filename_parser() (TestHistology method) test_filename_parts() (TestAlfParse method) test_filter() (TestONECache method) test_filter_by() (TestsAlfPartsFilters method) test_filter_lp_hp() (TestFFT method) test_filter_wildcards() (TestONECache method) test_find_pairs() (TestScanFixPassiveFiles method) test_find_trial_ids() (TestTrials method) test_firing_rate() (in module brainbox.tests.test_singlecell) test_firstlast_slices() (TestWindowGenerator method) test_fit_phase1d() (TestPhaseRegression method) test_fit_phase2d() (TestPhaseRegression method) test_fix_meta_file() (TestsSpikeGLX_Meta method) test_fk() (TestVoltage method) test_format_date_range() (TestUtils method) test_frame2ttl_flickers() (TestEphysFPGA_TTLsExtraction method) test_frame_diff() (TestVideo method) test_frame_diffs() (TestVideo method) test_freduce() (TestFFT method) test_fscale() (TestFFT method) test_generate_pseudo_blocks() (TestTask method) test_generate_pseudo_session() (TestTask method) test_generate_pseudo_stimuli() (TestTask method) test_generic_request() (TestDownloadHTTP method) test_get() (TestBrainRegions method) test_get_alf_path() (TestALFGet method) test_get_brain_exit_entry() (TestHistology method) test_get_channel_map() (TestSpikeGLX_hardwareInfo method) test_get_choice() (TestExtractTrialData method) test_get_contrastLR() (TestExtractTrialData method) test_get_default_client() (TestONEParamUtil method) test_get_details() (TestONECache 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_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_iti_duration() (TestExtractTrialData method) test_get_new_filename() (TestPipesMisc method) test_get_params_dir() (TestONEParamUtil method) test_get_probabilityLeft() (TestEphysBehaviorExtraction method) (TestExtractTrialData method) test_get_repNum() (TestExtractTrialData method) test_get_response_times() (TestExtractTrialData method) test_get_rest_dir() (TestONEParamUtil method) test_get_rewardVolume() (TestExtractTrialData method) test_get_session_folder() (TestALFGet method) test_get_spike_counts_in_bins() (TestPopulation method) test_get_stimOn_times_ge5() (TestExtractTrialData method) test_get_stimOn_times_lt5() (TestExtractTrialData method) test_get_stimOnTrigger_times() (TestExtractTrialData method) test_get_unit_bunches() (in module brainbox.tests.test_processing) test_get_wiring() (TestSpikeGLX_hardwareInfo method) test_glob_ephys() (TestSpikeGLX_glob_ephys method) test_groom_pin_state() (TestCameraExtractors method) test_guiinput_ins() (TestUserPmtSess method) test_hash_ids() (TestsONEParquet method) test_histology_get_brain_regions() (TestHistology method) test_histology_insertion_from_track() (TestHistology method) test_ibl_sync_maps() (TestIblChannelMaps method) test_image() (TestPlotBase method) test_impeccable_dataset() (TestFpgaTask method) test_imports() (TestFFT method) test_in_training() (TestTraining method) test_index_last_before() (TestOneMisc method) test_index_type() (TestONECache method) test_init_from_dict() (TestInsertion method) test_init_from_track() (TestInsertion method) test_interpolate_rf_mapping_stimulus() (TestsPassiveExtractor method) test_is_exp_ref() (TestConverters method) test_is_session_folder() (TestALFSpec method) test_is_uuid() (TestALFSpec method) test_is_uuid_string() (TestALFSpec method) test_is_valid() (TestALFSpec method) test_isdatetime() (TestALFGet method) test_isostr2date() (TestUtils method) test_json_methods() (TestJsonFieldMethods method) test_key_from_url() (TestONEParamUtil method) test_label_from_path() (TestVideo method) test_layouts() (TestNeuropixel method) test_LazyID() (TestOneMisc method) test_levels() (TestLoggingSystem method) test_line() (TestPlotBase method) test_linear_scaling() (TestsEphysAlignment method) test_list_collections() (TestONECache method) test_list_datasets() (TestONECache method) (TestOneRemote method) test_list_pk_query() (Tests_REST method) test_list_revisions() (TestONECache method) test_list_subjects() (TestONECache method) test_load_cache() (TestONECache 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_dataset() (TestONECache method) (TestOneRemote method) test_load_dataset_from_id() (TestONECache method) test_load_datasets() (TestONECache 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_file_content() (TestsLoadFile method) test_load_object() (TestONECache method) (TestOneRemote method) (TestsAlf method) test_load_passive_stim_meta() (TestsPassiveExtractor method) test_loads_cached() (TestRestCache method) test_login_auto() (TestsGlobus method) test_lookups() (TestAtlasSlicesConversion method) test_mappings_lateralized() (TestBrainRegions method) test_mappings_not_lateralized() (TestBrainRegions method) test_metadata_columns() (TestsAlf method) test_metadata_columns_UUID() (TestsAlf method) test_mle_fit_psycho() (PsychofitTest method) test_move_rename_pairs() (TestScanFixPassiveFiles method) test_movement_log() (TestWheelMovesExtraction method) test_movements() (TestWheel method) test_movements_FPGA() (TestWheel method) test_named_group() (TestALFSpec method) test_nech_optim() (TestFFT method) test_neg_likelihood() (PsychofitTest method) test_new_default_param() (TestsParams method) test_next_num_folder() (TestALFFolders method) test_no_pad() (TestArrangeChannels2Bank method) test_no_scaling() (TestsEphysAlignment method) test_note_probe_ins() (TestUserPmtSess method) test_note_with_picture_upload() (Tests_REST method) test_npy_parts_and_file_filters() (TestsAlfPartsFilters method)

test_nwindows_computation() (TestWindowGenerator method) test_offline_repr() (TestONECache method) test_offset() (TestsEphysAlignment method) test_one_factory() (TestOneSetup method) test_one_search() (TestONECache method) test_online_repr() (TestOneRemote method) test_outcome_from_dict() (TestAggregateOutcome method) test_outcome_setter() (TestQC method) test_overall_outcome() (TestQC method) test_pad() (TestArrangeChannels2Bank method) test_paginated_request() (TestDownloadHTTP method) test_param_get_file() (TestsParams method) test_params() (TestsParams method) test_parquet() (TestsONEParquet method) test_parse() (TestsONEParquet method) test_parse_id() (TestOneMisc method) test_patch_params() (TestOneSetup method) test_path2eid() (TestConverters method) test_path2record() (TestConverters method) test_path2ref() (TestConverters method) test_path_pattern() (TestALFSpec method) test_patterns() (TestALFSpec method) test_peths_synthetic() (TestPeths method) test_pid2eid() (TestOneAlyx method) test_pipeline_alyx() (TestPipelineAlyx method) test_plotting() (TestBunch method) test_probe() (TestPlotBase method) test_project_mindist() (TestTrajectory method) test_psychometric_insufficient_data() (TestTraining method) test_read_3A() (TestsSpikeGLX_Meta method) test_read_3B() (TestsSpikeGLX_Meta method) test_read_corrupt() (TestsSpikeGLX_Meta method) test_read_nidq() (TestsSpikeGLX_Meta method) test_read_slices() (TestsSpikeGLX_compress method) test_read_ts() (TestsAlf method) test_ready4delay() (TestTraining method) test_ready4ephys() (TestTraining method) test_ready4recording() (TestTraining method) test_reason_addnumberstr() (TestUserPmtSess method) test_record2path() (TestOnlineConverters method) test_record2url() (TestOnlineConverters method) test_recurse() (TestWrappers method) test_ref2dict() (TestConverters method) test_ref2dj() (TestOnlineConverters method) test_ref2path() (TestConverters method) test_refresh_cache() (TestONECache method) test_regex() (TestALFSpec method) test_registration_datasets() (TestRegistration method) test_registration_session() (TestRegistration method) test_regress() (TestPopulation method) test_rel_path_parts() (TestAlfParse method) test_remove_empty_folders() (TestALFFolders method) test_remove_uuid() (TestUUID_Files method) test_remove_uuid_recusive() (TestUUID_Files method) test_rename_and_move() (TestPipesMisc method) test_rename_session() (TestPipesMisc method) test_responsive_units() (TestTask method) test_rest_all_actions() (TestDownloadHTTP method) test_rest_endpoint_read_only() (TestDownloadHTTP method) test_rest_endpoint_write() (TestDownloadHTTP method) test_reverse_directions() (TestsCoordinatesSimples method) test_revision_last_before() (TestOneMisc method) test_rf_map() (TestPassive method) test_RGB_conversion() (TestScatterXYC method) test_RGB_conversion_with_clim() (TestScatterXYC method) test_rises_falls() (TestWindowGenerator method) test_roc_between_two_events() (TestTask method) test_roc_single_event() (TestTask method) test_save_npy() (TestsAlf method) test_saving_method() (TestBaseExtractorSavingMethods method) test_scan_fix() (TestScanFixPassiveFiles method) test_scatter() (TestPlotBase method) test_search() (TestOneRemote method) test_ses2records() (TestOneAlyx method) test_session_path_parts() (TestAlfParse method) test_sessions_df() (TestsONEParquet method) test_setup() (TestFTPPatcher method) (TestOneSetup method) test_setup_silent() (TestOneSetup method) test_shift_1d() (TestShift method) test_shift_2d() (TestShift method) test_shift_already_fft() (TestShift method) test_shift_floats() (TestShift method) test_sigtest_linshift() (TestPopulation method) test_sigtest_pseudosessions() (TestPopulation method) test_simple_print() (TestPrintProgress method) test_size_outputs() (TestExtractTrialData method) test_slice() (TestAtlasSlicesConversion method) test_smooth_lp() (TestSmooth method) test_spectral_convolution() (TestFFT method) test_sph2cart_and_back() (TestsCoordinatesSimples method) test_stim_aligned() (TestPassive method) test_stimOnOffFreeze_times() (TestExtractTrialData method) test_sync() (TestProcessing method) test_sync_3A() (TestSyncExtraction method) test_sync_3B() (TestSyncExtraction method) test_sync_bpod_bonsai_poor_quality_timestamps() (TestSyncWheelBpod method) test_sync_nidq() (TestSyncExtraction method) test_task_names_extractors() (TestExtractors2Tasks method) (TestRegistrationEndpoint method) test_task_to_pipeline() (TestExtractors2Tasks method) test_timestamps_lin() (TestSyncTimestamps method) test_to_alf() (TestALFSpec method) test_to_dataframe_scalars() (TestAlfBunch method) test_to_dataframe_vectors() (TestAlfBunch method) test_to_eid() (TestConverters method) (TestOnlineConverters method) test_traces_by_trial() (TestWheel method) test_tracing_exists() (TestTracingQc method) test_tracing_not_exists() (TestTracingQc method) test_trained_1a() (TestTraining method) test_trained_1b() (TestTraining method) test_training_to_bias() (TestTraining method) test_trajectory() (TestTrajectory method) test_ts2vec() (TestsAlf method) test_tscale() (TestWindowGenerator method) test_ttl_bpod_gaelle_writes_protocols_but_guido_doesnt_read_them() (TestEphysFPGA_TTLsExtraction method) test_type2datasets() (TestOneAlyx method) test_uniform_scaling() (TestsEphysAlignment method) test_update() (TestQC method) test_update_url_params() (TestDownloadHTTP method) (TestMisc method) test_upload_to_flatiron() (TestUploadToFlatIron method) test_url_from_eid() (TestVideo method) test_url_from_path() (TestOneAlyx method) test_url_from_record() (TestOneAlyx method) test_userinput_ins() (TestUserPmtSess method) test_userinput_sess() (TestUserPmtSess method) test_validate_date_range() (TestOneMisc method) test_walk() (TestsONEParquet method) test_walk_session() (TestsONEParquet method) test_water_restriction() (Tests_REST method) test_weibull() (PsychofitTest method) test_weibull50() (PsychofitTest method) test_wheel_folders() (TestExtractTrialData method) test_wheel_trace_from_sync() (TestEphysSyncExtraction method) test_window_simple() (TestWindowGenerator method) test_with_depth() (TestArrangeChannels2Bank method) test_without_RGB_conversion() (TestScatterXYC method) test_x1_decoding() (TestWheelExtraction method) test_x2_decoding() (TestWheelExtraction method) test_x4_decoding() (TestWheelExtraction method) test_xcorr_0() (TestPopulation method) test_xcorr_1() (TestPopulation method) test_xcorr_2() (TestPopulation method) TestAggregateOutcome (class in ibllib.tests.qc.test_task_metrics) TestAlfBunch (class in one.tests.alf.test_alf_io) TestALFFolders (class in one.tests.alf.test_alf_io) TestALFGet (class in one.tests.alf.test_alf_files) TestAlfParse (class in one.tests.alf.test_alf_files) TestALFSpec (class in one.tests.alf.test_alf_spec) 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) (class in one.tests.test_converters) testAppendFlagFile() (TestsRawDataLoaders method) TestArrangeChannels2Bank (class in brainbox.tests.test_plot_base) TestAtlasSlicesConversion (class in ibllib.tests.test_atlas) TestAuthentication (class in one.tests.test_alyxclient) TestBaseExtractorSavingMethods (class in ibllib.tests.extractors.test_extractors) TestBrainRegions (class in ibllib.tests.test_atlas) TestBunch (class in brainbox.tests.test_cca) TestCadzow (class in ibllib.tests.test_dsp) TestCameraExtractors (class in ibllib.tests.extractors.test_extractors) TestCameraQC (class in ibllib.tests.qc.test_camera_qc) TestConverters (class in one.tests.test_converters) TestDlcQC (class in ibllib.tests.qc.test_dlc_qc) TestDownloadHTTP (class in one.tests.test_alyxclient) TestDspMisc (class in ibllib.tests.test_dsp) TestEphysBehaviorExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestEphysFPGA_TTLsExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestEphysSyncExtraction (class in ibllib.tests.extractors.test_ephys_trials) TestExtractedWheelUnits (class in ibllib.tests.extractors.test_ephys_fpga) TestExtractors2Tasks (class in ibllib.tests.test_pipes) TestExtractTrialData (class in ibllib.tests.extractors.test_extractors) TestFFT (class in ibllib.tests.test_dsp) testFlagFileRead() (TestsRawDataLoaders method) TestFpgaTask (class in ibllib.tests.test_ephys) TestFTPPatcher (class in ibllib.tests.test_oneibl) testGetAnalogSyncIndex() (TestsSpikeGLX_Meta method) testGetRevisionAndType() (TestsSpikeGLX_Meta method) testGetSerialNumber() (TestsSpikeGLX_Meta method) TestHabituationQC (class in ibllib.tests.qc.test_task_metrics) TestHistology (class in ibllib.tests.test_histology) TestIblChannelMaps (class in ibllib.tests.extractors.test_ephys_fpga) TestInsertion (class in ibllib.tests.test_atlas) TestIO_ALF (class in brainbox.tests.test_io) TestJsonFieldMethods (class in one.tests.test_alyxclient) TestLoggingSystem (class in ibllib.tests.test_misc) TestMisc (class in one.tests.test_alyxclient) TestNeuropixel (class in ibllib.tests.test_ephys) TestOneAlyx (class in one.tests.test_one) TestONECache (class in one.tests.test_one) TestOneDownload (class in one.tests.test_one) TestOneMisc (class in one.tests.test_one) TestONEParamUtil (class in one.tests.test_params) TestOneRemote (class in one.tests.test_one) TestOneSetup (class in one.tests.test_one) TestOnlineConverters (class in one.tests.test_converters) TestParabolicMax (class in ibllib.tests.test_dsp) TestPassive (class in brainbox.tests.test_passive) TestPeths (class in brainbox.tests.test_singlecell) TestPhaseRegression (class in ibllib.tests.test_dsp) 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) TestPrintProgress (class in ibllib.tests.test_misc) TestProbeInsertion (class in ibllib.tests.qc.test_alignment_qc) TestProcessing (class in brainbox.tests.test_processing) TestQC (class in ibllib.tests.qc.test_base_qc) testReadChannelGainAPLF() (TestsSpikeGLX_Meta method) testReadChannelGainNIDQ() (TestsSpikeGLX_Meta method) testReadChannelMap() (TestsSpikeGLX_Meta method) TestRegistration (class in ibllib.tests.test_oneibl) TestRegistrationEndpoint (class in ibllib.tests.test_oneibl) TestRestCache (class in one.tests.test_alyxclient) tests_db() (TestsONEParquet method) tests_headers() (TestNeuropixel method) Tests_REST (class in one.tests.test_alyxrest) TestsAlf (class in one.tests.alf.test_alf_io) TestsAlfPartsFilters (class in one.tests.alf.test_alf_io) TestScanFixPassiveFiles (class in ibllib.tests.test_pipes) TestScatterXYC (class in brainbox.tests.test_plot_base) TestsCoordinatesSimples (class in ibllib.tests.test_atlas) TestsEphysAlignment (class in ibllib.tests.test_histology) TestsEphysReconstruction (class in ibllib.tests.test_histology) TestsFolderStructure (class in ibllib.tests.extractors.test_ephys_fpga) TestsGlobus (class in ibllib.tests.test_io) TestShift (class in ibllib.tests.test_dsp) TestsLoadFile (class in one.tests.alf.test_alf_io) TestsMisc (class in ibllib.tests.test_io) TestSmooth (class in ibllib.tests.test_dsp) TestsONEParquet (class in one.tests.alf.test_cache) TestsParams (class in ibllib.tests.test_io) TestsPassiveExtractor (class in ibllib.tests.extractors.test_ephys_passive) TestSpikeGLX_glob_ephys (class in ibllib.tests.test_spikeglx) TestSpikeGLX_hardwareInfo (class in ibllib.tests.test_spikeglx) testSplitSyncTrace() (TestsSpikeGLX_Meta method) TestsRawDataLoaders (class in ibllib.tests.test_io) TestsSpikeGLX_compress (class in ibllib.tests.test_spikeglx) TestsSpikeGLX_Meta (class in ibllib.tests.test_spikeglx) TestSyncExtraction (class in ibllib.tests.extractors.test_ephys_fpga) TestSyncTimestamps (class in ibllib.tests.test_dsp) TestSyncWheelBpod (class in ibllib.tests.extractors.test_extractors) TestTask (class in brainbox.tests.test_task) TestTaskMetrics (class in ibllib.tests.qc.test_task_metrics) TestTracingQc (class in ibllib.tests.qc.test_alignment_qc) TestTraining (class in brainbox.tests.test_behavior) TestTrajectory (class in ibllib.tests.test_atlas) TestTrials (class in brainbox.tests.test_trials) TestUploadToFlatIron (class in ibllib.tests.qc.test_alignment_qc) TestUserPmtSess (class in ibllib.tests.qc.test_critical_reasons) TestUtils (class in ibllib.tests.test_time) TestUUID_Files (class in one.tests.alf.test_alf_io) TestVersionTags (class in ibllib.tests.test_misc) TestVideo (class in brainbox.tests.test_video) (class in ibllib.tests.test_io) TestVoltage (class in ibllib.tests.test_dsp) 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) TestWindowGenerator (class in ibllib.tests.test_dsp) TestWrappers (class in one.tests.test_converters) theta (Insertion attribute) tilted_slice() (BrainAtlas method) time (ViewerModel attribute) time_diff() (in module iblviewer.utils) time_elapsed_secs (Task attribute) time_out_secs (Task attribute) time_series_context() (Viewer method) timer_id (ViewerModel attribute) TimeSeries (class in brainbox.core) timing() (in module ibllib.misc.timing) tip() (Insertion property) title (ViewerModel attribute) to_alf() (in module one.alf.spec) to_df() (AlfBunch method) (Bunch method) to_eid() (ConversionMixin method) toggle_autofocus() (Viewer method) toggle_box_widget() (Viewer method) toggle_color_bar() (Viewer method) toggle_config (UIModel attribute) toggle_context() (UIModel method) toggle_dark_mode() (Viewer method) toggle_global_slicer() (Viewer method) toggle_hollow() (VolumeController method) toggle_hollow_mode() (Viewer method) toggle_info() (Viewer method) toggle_info_text() (Viewer method) toggle_marker() (Viewer method) toggle_marker_type() (Viewer method) toggle_menu() (Viewer method) toggle_orthographic_view() (Viewer method) toggle_outline() (Viewer method) toggle_pickable() (Viewer method) toggle_slices() (Viewer method) toggle_slices_visibility() (VolumeController method) toggle_ui() (Viewer method) toggle_volumetric_lod() (Viewer method) trace_header() (in module ibllib.ephys.neuropixel) 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) traj_matrix_indices() (in module ibllib.dsp.cadzow) Trajectory (class in ibllib.atlas.atlas) trajectory() (in module ibllib.dsp.cadzow) (Insertion property) trajectory_matrixes() (TestCadzow method) transfer_folder() (in module ibllib.pipes.misc) transpose() (VolumeModel method) transpose_shape (VolumeModel attribute) trial_times_to_times() (in module ibllib.io.raw_data_loaders) TrialType (class in ibllib.io.extractors.training_trials) ts2vec() (in module one.alf.io) tscale() (WindowGenerator method) type() (CameraQC property) (Reader property) type2datasets() (OneAlyx method)

U

UI (ViewerModel attribute) ui (ViewerModel attribute) UIModel (class in iblviewer.application) uncycle_pgts() (in module ibllib.time) unique_name() (SlicerModel method) (VolumeModel method) unit_stability() (in module brainbox.metrics.single_units) units (VolumeModel attribute) unregister_object() (Viewer method) update() (QC method) (SlicerModel method) (SlicerView method) update_camera() (Viewer method) update_current_probe() (Viewer method) update_data() (Points method) update_data_ui() (Viewer method) update_element_color() (Viewer method) update_experimenter_evaluation() (AlignmentQC method) update_extended_qc() (QC method) update_nx_slicer() (Viewer method) update_ny_slicer() (Viewer method) update_nz_slicer() (Viewer method)

update_object_ui() (Viewer method) update_opacity() (Viewer method) update_probe() (VolumeController method) update_px_slicer() (Viewer method) update_py_slicer() (Viewer method) update_pz_slicer() (Viewer method) update_scalar_bar() (in module iblviewer.utils) update_scene_ui() (Viewer method) update_selection_info() (Viewer method) update_selection_slider() (Viewer method) update_slicer() (VolumeController method) update_slices_opacity() (Viewer method) update_statistics() (ViewerWindow method) update_time_series() (Viewer method) update_ui() (Viewer method) (ViewerWindow method) update_url_params() (in module one.webclient) update_video_duration() (Viewer method) update_video_end_angle() (Viewer method) update_video_start_angle() (Viewer method) upload_channels() (AlignmentQC method) url_from_eid() (in module ibllib.io.video) user (AlyxClient attribute)

V

validate_date_range() (in module one.util) validate_ttl_test() (in module ibllib.ephys.ephysqc) value (SlicerModel attribute) var_name (TrialType attribute) var_names (CameraTimestampsBpod attribute) (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) (LaserBool attribute) (MockExtracor attribute) (PassiveChoiceWorld attribute) (ProbabilityLeft attribute) (ProbaContrasts attribute) (RepNum attribute) (ResponseTimes attribute) (RewardVolume attribute) (StimFreezeTriggerTimes attribute) (StimOffTriggerTimes attribute) (StimOnOffFreezeTimes attribute) (StimOnTimes_deprecated attribute) (StimOnTriggerTimes attribute) (Wheel attribute)

vector (Trajectory attribute) velocity_smoothed() (in module brainbox.behavior.wheel) verify_hash() (Reader method) version (Task attribute) (Task00 attribute) version() (Reader property) version3A() (in module ibllib.ephys.sync_probes) version3B() (in module ibllib.ephys.sync_probes) vertical_lines() (in module ibllib.plots) video_duration (ViewerModel attribute) video_end_angle (ViewerModel attribute) VIDEO_EXPORT (UIModel attribute) video_export_context() (Viewer method) video_meta (CameraQC attribute) video_start_angle (ViewerModel attribute) VideoStreamer (class in ibllib.io.video) (class in ibllib.oneibl.stream) view_selected() (Viewer method) Viewer (class in iblviewer.application) ViewerApp (class in iblviewer.qt_application) ViewerModel (class in iblviewer.application) ViewerWindow (class in iblviewer.qt_application) visible (UIModel attribute) Volume (class in iblviewer.volume) VOLUME (ViewerModel attribute) volume_visible (VolumeModel attribute) VolumeController (class in iblviewer.volume) VolumeModel (class in iblviewer.volume) volumes (ViewerModel attribute) volumetric_lod() (Viewer method)

W

web_ui (ViewerModel attribute) web_window_size (ViewerModel attribute) weibull() (in module brainbox.behavior.pyschofit) weibull50() (in module brainbox.behavior.pyschofit) welchogram() (in module ibllib.io.extractors.training_audio) wf_comp() (in module brainbox.plot) wf_similarity() (in module brainbox.metrics.single_units)

Wheel (class in ibllib.io.extractors.training_wheel) wheel_radius_cm (TestExtractedWheelUnits attribute) wheelMoves_fixture() (in module ibllib.tests.extractors.test_extractors) wiggle() (in module ibllib.plots) window_size (ViewerModel attribute) WindowGenerator (class in ibllib.dsp.utils) within_ranges() (in module brainbox.numerical) write_flag_file() (in module ibllib.io.flags)

X

x (Insertion attribute) (TestParabolicMax attribute) x2i() (BrainCoordinates method) X_DOWN (ViewerModel attribute) x_slice() (SlicerView method) X_UP (ViewerModel attribute)

xcorr() (in module brainbox.population.decode) xlim() (BrainCoordinates property) xscale() (BrainCoordinates property) xyz() (Insertion property) xyz2ccf() (AllenAtlas method) xyz2i() (BrainCoordinates method)

Y

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

y_slice() (SlicerView method) Y_UP (ViewerModel attribute) ylim() (BrainCoordinates property) yscale() (BrainCoordinates property)

Z

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

z_slice() (SlicerView method) Z_UP (ViewerModel attribute) zlim() (BrainCoordinates property) zscale() (BrainCoordinates property)