Index

A

add_recording_segment() (spikeinterface.core.BaseRecording method) add_synchrony_to_sorting() (in module spikeinterface.generation) align_sorting() (in module spikeinterface.postprocessing) append_recordings() (in module spikeinterface.core) append_sortings() (in module spikeinterface.core) AppendSegmentRecording (class in spikeinterface.core)

AppendSegmentSorting (class in spikeinterface.core) apply_curation() (in module spikeinterface.curation) apply_merges_to_sorting() (in module spikeinterface.core) apply_sortingview_curation() (in module spikeinterface.curation) astype() (in module spikeinterface.preprocessing) available_sorters() (in module spikeinterface.sorters) average_across_direction() (in module spikeinterface.preprocessing)

B

bandpass_filter() (in module spikeinterface.preprocessing) BaseEvent (class in spikeinterface.core) BaseRecording (class in spikeinterface.core) BaseSnippets (class in spikeinterface.core) BaseSorter (class in spikeinterface.sorters)

BaseSorting (class in spikeinterface.core) binary_compatible_with() (spikeinterface.core.BaseRecording method) BinaryFolderRecording (class in spikeinterface.core) BinaryRecordingExtractor (class in spikeinterface.core) blank_staturation() (in module spikeinterface.preprocessing)

C

causal_filter() (in module spikeinterface.preprocessing) center() (in module spikeinterface.preprocessing) ChannelSparsity (class in spikeinterface.core) ChunkRecordingExecutor (class in spikeinterface.core) clean_motion_vector() (in module spikeinterface.sortingcomponents.motion) clip() (in module spikeinterface.preprocessing) CollisionGTComparison (class in spikeinterface.comparison) common_reference() (in module spikeinterface.preprocessing) compare_multiple_sorters() (in module spikeinterface.comparison) compare_multiple_templates() (in module spikeinterface.comparison) compare_sorter_to_ground_truth() (in module spikeinterface.comparison) compare_templates() (in module spikeinterface.comparison) compare_two_sorters() (in module spikeinterface.comparison) compute() (spikeinterface.core.SortingAnalyzer method) compute_amplitude_cutoffs() (in module spikeinterface.qualitymetrics.misc_metrics) compute_amplitude_cv_metrics() (in module spikeinterface.qualitymetrics.misc_metrics) compute_amplitude_medians() (in module spikeinterface.qualitymetrics.misc_metrics) compute_correlograms() (in module spikeinterface.postprocessing) compute_drift_metrics() (in module spikeinterface.qualitymetrics.misc_metrics) compute_firing_ranges() (in module spikeinterface.qualitymetrics.misc_metrics) compute_firing_rates() (in module spikeinterface.qualitymetrics.misc_metrics) compute_isi_histograms() (in module spikeinterface.postprocessing) compute_isi_violations() (in module spikeinterface.qualitymetrics.misc_metrics) compute_noise_levels() (in module spikeinterface.postprocessing) compute_one_extension() (spikeinterface.core.SortingAnalyzer method) compute_presence_ratios() (in module spikeinterface.qualitymetrics.misc_metrics) compute_principal_components() (in module spikeinterface.postprocessing) compute_quality_metrics() (in module spikeinterface.qualitymetrics) compute_refrac_period_violations() (in module spikeinterface.qualitymetrics.misc_metrics) compute_sd_ratio() (in module spikeinterface.qualitymetrics.misc_metrics)

compute_several_extensions() (spikeinterface.core.SortingAnalyzer method) compute_sliding_rp_violations() (in module spikeinterface.qualitymetrics.misc_metrics) compute_snrs() (in module spikeinterface.qualitymetrics.misc_metrics) compute_sparsity() (in module spikeinterface.core) compute_spike_amplitudes() (in module spikeinterface.postprocessing) compute_spike_locations() (in module spikeinterface.postprocessing) compute_synchrony_metrics() (in module spikeinterface.qualitymetrics.misc_metrics) compute_template_metrics() (in module spikeinterface.postprocessing) compute_template_similarity() (in module spikeinterface.postprocessing) compute_unit_locations() (in module spikeinterface.postprocessing) concatenate_recordings() (in module spikeinterface.core) ConcatenateSegmentRecording (class in spikeinterface.core) copy() (spikeinterface.core.SortingAnalyzer method) correct_lsb() (in module spikeinterface.preprocessing) correct_motion() (in module spikeinterface.preprocessing) correct_motion_on_peaks() (in module spikeinterface.sortingcomponents.motion) CorrelogramGTComparison (class in spikeinterface.comparison) count_bad_units() (spikeinterface.comparison.GroundTruthComparison method) count_false_positive_units() (spikeinterface.comparison.GroundTruthComparison method) count_num_spikes_per_unit() (spikeinterface.core.BaseSorting method) count_overmerged_units() (spikeinterface.comparison.GroundTruthComparison method) count_redundant_units() (spikeinterface.comparison.GroundTruthComparison method) count_total_num_spikes() (spikeinterface.core.BaseSorting method) count_well_detected_units() (spikeinterface.comparison.GroundTruthComparison method) create() (spikeinterface.comparison.GroundTruthStudy class method) create_dense() (spikeinterface.core.ChannelSparsity class method) create_hybrid_spikes_recording() (in module spikeinterface.comparison) create_hybrid_units_recording() (in module spikeinterface.comparison) create_sorting_analyzer() (in module spikeinterface.core) CurationSorting (class in spikeinterface.curation)

D

delete_extension() (spikeinterface.core.SortingAnalyzer method) densify_waveforms() (spikeinterface.core.ChannelSparsity method) depth_order() (in module spikeinterface.preprocessing) detect_bad_channels() (in module spikeinterface.preprocessing)

detect_peaks() (in module spikeinterface.sortingcomponents.peak_detection) directional_derivative() (in module spikeinterface.preprocessing) download_dataset() (in module spikeinterface.core) DriftingTemplates (class in spikeinterface.generation)

E

estimate_motion() (in module spikeinterface.sortingcomponents.motion) estimate_sparsity() (in module spikeinterface.core) estimate_templates_from_recording() (in module spikeinterface.generation)

export_report() (in module spikeinterface.exporters) export_to_phy() (in module spikeinterface.exporters) extract_waveforms() (in module spikeinterface.core)

F

fetch_template_object_from_database() (in module spikeinterface.generation) fetch_templates_database_info() (in module spikeinterface.generation) filter() (in module spikeinterface.preprocessing) find_cluster_from_peaks() (in module spikeinterface.sortingcomponents.clustering) find_redundant_units() (in module spikeinterface.curation) find_spikes_from_templates() (in module spikeinterface.sortingcomponents.matching) frame_slice() (spikeinterface.core.BaseRecording method)

from_amplitude() (spikeinterface.core.ChannelSparsity class method) from_best_channels() (spikeinterface.core.ChannelSparsity class method) from_energy() (spikeinterface.core.ChannelSparsity class method) from_property() (spikeinterface.core.ChannelSparsity class method) from_ptp() (spikeinterface.core.ChannelSparsity class method) from_radius() (spikeinterface.core.ChannelSparsity class method) from_snr() (spikeinterface.core.ChannelSparsity class method) from_unit_id_to_channel_ids() (spikeinterface.core.ChannelSparsity class method)

G

gaussian_filter() (in module spikeinterface.preprocessing) generate_displacement_vector() (in module spikeinterface.generation) generate_drifting_recording() (in module spikeinterface.generation) generate_ground_truth_recording() (in module spikeinterface.generation) generate_hybrid_recording() (in module spikeinterface.generation) generate_noise() (in module spikeinterface.generation) generate_recording() (in module spikeinterface.generation) generate_recording_by_size() (in module spikeinterface.generation) generate_snippets() (in module spikeinterface.generation) generate_sorting() (in module spikeinterface.generation) generate_templates() (in module spikeinterface.generation) get_agreement_fraction() (spikeinterface.comparison.SymmetricSortingComparison method) get_agreement_sorting() (spikeinterface.comparison.MultiSortingComparison method) get_all_spike_trains() (spikeinterface.core.BaseSorting method) get_bad_units() (spikeinterface.comparison.GroundTruthComparison method) get_best_unit_match1() (spikeinterface.comparison.SymmetricSortingComparison method) get_best_unit_match2() (spikeinterface.comparison.SymmetricSortingComparison method) get_binary_description() (spikeinterface.core.BaseRecording method) get_channel_distances() (in module spikeinterface.core) get_channel_locations() (spikeinterface.core.BaseRecording method) get_chunk_with_margin() (in module spikeinterface.core) get_closest_channels() (in module spikeinterface.core) get_computable_extensions() (spikeinterface.core.SortingAnalyzer method) get_confusion_matrix() (spikeinterface.comparison.GroundTruthComparison method) get_default_extension_params() (spikeinterface.core.SortingAnalyzer method) get_default_plotter_backend() (in module spikeinterface.widgets) get_default_qm_params() (in module spikeinterface.qualitymetrics) get_default_sorter_params() (in module spikeinterface.sorters) get_duration() (spikeinterface.core.BaseRecording method) get_event_times() (spikeinterface.core.BaseEvent method) get_events() (spikeinterface.core.BaseEvent method) get_extension() (spikeinterface.core.SortingAnalyzer method) get_false_positive_units() (spikeinterface.comparison.GroundTruthComparison method) get_loaded_extension_names() (spikeinterface.core.SortingAnalyzer method) get_matching() (spikeinterface.comparison.SymmetricSortingComparison method) get_matching_event_count() (spikeinterface.comparison.SymmetricSortingComparison method) get_matching_unit_list1() (spikeinterface.comparison.SymmetricSortingComparison method)

get_matching_unit_list2() (spikeinterface.comparison.SymmetricSortingComparison method) get_memory_size() (spikeinterface.core.BaseRecording method) get_motion_parameters_preset() (in module spikeinterface.preprocessing) get_motion_presets() (in module spikeinterface.preprocessing) get_noise_levels() (in module spikeinterface.core) get_num_frames() (spikeinterface.core.BaseRecording method) get_num_samples() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSorting method) get_num_segments() (spikeinterface.core.BaseRecording method) get_overmerged_units() (spikeinterface.comparison.GroundTruthComparison method) get_performance() (spikeinterface.comparison.GroundTruthComparison method) get_potential_auto_merge() (in module spikeinterface.curation) get_quality_metric_list() (in module spikeinterface.qualitymetrics) get_quality_pca_metric_list() (in module spikeinterface.qualitymetrics) get_random_data_chunks() (in module spikeinterface.core) get_redundant_units() (spikeinterface.comparison.GroundTruthComparison method) get_saved_extension_names() (spikeinterface.core.SortingAnalyzer method) get_sorter_description() (in module spikeinterface.sorters) get_sorter_params_description() (in module spikeinterface.sorters) get_sorting_provenance() (spikeinterface.core.SortingAnalyzer method) get_template_amplitudes() (in module spikeinterface.core) get_template_extremum_amplitude() (in module spikeinterface.core) get_template_extremum_channel() (in module spikeinterface.core) get_template_extremum_channel_peak_shift() (in module spikeinterface.core) get_template_metric_names() (in module spikeinterface.postprocessing) get_time_info() (spikeinterface.core.BaseRecording method) get_times() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSorting method) get_total_duration() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSorting method) get_total_memory_size() (spikeinterface.core.BaseRecording method) get_total_samples() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSorting method) get_traces() (spikeinterface.core.BaseRecording method) get_well_detected_units() (spikeinterface.comparison.GroundTruthComparison method) GroundTruthComparison (class in spikeinterface.comparison) GroundTruthStudy (class in spikeinterface.comparison)

H

has_extension() (spikeinterface.core.SortingAnalyzer method) has_scaled_traces() (spikeinterface.core.BaseRecording method) has_time_vector() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSorting method)

highpass_filter() (in module spikeinterface.preprocessing) highpass_spatial_filter() (in module spikeinterface.preprocessing)

I

inject_some_duplicate_units() (in module spikeinterface.generation) inject_some_split_units() (in module spikeinterface.generation) inject_templates() (in module spikeinterface.generation) InjectDriftingTemplatesRecording (class in spikeinterface.generation) InjectTemplatesRecording (class in spikeinterface.generation) installed_sorters() (in module spikeinterface.sorters)

interpolate_bad_channels() (in module spikeinterface.preprocessing) interpolate_motion() (in module spikeinterface.sortingcomponents.motion) interpolate_motion_on_traces() (in module spikeinterface.sortingcomponents.motion) interpolate_templates() (in module spikeinterface.generation) InterpolateMotionRecording (class in spikeinterface.sortingcomponents.motion) is_binary_compatible() (spikeinterface.core.BaseRecording method)

L

lda_metrics() (in module spikeinterface.qualitymetrics.pca_metrics) list_available_datasets_in_template_database() (in module spikeinterface.generation) load() (spikeinterface.core.SortingAnalyzer class method) load_all_saved_extension() (spikeinterface.core.SortingAnalyzer method) load_extension() (spikeinterface.core.SortingAnalyzer method)

load_extractor() (in module spikeinterface.core) load_sorting_analyzer() (in module spikeinterface.core) load_sorting_analyzer_or_waveforms() (in module spikeinterface.core) load_waveforms() (in module spikeinterface.core) localize_peaks() (in module spikeinterface.sortingcomponents.peak_localization)

M

mahalanobis_metrics() (in module spikeinterface.qualitymetrics.pca_metrics) make_linear_displacement() (in module spikeinterface.generation) make_one_displacement_vector() (in module spikeinterface.generation) merge_units() (spikeinterface.core.SortingAnalyzer method) MergeUnitsSorting (class in spikeinterface.curation) module spikeinterface.comparison spikeinterface.core spikeinterface.curation spikeinterface.exporters spikeinterface.extractors spikeinterface.postprocessing spikeinterface.preprocessing spikeinterface.qualitymetrics spikeinterface.qualitymetrics.misc_metrics spikeinterface.sorters spikeinterface.sortingcomponents.clustering spikeinterface.sortingcomponents.matching spikeinterface.sortingcomponents.motion spikeinterface.sortingcomponents.peak_detection spikeinterface.sortingcomponents.peak_localization spikeinterface.widgets

Motion (class in spikeinterface.sortingcomponents.motion) move_dense_templates() (in module spikeinterface.generation) MultiSortingComparison (class in spikeinterface.comparison)

N

nearest_neighbors_isolation() (in module spikeinterface.qualitymetrics.pca_metrics) nearest_neighbors_metrics() (in module spikeinterface.qualitymetrics.pca_metrics) nearest_neighbors_noise_overlap() (in module spikeinterface.qualitymetrics.pca_metrics) noise_generator_recording() (in module spikeinterface.generation) NoiseGeneratorRecording (class in spikeinterface.generation) normalize_by_quantile() (in module spikeinterface.preprocessing)

notch_filter() (in module spikeinterface.preprocessing) NpyFolderSnippets (class in spikeinterface.core) NpzFolderSorting (class in spikeinterface.core) NumpyRecording (class in spikeinterface.core) NumpySnippets (class in spikeinterface.core) NumpySorting (class in spikeinterface.core)

O

order_channels_by_depth() (in module spikeinterface.core)

P

phase_shift() (in module spikeinterface.preprocessing) plot_agreement_matrix() (in module spikeinterface.widgets) plot_all_amplitudes_distributions() (in module spikeinterface.widgets) plot_amplitudes() (in module spikeinterface.widgets) plot_autocorrelograms() (in module spikeinterface.widgets) plot_comparison_collision_by_similarity() (in module spikeinterface.widgets) plot_confusion_matrix() (in module spikeinterface.widgets) plot_crosscorrelograms() (in module spikeinterface.widgets) plot_isi_distribution() (in module spikeinterface.widgets) plot_motion() (in module spikeinterface.widgets) plot_multicomparison_agreement() (in module spikeinterface.widgets) plot_multicomparison_agreement_by_sorter() (in module spikeinterface.widgets) plot_multicomparison_graph() (in module spikeinterface.widgets) plot_peak_activity() (in module spikeinterface.widgets) plot_probe_map() (in module spikeinterface.widgets) plot_quality_metrics() (in module spikeinterface.widgets) plot_rasters() (in module spikeinterface.widgets) plot_sorting_summary() (in module spikeinterface.widgets) plot_spike_locations() (in module spikeinterface.widgets) plot_spikes_on_traces() (in module spikeinterface.widgets)

plot_study_agreement_matrix() (in module spikeinterface.widgets) plot_study_comparison_collision_by_similarity() (in module spikeinterface.widgets) plot_study_performances() (in module spikeinterface.widgets) plot_study_run_times() (in module spikeinterface.widgets) plot_study_summary() (in module spikeinterface.widgets) plot_study_unit_counts() (in module spikeinterface.widgets) plot_template_metrics() (in module spikeinterface.widgets) plot_template_similarity() (in module spikeinterface.widgets) plot_traces() (in module spikeinterface.widgets) plot_unit_depths() (in module spikeinterface.widgets) plot_unit_locations() (in module spikeinterface.widgets) plot_unit_presence() (in module spikeinterface.widgets) plot_unit_probe_map() (in module spikeinterface.widgets) plot_unit_summary() (in module spikeinterface.widgets) plot_unit_templates() (in module spikeinterface.widgets) plot_unit_waveforms() (in module spikeinterface.widgets) plot_unit_waveforms_density_map() (in module spikeinterface.widgets) precompute_spike_trains() (spikeinterface.core.BaseSorting method) print_performance() (spikeinterface.comparison.GroundTruthComparison method) print_sorter_versions() (in module spikeinterface.sorters) print_summary() (spikeinterface.comparison.GroundTruthComparison method)

Q

query_templates_from_database() (in module spikeinterface.generation)

R

random_spikes_selection() (in module spikeinterface.core) read_alf_sorting() (in module spikeinterface.extractors) read_alphaomega() (in module spikeinterface.extractors) read_alphaomega_event() (in module spikeinterface.extractors) read_axona() (in module spikeinterface.extractors) read_bids() (in module spikeinterface.extractors) read_binary() (in module spikeinterface.core) (in module spikeinterface.extractors) read_biocam() (in module spikeinterface.extractors) read_blackrock() (in module spikeinterface.extractors) read_cbin_ibl() (in module spikeinterface.extractors) read_ced() (in module spikeinterface.extractors) read_combinato() (in module spikeinterface.extractors) read_hdsort() (in module spikeinterface.extractors) read_herdingspikes() (in module spikeinterface.extractors) read_ibl_recording() (in module spikeinterface.extractors) read_intan() (in module spikeinterface.extractors) read_kilosort() (in module spikeinterface.extractors) read_klusta() (in module spikeinterface.extractors) read_maxwell() (in module spikeinterface.extractors) read_mcsh5() (in module spikeinterface.extractors) read_mcsraw() (in module spikeinterface.extractors) read_mda_recording() (in module spikeinterface.extractors) read_mda_sorting() (in module spikeinterface.extractors) read_mearec() (in module spikeinterface.extractors) read_neuralynx() (in module spikeinterface.extractors) read_neuralynx_sorting() (in module spikeinterface.extractors) read_neuroexplorer() (in module spikeinterface.extractors) read_neuroscope() (in module spikeinterface.extractors) read_nix() (in module spikeinterface.extractors) read_nwb() (in module spikeinterface.extractors) read_openephys() (in module spikeinterface.extractors) read_openephys_event() (in module spikeinterface.extractors) read_phy() (in module spikeinterface.extractors)

read_plexon() (in module spikeinterface.extractors) read_plexon2() (in module spikeinterface.extractors) read_plexon2_sorting() (in module spikeinterface.extractors) read_plexon_sorting() (in module spikeinterface.extractors) read_shybrid_recording() (in module spikeinterface.extractors) read_shybrid_sorting() (in module spikeinterface.extractors) read_sorter_folder() (in module spikeinterface.sorters) read_spike2() (in module spikeinterface.extractors) read_spikegadgets() (in module spikeinterface.extractors) read_spikeglx() (in module spikeinterface.extractors) read_spykingcircus() (in module spikeinterface.extractors) read_tdt() (in module spikeinterface.extractors) read_tridesclous() (in module spikeinterface.extractors) read_waveclus() (in module spikeinterface.extractors) read_yass() (in module spikeinterface.extractors) read_zarr() (in module spikeinterface.core) (in module spikeinterface.extractors) rectify() (in module spikeinterface.preprocessing) register_recording() (spikeinterface.core.BaseSorting method) relocate_templates() (in module spikeinterface.generation) remove_artifacts() (in module spikeinterface.preprocessing) remove_duplicated_spikes() (in module spikeinterface.curation) remove_empty_units() (spikeinterface.core.BaseSorting method) remove_excess_spikes() (in module spikeinterface.curation) remove_redundant_units() (in module spikeinterface.curation) remove_units() (spikeinterface.core.BaseSorting method) (spikeinterface.core.SortingAnalyzer method) rename_channels() (spikeinterface.core.BaseRecording method) rename_units() (spikeinterface.core.BaseSorting method) resample() (in module spikeinterface.preprocessing) reset_times() (spikeinterface.core.BaseRecording method) run_sorter() (in module spikeinterface.sorters) run_sorter_by_property() (in module spikeinterface.sorters) run_sorter_jobs() (in module spikeinterface.sorters)

S

sample_index_to_time() (spikeinterface.core.BaseRecording method) save_as() (spikeinterface.core.SortingAnalyzer method) scale() (in module spikeinterface.preprocessing) scale_template_to_range() (in module spikeinterface.generation) select_channels() (spikeinterface.core.BaseRecording method) (spikeinterface.core.BaseSnippets method) select_segment_recording() (in module spikeinterface.core) select_segment_sorting() (in module spikeinterface.core) select_templates() (in module spikeinterface.generation) select_units() (spikeinterface.core.BaseSorting method) (spikeinterface.core.SortingAnalyzer method) SelectSegmentRecording (class in spikeinterface.core) SelectSegmentSorting (class in spikeinterface.core) set_default_plotter_backend() (in module spikeinterface.widgets) set_global_dataset_folder() (in module spikeinterface.core) set_global_job_kwargs() (in module spikeinterface.core) set_global_tmp_folder() (in module spikeinterface.core) set_temporary_recording() (spikeinterface.core.SortingAnalyzer method) set_times() (spikeinterface.core.BaseRecording method) silence_periods() (in module spikeinterface.preprocessing) silhouette_score() (in module spikeinterface.qualitymetrics.pca_metrics) simplified_silhouette_score() (in module spikeinterface.qualitymetrics.pca_metrics) SortingAnalyzer (class in spikeinterface.core) sparsify_waveforms() (spikeinterface.core.ChannelSparsity method) spike_vector_to_spike_trains() (in module spikeinterface.core) spikeinterface.comparison module spikeinterface.core module spikeinterface.curation module spikeinterface.exporters module

spikeinterface.extractors module spikeinterface.postprocessing module spikeinterface.preprocessing module spikeinterface.qualitymetrics module spikeinterface.qualitymetrics.misc_metrics module spikeinterface.sorters module spikeinterface.sortingcomponents.clustering module spikeinterface.sortingcomponents.matching module spikeinterface.sortingcomponents.motion module spikeinterface.sortingcomponents.peak_detection module spikeinterface.sortingcomponents.peak_localization module spikeinterface.widgets module split_recording() (in module spikeinterface.core) split_sorting() (in module spikeinterface.core) SplitSegmentSorting (class in spikeinterface.core) SplitUnitSorting (class in spikeinterface.curation) SymmetricSortingComparison (class in spikeinterface.comparison) synthesize_random_firings() (in module spikeinterface.generation) synthetize_spike_train_bad_isi() (in module spikeinterface.generation)

T

time_slice() (spikeinterface.core.BaseRecording method) to_dict() (spikeinterface.core.ChannelSparsity method) to_multiprocessing() (spikeinterface.core.BaseSorting method)

to_numpy_sorting() (spikeinterface.core.BaseSorting method) to_shared_memory_sorting() (spikeinterface.core.BaseSorting method) to_spike_vector() (spikeinterface.core.BaseSorting method) toy_example() (in module spikeinterface.extractors)

U

unsigned_to_signed() (in module spikeinterface.preprocessing)

W

whiten() (in module spikeinterface.preprocessing)

write_binary_recording() (in module spikeinterface.core)

Z

ZarrRecordingExtractor (class in spikeinterface.core)

zero_channel_pad() (in module spikeinterface.preprocessing) zscore() (in module spikeinterface.preprocessing)