SpikeInterface
0.100.2
Contents:
Overview
Installation
Importing SpikeInterface
Modules documentation
How to guides
Modules example gallery
Installing Spike Sorters
Viewers
Development
API
Release notes
Contact Us
SpikeInterface
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
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Z
A
add_recording_segment() (spikeinterface.core.BaseRecording method)
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_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)
BaseWaveformExtractorExtension (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
center() (in module spikeinterface.preprocessing)
ChannelSparsity (class in spikeinterface.core)
ChunkRecordingExecutor (class in spikeinterface.core)
clip() (in module spikeinterface.preprocessing)
CollisionGTComparison (class in spikeinterface.comparison)
CollisionGTStudy (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_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_metrics() (spikeinterface.comparison.GroundTruthStudy method)
compute_noise_levels() (in module spikeinterface.postprocessing)
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_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_sortings() (spikeinterface.comparison.GroundTruthStudy method)
correct_lsb() (in module spikeinterface.preprocessing)
correct_motion() (in module spikeinterface.preprocessing)
CorrelogramGTComparison (class in spikeinterface.comparison)
CorrelogramGTStudy (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)
CurationSorting (class in spikeinterface.curation)
D
delete_extension() (spikeinterface.core.WaveformExtractor method)
delete_waveforms() (spikeinterface.core.WaveformExtractor 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
export_report() (in module spikeinterface.exporters)
export_to_phy() (in module spikeinterface.exporters)
extract_waveforms() (in module spikeinterface.core)
extract_waveforms_gt() (spikeinterface.comparison.GroundTruthStudy method)
F
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)
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)
get_agreement_fraction() (spikeinterface.comparison.SymmetricSortingComparison method)
get_agreement_sorting() (spikeinterface.comparison.MultiSortingComparison method)
get_all_spike_trains() (spikeinterface.core.BaseSorting method)
get_all_templates() (spikeinterface.core.WaveformExtractor method)
get_available_extension_names() (spikeinterface.core.WaveformExtractor 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_chunk_with_margin() (in module spikeinterface.core)
get_closest_channels() (in module spikeinterface.core)
get_confusion_matrix() (spikeinterface.comparison.GroundTruthComparison method)
get_count_units() (spikeinterface.comparison.GroundTruthStudy 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_class() (spikeinterface.core.WaveformExtractor method)
get_false_positive_units() (spikeinterface.comparison.GroundTruthComparison 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_metrics() (spikeinterface.comparison.GroundTruthStudy method)
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_performance_by_unit() (spikeinterface.comparison.GroundTruthStudy 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_run_times() (spikeinterface.comparison.GroundTruthStudy method)
get_sampled_indices() (spikeinterface.core.WaveformExtractor method)
get_sorter_description() (in module spikeinterface.sorters)
get_sorter_params_description() (in module spikeinterface.sorters)
get_template() (spikeinterface.core.WaveformExtractor 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_template_segment() (spikeinterface.core.WaveformExtractor method)
get_templates() (spikeinterface.comparison.GroundTruthStudy method)
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_units_snr() (spikeinterface.comparison.GroundTruthStudy method)
get_waveform_extractor() (spikeinterface.comparison.GroundTruthStudy method)
get_waveforms() (spikeinterface.core.WaveformExtractor method)
get_waveforms_segment() (spikeinterface.core.WaveformExtractor method)
get_well_detected_units() (spikeinterface.comparison.GroundTruthComparison method)
GroundTruthComparison (class in spikeinterface.comparison)
GroundTruthStudy (class in spikeinterface.comparison)
H
has_extension() (spikeinterface.core.WaveformExtractor 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
InjectDriftingTemplatesRecording (class in spikeinterface.generation)
installed_sorters() (in module spikeinterface.sorters)
interpolate_bad_channels() (in module spikeinterface.preprocessing)
interpolate_templates() (in module spikeinterface.generation)
InterpolateMotionRecording (class in spikeinterface.sortingcomponents.motion_interpolation)
is_binary_compatible() (spikeinterface.core.BaseRecording method)
K
key_to_str() (spikeinterface.comparison.GroundTruthStudy method)
L
lda_metrics() (in module spikeinterface.qualitymetrics.pca_metrics)
load_extension() (spikeinterface.core.WaveformExtractor method)
load_extractor() (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)
MergeUnitsSorting (class in spikeinterface.curation)
module
spikeinterface.comparison
spikeinterface.core
spikeinterface.curation
spikeinterface.exporters
spikeinterface.extractors
spikeinterface.generation
spikeinterface.postprocessing
spikeinterface.preprocessing
spikeinterface.qualitymetrics
spikeinterface.qualitymetrics.misc_metrics
spikeinterface.sorters
spikeinterface.sortingcomponents.clustering
spikeinterface.sortingcomponents.matching
spikeinterface.sortingcomponents.motion_interpolation
spikeinterface.sortingcomponents.peak_detection
spikeinterface.sortingcomponents.peak_localization
spikeinterface.widgets
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)
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)
precompute_templates() (spikeinterface.core.WaveformExtractor method)
print_performance() (spikeinterface.comparison.GroundTruthComparison method)
print_sorter_versions() (in module spikeinterface.sorters)
print_summary() (spikeinterface.comparison.GroundTruthComparison method)
R
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_streaming_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_extension() (spikeinterface.core.WaveformExtractor class method)
register_recording() (spikeinterface.core.BaseSorting method)
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_sorting() (spikeinterface.comparison.GroundTruthStudy method)
remove_units() (spikeinterface.core.BaseSorting method)
rename_channels() (spikeinterface.core.BaseRecording method)
rename_units() (spikeinterface.core.BaseSorting method)
resample() (in module spikeinterface.preprocessing)
run_comparisons() (spikeinterface.comparison.GroundTruthStudy method)
run_sorter() (in module spikeinterface.sorters)
run_sorter_by_property() (in module spikeinterface.sorters)
run_sorter_jobs() (in module spikeinterface.sorters)
run_sorters() (spikeinterface.comparison.GroundTruthStudy method)
S
sample_index_to_time() (spikeinterface.core.BaseRecording method)
save() (spikeinterface.core.WaveformExtractor method)
scale() (in module spikeinterface.preprocessing)
scan_folder() (spikeinterface.comparison.GroundTruthStudy method)
select_segment_recording() (in module spikeinterface.core)
select_segment_sorting() (in module spikeinterface.core)
select_units() (spikeinterface.core.BaseSorting method)
(spikeinterface.core.WaveformExtractor 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_params() (spikeinterface.core.WaveformExtractor method)
set_recording() (spikeinterface.core.WaveformExtractor 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)
sparsify_waveforms() (spikeinterface.core.ChannelSparsity method)
spikeinterface.comparison
module
spikeinterface.core
module
spikeinterface.curation
module
spikeinterface.exporters
module
spikeinterface.extractors
module
spikeinterface.generation
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_interpolation
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)
T
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
WaveformExtractor (class in spikeinterface.core)
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)
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