spikeinterface
0.13.0
Contents:
Overview
Installation
Compatible Technology
Installing Spike Sorters
Getting started with SpikeInterface
Tutorials
Spike sorting comparison methods
Contribute
API
Release notes
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spikeinterface
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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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L
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M
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N
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P
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R
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S
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T
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W
A
add_epoch() (spikeextractors.baseextractor.BaseExtractor method)
aggregate_count_units() (spikecomparison.GroundTruthStudy method)
aggregate_dataframes() (spikecomparison.GroundTruthStudy method)
aggregate_performance_by_units() (spikecomparison.GroundTruthStudy method)
aggregate_run_times() (spikecomparison.GroundTruthStudy method)
allocate_array() (spikeextractors.baseextractor.BaseExtractor method)
annotate() (spikeextractors.baseextractor.BaseExtractor method)
available_sorters() (in module spikesorters)
B
bandpass_filter() (in module spiketoolkit.preprocessing)
BaseExtractor (class in spikeextractors.baseextractor)
blank_saturation() (in module spiketoolkit.preprocessing)
C
clear_channel_gains() (spikeextractors.RecordingExtractor method)
clear_channel_groups() (spikeextractors.RecordingExtractor method)
clear_channel_locations() (spikeextractors.RecordingExtractor method)
clear_channel_offsets() (spikeextractors.RecordingExtractor method)
clear_channel_property() (spikeextractors.RecordingExtractor method)
clear_channels_property() (spikeextractors.RecordingExtractor method)
clear_unit_property() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
clear_unit_spike_features() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
clear_units_property() (spikeextractors.SortingExtractor method)
clear_units_spike_features() (spikeextractors.SortingExtractor method)
clip() (in module spiketoolkit.preprocessing)
common_reference() (in module spiketoolkit.preprocessing)
compare_multiple_sorters() (in module spikecomparison)
compare_sorter_to_ground_truth() (in module spikecomparison)
compare_two_sorters() (in module spikecomparison)
compute_amplitude_cutoffs() (in module spiketoolkit.validation)
compute_d_primes() (in module spiketoolkit.validation)
compute_drift_metrics() (in module spiketoolkit.validation)
compute_firing_rates() (in module spiketoolkit.validation)
compute_isi_violations() (in module spiketoolkit.validation)
compute_isolation_distances() (in module spiketoolkit.validation)
compute_l_ratios() (in module spiketoolkit.validation)
compute_nn_metrics() (in module spiketoolkit.validation)
compute_num_spikes() (in module spiketoolkit.validation)
compute_presence_ratios() (in module spiketoolkit.validation)
compute_quality_metrics() (in module spiketoolkit.validation)
compute_silhouette_scores() (in module spiketoolkit.validation)
compute_snrs() (in module spiketoolkit.validation)
compute_unit_pca_scores() (in module spiketoolkit.postprocessing)
compute_unit_template_features() (in module spiketoolkit.postprocessing)
concat_all_snr() (spikecomparison.GroundTruthStudy method)
copy_annotations() (spikeextractors.baseextractor.BaseExtractor method)
copy_channel_properties() (spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
copy_epochs() (spikeextractors.baseextractor.BaseExtractor method)
copy_sortings() (spikecomparison.GroundTruthStudy method)
copy_times() (spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
copy_unit_properties() (spikeextractors.SortingExtractor method)
(spikeextractors.SubSortingExtractor method)
copy_unit_spike_features() (spikeextractors.SortingExtractor method)
(spikeextractors.SubSortingExtractor method)
count_bad_units() (spikecomparison.GroundTruthComparison method)
count_false_positive_units() (spikecomparison.GroundTruthComparison method)
count_overmerged_units() (spikecomparison.GroundTruthComparison method)
count_redundant_units() (spikecomparison.GroundTruthComparison method)
count_well_detected_units() (spikecomparison.GroundTruthComparison method)
create() (spikecomparison.GroundTruthStudy class method)
CurationSortingExtractor (class in spiketoolkit.curation)
D
del_memmap_file() (spikeextractors.baseextractor.BaseExtractor method)
dump_to_dict() (spikeextractors.baseextractor.BaseExtractor method)
dump_to_json() (spikeextractors.baseextractor.BaseExtractor method)
dump_to_pickle() (spikeextractors.baseextractor.BaseExtractor method)
E
exclude_units() (spiketoolkit.curation.CurationSortingExtractor method)
export_to_phy() (in module spiketoolkit.postprocessing)
F
frame_to_time() (spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
(spikeextractors.SubRecordingExtractor method)
(spikeextractors.SubSortingExtractor method)
G
get_agreement_fraction() (spikecomparison.SymmetricSortingComparison method)
get_annotation() (spikeextractors.baseextractor.BaseExtractor method)
get_annotation_keys() (spikeextractors.baseextractor.BaseExtractor method)
get_bad_units() (spikecomparison.GroundTruthComparison method)
get_best_unit_match1() (spikecomparison.SymmetricSortingComparison method)
get_best_unit_match2() (spikecomparison.SymmetricSortingComparison method)
get_channel_gains() (spikeextractors.RecordingExtractor method)
get_channel_groups() (spikeextractors.RecordingExtractor method)
get_channel_ids() (spikeextractors.MultiRecordingChannelExtractor method)
(spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
get_channel_locations() (spikeextractors.RecordingExtractor method)
get_channel_offsets() (spikeextractors.RecordingExtractor method)
get_channel_property() (spikeextractors.RecordingExtractor method)
get_channel_property_names() (spikeextractors.RecordingExtractor method)
get_confusion_matrix() (spikecomparison.GroundTruthComparison method)
get_default_params() (in module spikesorters)
get_dtype() (spikeextractors.RecordingExtractor method)
get_epoch() (spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
get_epoch_info() (spikeextractors.baseextractor.BaseExtractor method)
get_epoch_names() (spikeextractors.baseextractor.BaseExtractor method)
get_false_positive_units() (spikecomparison.GroundTruthComparison method)
get_ground_truth() (spikecomparison.GroundTruthStudy method)
get_mapped_sorting1() (spikecomparison.SymmetricSortingComparison method)
get_mapped_sorting2() (spikecomparison.SymmetricSortingComparison method)
get_matching_event_count() (spikecomparison.SymmetricSortingComparison method)
get_matching_unit_list1() (spikecomparison.SymmetricSortingComparison method)
get_matching_unit_list2() (spikecomparison.SymmetricSortingComparison method)
get_num_channels() (spikeextractors.RecordingExtractor method)
get_num_frames() (spikeextractors.MultiRecordingChannelExtractor method)
(spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
get_overmerged_units() (spikecomparison.GroundTruthComparison method)
get_performance() (spikecomparison.GroundTruthComparison method)
get_recording() (spikecomparison.GroundTruthStudy method)
get_redundant_units() (spikecomparison.GroundTruthComparison method)
get_sampling_frequency() (spikeextractors.MultiRecordingChannelExtractor method)
(spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.MultiSortingExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
(spikeextractors.SubRecordingExtractor method)
(spikeextractors.SubSortingExtractor method)
get_shared_channel_property_names() (spikeextractors.RecordingExtractor method)
get_shared_unit_property_names() (spikeextractors.SortingExtractor method)
get_shared_unit_spike_feature_names() (spikeextractors.SortingExtractor method)
get_snippets() (spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
get_sorting() (spikecomparison.GroundTruthStudy method)
get_sub_extractors_by_property() (in module spikeextractors)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
get_tmp_folder() (spikeextractors.baseextractor.BaseExtractor method)
get_traces() (spikeextractors.MultiRecordingChannelExtractor method)
(spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
get_ttl_events() (spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SubRecordingExtractor method)
get_unit_amplitudes() (in module spiketoolkit.postprocessing)
get_unit_ids() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
(spikeextractors.SubSortingExtractor method)
(spiketoolkit.curation.CurationSortingExtractor method)
get_unit_max_channels() (in module spiketoolkit.postprocessing)
get_unit_property() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
get_unit_property_names() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
get_unit_spike_feature_names() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
get_unit_spike_features() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
get_unit_spike_train() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
(spikeextractors.SubSortingExtractor method)
(spiketoolkit.curation.CurationSortingExtractor method)
get_unit_templates() (in module spiketoolkit.postprocessing)
get_unit_waveforms() (in module spiketoolkit.postprocessing)
get_units_property() (spikeextractors.SortingExtractor method)
get_units_snr() (spikecomparison.GroundTruthStudy method)
get_units_spike_train() (spikeextractors.SortingExtractor method)
get_unsorted_spike_train() (spikeextractors.SortingExtractor method)
get_well_detected_units() (spikecomparison.GroundTruthComparison method)
GroundTruthComparison (class in spikecomparison)
GroundTruthStudy (class in spikecomparison)
L
load_extractor_from_dict() (in module spikeextractors)
(spikeextractors.baseextractor.BaseExtractor static method)
load_extractor_from_json() (in module spikeextractors)
(spikeextractors.baseextractor.BaseExtractor static method)
load_extractor_from_pickle() (in module spikeextractors)
(spikeextractors.baseextractor.BaseExtractor static method)
load_probe_file() (in module spikeextractors)
(spikeextractors.RecordingExtractor method)
M
make_serialized_dict() (spikeextractors.baseextractor.BaseExtractor method)
merge_units() (spiketoolkit.curation.CurationSortingExtractor method)
MultiRecordingChannelExtractor (class in spikeextractors)
MultiRecordingTimeExtractor (class in spikeextractors)
MultiSortingExtractor (class in spikeextractors)
N
normalize_by_quantile() (in module spiketoolkit.preprocessing)
notch_filter() (in module spiketoolkit.preprocessing)
P
plot_activity_map() (in module spikewidgets)
plot_agreement_matrix() (in module spikewidgets)
plot_amplitudes_distribution() (in module spikewidgets)
plot_amplitudes_timeseries() (in module spikewidgets)
plot_autocorrelograms() (in module spikewidgets)
plot_confusion_matrix() (in module spikewidgets)
plot_crosscorrelograms() (in module spikewidgets)
plot_electrode_geometry() (in module spikewidgets)
plot_isi_distribution() (in module spikewidgets)
plot_multicomp_agreement() (in module spikewidgets)
plot_multicomp_agreement_by_sorter() (in module spikewidgets)
plot_multicomp_graph() (in module spikewidgets)
plot_rasters() (in module spikewidgets)
plot_sorting_performance() (in module spikewidgets)
plot_spectrogram() (in module spikewidgets)
plot_spectrum() (in module spikewidgets)
plot_timeseries() (in module spikewidgets)
plot_unit_template_maps() (in module spikewidgets)
plot_unit_templates() (in module spikewidgets)
plot_unit_waveforms() (in module spikewidgets)
print_curation_tree() (spiketoolkit.curation.CurationSortingExtractor method)
print_performance() (spikecomparison.GroundTruthComparison method)
print_summary() (spikecomparison.GroundTruthComparison method)
R
RecordingExtractor (class in spikeextractors)
rectify() (in module spiketoolkit.preprocessing)
remove_artifacts() (in module spiketoolkit.preprocessing)
remove_bad_channels() (in module spiketoolkit.preprocessing)
remove_epoch() (spikeextractors.baseextractor.BaseExtractor method)
resample() (in module spiketoolkit.preprocessing)
run_comparisons() (spikecomparison.GroundTruthStudy method)
run_sorter() (in module spikesorters)
run_sorters() (in module spikesorters)
(spikecomparison.GroundTruthStudy method)
S
save_to_probe_file() (in module spikeextractors)
(spikeextractors.RecordingExtractor method)
scan_folder() (spikecomparison.GroundTruthStudy method)
set_channel_gains() (spikeextractors.RecordingExtractor method)
set_channel_groups() (spikeextractors.RecordingExtractor method)
set_channel_locations() (spikeextractors.RecordingExtractor method)
set_channel_offsets() (spikeextractors.RecordingExtractor method)
set_channel_property() (spikeextractors.RecordingExtractor method)
set_sampling_frequency() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
set_times() (spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
set_tmp_folder() (spikeextractors.baseextractor.BaseExtractor method)
set_unit_properties_by_max_channel_properties() (in module spiketoolkit.postprocessing)
set_unit_property() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
set_unit_spike_features() (spikeextractors.MultiSortingExtractor method)
(spikeextractors.SortingExtractor method)
set_units_property() (spikeextractors.SortingExtractor method)
SortingExtractor (class in spikeextractors)
spikecomparison (module)
spikeextractors (module)
spikesorters (module)
spiketoolkit.curation (module)
spiketoolkit.postprocessing (module)
spiketoolkit.preprocessing (module)
spiketoolkit.validation (module)
spikewidgets (module)
split_unit() (spiketoolkit.curation.CurationSortingExtractor method)
SubRecordingExtractor (class in spikeextractors)
SubSortingExtractor (class in spikeextractors)
SymmetricSortingComparison (class in spikecomparison)
T
threshold_amplitude_cutoffs() (in module spiketoolkit.curation)
threshold_d_primes() (in module spiketoolkit.curation)
threshold_drift_metrics() (in module spiketoolkit.curation)
threshold_firing_rates() (in module spiketoolkit.curation)
threshold_isi_violations() (in module spiketoolkit.curation)
threshold_isolation_distances() (in module spiketoolkit.curation)
threshold_l_ratios() (in module spiketoolkit.curation)
threshold_nn_metrics() (in module spiketoolkit.curation)
threshold_num_spikes() (in module spiketoolkit.curation)
threshold_presence_ratios() (in module spiketoolkit.curation)
threshold_silhouette_scores() (in module spiketoolkit.curation)
threshold_snrs() (in module spiketoolkit.curation)
time_to_frame() (spikeextractors.MultiRecordingTimeExtractor method)
(spikeextractors.RecordingExtractor method)
(spikeextractors.SortingExtractor method)
(spikeextractors.SubRecordingExtractor method)
(spikeextractors.SubSortingExtractor method)
transform() (in module spiketoolkit.preprocessing)
W
whiten() (in module spiketoolkit.preprocessing)
write_recording() (spikeextractors.RecordingExtractor static method)
write_sorting() (spikeextractors.SortingExtractor static method)
write_to_binary_dat_format() (in module spikeextractors)
(spikeextractors.RecordingExtractor method)
write_to_h5_dataset_format() (spikeextractors.RecordingExtractor method)
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