Index

A

adaptation_index (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute) add_step() (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) AnalysisRegistry (class in Synaptipy.core.analysis.registry)

analyze_multi_sweep_spikes() (in module Synaptipy.core.analysis.single_spike) analyze_spikes_and_bursts() (in module Synaptipy.core.analysis.firing_dynamics) apply_ljp_correction() (in module Synaptipy.core.analysis.passive_properties) apply_trace_corrections() (in module Synaptipy.core.processing_pipeline)

B

bandpass_filter() (in module Synaptipy.core.signal_processor)

BatchAnalysisEngine (class in Synaptipy.core.analysis.batch_engine) blank_artifact() (in module Synaptipy.core.signal_processor)

C

calculate_baseline_stats() (in module Synaptipy.core.analysis.passive_properties) calculate_bursts_logic() (in module Synaptipy.core.analysis.firing_dynamics) calculate_capacitance_cc() (in module Synaptipy.core.analysis.passive_properties) calculate_capacitance_vc() (in module Synaptipy.core.analysis.passive_properties) calculate_cc_series_resistance_fast() (in module Synaptipy.core.analysis.passive_properties) calculate_conductance() (in module Synaptipy.core.analysis.passive_properties) calculate_dvdt() (in module Synaptipy.core.analysis.single_spike) calculate_event_charge_dynamic() (in module Synaptipy.core.analysis.synaptic_events) calculate_fi_curve() (in module Synaptipy.core.analysis.firing_dynamics) calculate_isi() (in module Synaptipy.core.analysis.single_spike) calculate_iv_curve() (in module Synaptipy.core.analysis.passive_properties) calculate_optogenetic_sync() (in module Synaptipy.core.analysis.evoked_responses) calculate_paired_pulse_ratio() (in module Synaptipy.core.analysis.evoked_responses) (in module Synaptipy.core.analysis.synaptic_events) calculate_rin() (in module Synaptipy.core.analysis.passive_properties) calculate_rmp() (in module Synaptipy.core.analysis.passive_properties) calculate_sag_ratio() (in module Synaptipy.core.analysis.passive_properties) calculate_spike_features() (in module Synaptipy.core.analysis.single_spike) calculate_stimulus_train_stp() (in module Synaptipy.core.analysis.evoked_responses) calculate_tau() (in module Synaptipy.core.analysis.passive_properties)

calculate_train_dynamics() (in module Synaptipy.core.analysis.firing_dynamics) calculate_vc_transient_parameters() (in module Synaptipy.core.analysis.passive_properties) can_undo (Synaptipy.core.data_model.Channel property) can_undo() (Synaptipy.core.data_model.UndoStack method) cancel() (Synaptipy.core.analysis.batch_engine.BatchAnalysisEngine method) Channel (class in Synaptipy.core.data_model) channel_names (Synaptipy.core.data_model.Recording property) check_trace_quality() (in module Synaptipy.core.signal_processor) clear() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) (Synaptipy.core.data_model.UndoStack method) (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) close() (Synaptipy.core.data_model.Recording method) comb_filter() (in module Synaptipy.core.signal_processor) compute_local_pre_event_baseline() (in module Synaptipy.core.analysis.synaptic_events) compute_psd() (in module Synaptipy.core.signal_processor) create_plugin_directory() (Synaptipy.application.plugin_manager.PluginManager class method) CurrentClampSeries (class in Synaptipy.infrastructure.exporters.nwb_exporter) CurrentClampStimulusSeries (class in Synaptipy.infrastructure.exporters.nwb_exporter) cv (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute) cv2 (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute)

D

depth (Synaptipy.core.data_model.UndoStack property) detect_events_baseline_peak_kinetics() (in module Synaptipy.core.analysis.synaptic_events) detect_events_template() (in module Synaptipy.core.analysis.synaptic_events)

detect_events_threshold() (in module Synaptipy.core.analysis.synaptic_events) detect_minis_threshold() (in module Synaptipy.core.analysis.synaptic_events) detect_spikes_threshold() (in module Synaptipy.core.analysis.single_spike) detect_threshold_kink() (in module Synaptipy.core.analysis.single_spike)

E

evoked_responses_module() (in module Synaptipy.core.analysis.evoked_responses) Experiment (class in Synaptipy.core.data_model)

export() (Synaptipy.infrastructure.exporters.nwb_exporter.NWBExporter method) extract_ttl_epochs() (in module Synaptipy.core.analysis.evoked_responses)

F

failure_count (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) find_artifact_windows() (in module Synaptipy.core.signal_processor) find_quiescent_baseline_rms() (in module Synaptipy.core.analysis.synaptic_events)

find_stable_baseline() (in module Synaptipy.core.analysis.passive_properties) firing_dynamics_module() (in module Synaptipy.core.analysis.firing_dynamics) fit_biexponential_decay() (in module Synaptipy.core.analysis.synaptic_events)

G

get_analysis_info() (Synaptipy.core.analysis.batch_engine.BatchAnalysisEngine static method) get_averaged_current_data() (Synaptipy.core.data_model.Channel method) get_averaged_data() (Synaptipy.core.data_model.Channel method) get_averaged_time_vector() (Synaptipy.core.data_model.Channel method) get_consistent_samples() (Synaptipy.core.data_model.Channel method) get_current_data() (Synaptipy.core.data_model.Channel method) get_data() (Synaptipy.core.data_model.Channel method) get_data_bounds() (Synaptipy.core.data_model.Channel method) get_finite_data_bounds() (Synaptipy.core.data_model.Channel method) get_function() (Synaptipy.core.analysis.registry.AnalysisRegistry class method)

get_metadata() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) get_phase_plane_trajectory() (in module Synaptipy.core.analysis.single_spike) get_plugin_files() (Synaptipy.application.plugin_manager.PluginManager class method) get_primary_data_label() (Synaptipy.core.data_model.Channel method) get_relative_averaged_time_vector() (Synaptipy.core.data_model.Channel method) get_relative_time_vector() (Synaptipy.core.data_model.Channel method) get_steps() (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) get_supported_extensions() (Synaptipy.infrastructure.file_readers.neo_adapter.NeoAdapter method) get_supported_file_filter() (Synaptipy.infrastructure.file_readers.neo_adapter.NeoAdapter method) get_time_vector() (Synaptipy.core.data_model.Channel method)

H

highpass_filter() (in module Synaptipy.core.signal_processor)

I

IntracellularElectrode (class in Synaptipy.infrastructure.exporters.nwb_exporter)

isis (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute)

L

list_analysis() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) list_available_analyses() (Synaptipy.core.analysis.batch_engine.BatchAnalysisEngine static method) list_by_type() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) list_preprocessing() (Synaptipy.core.analysis.registry.AnalysisRegistry class method)

list_registered() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) load_plugins() (Synaptipy.application.plugin_manager.PluginManager class method) lowpass_filter() (in module Synaptipy.core.signal_processor) lv (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute)

M

mark_core_snapshot() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) max_trials (Synaptipy.core.data_model.Recording property) mean_isi_s (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute) module Synaptipy.application.plugin_manager Synaptipy.core.analysis.batch_engine Synaptipy.core.analysis.evoked_responses Synaptipy.core.analysis.firing_dynamics Synaptipy.core.analysis.passive_properties Synaptipy.core.analysis.registry Synaptipy.core.analysis.single_spike Synaptipy.core.analysis.synaptic_events Synaptipy.core.data_model Synaptipy.core.processing_pipeline Synaptipy.core.signal_processor Synaptipy.infrastructure.exporters.nwb_exporter Synaptipy.infrastructure.file_readers.neo_adapter

multi_harmonic_notch() (in module Synaptipy.core.signal_processor)

N

NeoAdapter (class in Synaptipy.infrastructure.file_readers.neo_adapter) notch_filter() (in module Synaptipy.core.signal_processor) num_channels (Synaptipy.core.data_model.Recording property) num_samples (Synaptipy.core.data_model.Channel property)

num_trials (Synaptipy.core.data_model.Channel property) NWBExporter (class in Synaptipy.infrastructure.exporters.nwb_exporter) NWBFile (class in Synaptipy.infrastructure.exporters.nwb_exporter) NWBHDF5IO (class in Synaptipy.infrastructure.exporters.nwb_exporter)

O

optical_latency_ms (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute)

OptoSyncResult (class in Synaptipy.core.analysis.evoked_responses)

P

parameters (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute) passive_properties_module() (in module Synaptipy.core.analysis.passive_properties) PatchClampSeries (class in Synaptipy.infrastructure.exporters.nwb_exporter) phase_plane_analysis() (in module Synaptipy.core.analysis.single_spike)

phase_plane_analysis_wrapper() (in module Synaptipy.core.analysis.single_spike) PluginManager (class in Synaptipy.application.plugin_manager) pop() (Synaptipy.core.data_model.UndoStack method) process() (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) push() (Synaptipy.core.data_model.UndoStack method) push_undo() (Synaptipy.core.data_model.Channel method)

R

read_recording() (Synaptipy.infrastructure.file_readers.neo_adapter.NeoAdapter method) Recording (class in Synaptipy.core.data_model) register() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) register_processor() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) reload_plugins() (Synaptipy.application.plugin_manager.PluginManager class method) remove_step_by_type() (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) reset_to_factory() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) responding_spikes (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) response_probability (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) run_batch() (Synaptipy.core.analysis.batch_engine.BatchAnalysisEngine method) run_burst_analysis_wrapper() (in module Synaptipy.core.analysis.firing_dynamics) run_capacitance_analysis_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_event_detection_baseline_peak_wrapper() (in module Synaptipy.core.analysis.synaptic_events)

run_event_detection_template_wrapper() (in module Synaptipy.core.analysis.synaptic_events) run_event_detection_threshold_wrapper() (in module Synaptipy.core.analysis.synaptic_events) run_excitability_analysis_wrapper() (in module Synaptipy.core.analysis.firing_dynamics) run_iv_curve_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_opto_sync_wrapper() (in module Synaptipy.core.analysis.evoked_responses) run_ppr_wrapper() (in module Synaptipy.core.analysis.evoked_responses) run_rin_analysis_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_rmp_analysis_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_sag_ratio_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_spike_detection_wrapper() (in module Synaptipy.core.analysis.single_spike) run_stimulus_train_stp_wrapper() (in module Synaptipy.core.analysis.evoked_responses) run_tau_analysis_wrapper() (in module Synaptipy.core.analysis.passive_properties) run_train_dynamics_wrapper() (in module Synaptipy.core.analysis.firing_dynamics)

S

set_steps() (Synaptipy.core.processing_pipeline.SignalProcessingPipeline method) SignalProcessingPipeline (class in Synaptipy.core.processing_pipeline) single_spike_module() (in module Synaptipy.core.analysis.single_spike) spike_count (Synaptipy.core.analysis.firing_dynamics.TrainDynamicsResult attribute) spike_jitter_ms (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) stimulus_count (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) stimulus_offsets (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) stimulus_onsets (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) subtract_baseline_linear() (in module Synaptipy.core.signal_processor) subtract_baseline_mean() (in module Synaptipy.core.signal_processor) subtract_baseline_median() (in module Synaptipy.core.signal_processor) subtract_baseline_mode() (in module Synaptipy.core.signal_processor) subtract_baseline_region() (in module Synaptipy.core.signal_processor) success_count (Synaptipy.core.analysis.evoked_responses.OptoSyncResult attribute) synaptic_events_module() (in module Synaptipy.core.analysis.synaptic_events) Synaptipy.application.plugin_manager module Synaptipy.core.analysis.batch_engine module Synaptipy.core.analysis.evoked_responses module

Synaptipy.core.analysis.firing_dynamics module Synaptipy.core.analysis.passive_properties module Synaptipy.core.analysis.registry module Synaptipy.core.analysis.single_spike module Synaptipy.core.analysis.synaptic_events module Synaptipy.core.data_model module Synaptipy.core.processing_pipeline module Synaptipy.core.signal_processor module Synaptipy.infrastructure.exporters.nwb_exporter module Synaptipy.infrastructure.file_readers.neo_adapter module

T

TrainDynamicsResult (class in Synaptipy.core.analysis.firing_dynamics)

U

undo() (Synaptipy.core.data_model.Channel method) UndoStack (class in Synaptipy.core.data_model)

unregister_plugins() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) update_default_params() (Synaptipy.core.analysis.registry.AnalysisRegistry class method) update_performance_settings() (Synaptipy.core.analysis.batch_engine.BatchAnalysisEngine method)

V

validate_sampling_rate() (in module Synaptipy.core.signal_processor)

VoltageClampSeries (class in Synaptipy.infrastructure.exporters.nwb_exporter) VoltageClampStimulusSeries (class in Synaptipy.infrastructure.exporters.nwb_exporter)