Index

A

abs_gain (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) ADAPTATION_FIT_START_S (in module arista.constants) AdaptationFit (class in arista.processing) (class in arista.processing.adaptation) AdaptationTaus (class in arista.viz) (class in arista.viz.adaptation_taus) aggregate_response_data() (in module arista.viz) (in module arista.viz.response_curves) aic (arista.preprocess.drift.DriftFit attribute) (arista.preprocess.DriftFit attribute) amplitude (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) animal_number (arista.ingest.AnimalLabel attribute), [1] (arista.ingest.IngestRecord attribute) (arista.ingest.metadata.AnimalLabel attribute), [1] (arista.ingest.parsers.alex.IngestRecord attribute) AnimalLabel (class in arista.ingest) (class in arista.ingest.metadata) apply_drift() (in module arista.preprocess) (in module arista.preprocess.drift) arista module arista.cli module arista.cli.figs module arista.cli.ingest module arista.cli.preprocess module arista.constants module arista.db module arista.db.connection module arista.db.schema module arista.db.seeds module arista.fitting module arista.ingest module arista.ingest.metadata module arista.ingest.orchestrator module arista.ingest.parsers module arista.ingest.parsers.alex module

arista.ingest.parsers.laurin module arista.ingest.parsers.robert module arista.preprocess module arista.preprocess.align module arista.preprocess.drift module arista.preprocess.interpolate module arista.preprocess.io module arista.preprocess.template_rescue module arista.processing module arista.processing.adaptation module arista.processing.gain module arista.processing.orchestrator module arista.processing.sigmoid module arista.processing.stimulus_response module arista.viz module arista.viz.adaptation_taus module arista.viz.gain_comparison module arista.viz.nompc_dosage module arista.viz.recording_overview module arista.viz.response_curves module arista.viz.sigmoid_fits module arista_suffix (arista.ingest.AnimalLabel attribute), [1] (arista.ingest.IngestRecord attribute) (arista.ingest.metadata.AnimalLabel attribute), [1] (arista.ingest.parsers.alex.IngestRecord attribute) as_dict() (arista.ingest.IngestStats method) (arista.ingest.orchestrator.IngestStats method) (arista.processing.orchestrator.ProcessingStats method) (arista.processing.ProcessingStats method) assemble_recording() (in module arista.preprocess) (in module arista.preprocess.align) asymptote (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute)

B

baseline_duration_s (arista.constants.StimulusProtocol attribute) baseline_t_c (arista.constants.StimulusProtocol attribute) bottom (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute)

build_schema() (in module arista.db) (in module arista.db.schema) by_x (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute)

C

cell_linewidth (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.SessionOverview attribute) cell_number (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) cell_type_code (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) cell_types (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute) (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute)

CellTypeInfo (class in arista.constants) code (arista.constants.CellTypeInfo attribute) collapse_to_frames() (in module arista.preprocess) (in module arista.preprocess.align) colour_for_cell() (in module arista.constants) compute_gains_table() (in module arista.processing) (in module arista.processing.gain) compute_recording_gain() (in module arista.processing) (in module arista.processing.gain) compute_stimulus_responses() (in module arista.processing) (in module arista.processing.stimulus_response) connect_tiers (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) correct_drift() (in module arista.preprocess) (in module arista.preprocess.drift) csv_path (arista.ingest.DiscoveryResult attribute) (arista.ingest.parsers.alex.DiscoveryResult attribute)

D

DEFAULT_DOSAGE_STIMULI (in module arista.viz.nompc_dosage) DEFAULT_FPS (in module arista.ingest.parsers.laurin) (in module arista.ingest.parsers.robert) delta_target_c (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute) description (arista.constants.CellTypeInfo attribute) (arista.constants.StimulusProtocol attribute) dfbf (arista.preprocess.FijiRecording attribute) (arista.preprocess.io.FijiRecording attribute) (arista.preprocess.io.Recording attribute) (arista.preprocess.Recording attribute) dfbf_drift_corrected (arista.preprocess.io.Recording attribute) (arista.preprocess.Recording attribute) dfbf_response_median (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute) discover_adaptation_stimuli() (in module arista.viz) (in module arista.viz.adaptation_taus) discover_alex_records() (in module arista.ingest) (in module arista.ingest.parsers.alex) discover_laurin_records() (in module arista.ingest) (in module arista.ingest.parsers.laurin) discover_robert_records() (in module arista.ingest) (in module arista.ingest.parsers.robert) DiscoveryResult (class in arista.ingest) (class in arista.ingest.parsers.alex)

dpi (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute) (arista.viz.SessionOverview attribute) (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute) drift_method (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) (arista.preprocess.io.Recording attribute) (arista.preprocess.Recording attribute) DriftFit (class in arista.preprocess) (class in arista.preprocess.drift) drive_t_c (arista.preprocess.io.Recording attribute) (arista.preprocess.io.SensorRecord attribute) (arista.preprocess.Recording attribute) (arista.preprocess.SensorRecord attribute) duration_s (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute)

E

epoch_time (arista.preprocess.io.SensorRecord attribute) (arista.preprocess.SensorRecord attribute) error (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute)

errors (arista.ingest.IngestStats attribute) (arista.ingest.orchestrator.IngestStats attribute)

F

failed_adaptations (arista.processing.orchestrator.ProcessingStats attribute) (arista.processing.ProcessingStats attribute) family (arista.constants.StimulusProtocol attribute) fetch_adaptation_taus() (in module arista.viz) (in module arista.viz.adaptation_taus) fetch_dosage_gains() (in module arista.viz) (in module arista.viz.nompc_dosage) fetch_recording_gains() (in module arista.viz) (in module arista.viz.gain_comparison) fetch_response_data() (in module arista.viz) (in module arista.viz.response_curves) figsize (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute) (arista.viz.SessionOverview attribute) (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute) FIJI_NAME_PATTERN (in module arista.constants) FijiRecording (class in arista.preprocess) (class in arista.preprocess.io) fit_adaptation() (in module arista.processing) (in module arista.processing.adaptation)

fit_all() (in module arista.preprocess) (in module arista.preprocess.drift) fit_exponential() (in module arista.preprocess) (in module arista.preprocess.drift) fit_linear() (in module arista.preprocess) (in module arista.preprocess.drift) fit_polynomial() (in module arista.preprocess) (in module arista.preprocess.drift) fit_sigmoid() (in module arista.processing) (in module arista.processing.sigmoid) fit_sigmoids_by_group() (in module arista.processing) (in module arista.processing.sigmoid) fit_window_end_s (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) fit_window_start_s (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) fitted (arista.preprocess.drift.DriftFit attribute) (arista.preprocess.DriftFit attribute) four_pl() (in module arista.processing) (in module arista.processing.sigmoid) fps (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) frame (arista.preprocess.FijiRecording attribute) (arista.preprocess.io.FijiRecording attribute) (arista.preprocess.io.Recording attribute) (arista.preprocess.io.SensorRecord attribute) (arista.preprocess.Recording attribute) (arista.preprocess.SensorRecord attribute)

G

GainComparison (class in arista.viz) (class in arista.viz.gain_comparison)

H

hello() (in module arista.cli.preprocess)

hemisphere (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute)

I

infer_cell_type_from_filename() (in module arista.constants) ingest_one() (in module arista.ingest) (in module arista.ingest.orchestrator) ingest_stream() (in module arista.ingest) (in module arista.ingest.orchestrator) IngestRecord (class in arista.ingest) (class in arista.ingest.parsers.alex) IngestStats (class in arista.ingest) (class in arista.ingest.orchestrator) inserted_adaptations (arista.processing.orchestrator.ProcessingStats attribute) (arista.processing.ProcessingStats attribute) inserted_recordings (arista.ingest.IngestStats attribute) (arista.ingest.orchestrator.IngestStats attribute)

inserted_responses (arista.processing.orchestrator.ProcessingStats attribute) (arista.processing.ProcessingStats attribute) inserted_samples (arista.ingest.IngestStats attribute) (arista.ingest.orchestrator.IngestStats attribute) intercept (arista.processing.gain.RecordingGain attribute) (arista.processing.RecordingGain attribute) interpolate_missing_frames() (in module arista.preprocess) (in module arista.preprocess.interpolate) is_broken_sensor() (in module arista.preprocess) (in module arista.preprocess.template_rescue) is_fiji_filename() (in module arista.constants)

L

load_template() (in module arista.preprocess) (in module arista.preprocess.template_rescue)

log_tau (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute)

M

marker_for_hemisphere() (in module arista.constants) method (arista.preprocess.drift.DriftFit attribute) (arista.preprocess.DriftFit attribute) midpoint_c (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute) min_r_squared (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) min_steps (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) module arista arista.cli arista.cli.figs arista.cli.ingest arista.cli.preprocess arista.constants arista.db arista.db.connection arista.db.schema arista.db.seeds arista.fitting arista.ingest arista.ingest.metadata arista.ingest.orchestrator arista.ingest.parsers arista.ingest.parsers.alex arista.ingest.parsers.laurin arista.ingest.parsers.robert arista.preprocess arista.preprocess.align arista.preprocess.drift arista.preprocess.interpolate arista.preprocess.io arista.preprocess.template_rescue arista.processing arista.processing.adaptation arista.processing.gain arista.processing.orchestrator arista.processing.sigmoid arista.processing.stimulus_response arista.viz arista.viz.adaptation_taus arista.viz.gain_comparison arista.viz.nompc_dosage arista.viz.recording_overview arista.viz.response_curves arista.viz.sigmoid_fits

N

n_curve (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute) n_frames (arista.preprocess.FijiRecording property) (arista.preprocess.io.FijiRecording property) (arista.preprocess.io.Recording property) (arista.preprocess.Recording property) n_frames_in_window (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute) n_points (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) (arista.processing.gain.RecordingGain attribute) (arista.processing.RecordingGain attribute) (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute)

n_samples (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) (arista.preprocess.io.SensorRecord property) (arista.preprocess.SensorRecord property) name (arista.constants.CellTypeInfo attribute) (arista.constants.StimulusProtocol attribute) nompc_dosage() (in module arista.constants) NompCDosage (class in arista.viz) (class in arista.viz.nompc_dosage) normalise_stimulus() (in module arista.constants) normalise_strain() (in module arista.constants) notes (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute)

O

observed_temp_median (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute)

open_db() (in module arista.db) (in module arista.db.connection)

P

params (arista.preprocess.drift.DriftFit attribute) (arista.preprocess.DriftFit attribute) parse_animal_label() (in module arista.ingest) (in module arista.ingest.metadata) parse_fiji_filename() (in module arista.constants) pick_best() (in module arista.preprocess) (in module arista.preprocess.drift) plot() (arista.viz.adaptation_taus.AdaptationTaus method) (arista.viz.AdaptationTaus method) (arista.viz.gain_comparison.GainComparison method) (arista.viz.GainComparison method) (arista.viz.nompc_dosage.NompCDosage method) (arista.viz.NompCDosage method) (arista.viz.recording_overview.SessionOverview method) (arista.viz.response_curves.ResponseCurves method) (arista.viz.ResponseCurves method) (arista.viz.SessionOverview method) (arista.viz.sigmoid_fits.SigmoidFits method) (arista.viz.SigmoidFits method)

plot_adaptation_taus() (in module arista.viz) (in module arista.viz.adaptation_taus) plot_gain_comparison() (in module arista.viz) (in module arista.viz.gain_comparison) plot_nompc_dosage() (in module arista.viz) (in module arista.viz.nompc_dosage) plot_response_curves() (in module arista.viz) (in module arista.viz.response_curves) plot_session_overview() (in module arista.viz) (in module arista.viz.recording_overview) plot_sigmoid_fits() (in module arista.viz) (in module arista.viz.sigmoid_fits) prepare_db() (in module arista.ingest) (in module arista.ingest.orchestrator) process_all() (in module arista.processing) (in module arista.processing.orchestrator) ProcessingStats (class in arista.processing) (class in arista.processing.orchestrator)

R

r_squared (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) (arista.processing.gain.RecordingGain attribute) (arista.processing.RecordingGain attribute) (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute) read_fiji_csv() (in module arista.preprocess) (in module arista.preprocess.io) read_recording_csv() (in module arista.preprocess) (in module arista.preprocess.io) read_sensor_mat() (in module arista.preprocess) (in module arista.preprocess.io) reason (arista.ingest.DiscoveryResult attribute) (arista.ingest.parsers.alex.DiscoveryResult attribute) record (arista.ingest.DiscoveryResult attribute) (arista.ingest.parsers.alex.DiscoveryResult attribute) Recording (class in arista.preprocess) (class in arista.preprocess.io) recording_date (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) (arista.preprocess.io.Recording attribute) (arista.preprocess.Recording attribute)

RecordingGain (class in arista.processing) (class in arista.processing.gain) researcher_name (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) residual_ssq (arista.preprocess.drift.DriftFit attribute) (arista.preprocess.DriftFit attribute) resolve_db_path() (in module arista.db) (in module arista.db.connection) ResponseCurves (class in arista.viz) (class in arista.viz.response_curves) rng_seed (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute)

S

samples_df (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) save() (arista.viz.adaptation_taus.AdaptationTaus method) (arista.viz.AdaptationTaus method) (arista.viz.gain_comparison.GainComparison method) (arista.viz.GainComparison method) (arista.viz.nompc_dosage.NompCDosage method) (arista.viz.NompCDosage method) (arista.viz.recording_overview.SessionOverview method) (arista.viz.response_curves.ResponseCurves method) (arista.viz.ResponseCurves method) (arista.viz.SessionOverview method) (arista.viz.sigmoid_fits.SigmoidFits method) (arista.viz.SigmoidFits method) save_figure() (in module arista.constants) scatter_alpha (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute) scatter_size (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute) seed_cell_types() (in module arista.db.seeds) seed_dimensions() (in module arista.db) (in module arista.db.seeds) seed_researchers() (in module arista.db.seeds) seed_stimulus_protocols() (in module arista.db.seeds) seed_strains() (in module arista.db.seeds) sensor_alpha (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.SessionOverview attribute) sensor_t_c (arista.preprocess.io.Recording attribute) (arista.preprocess.io.SensorRecord attribute) (arista.preprocess.Recording attribute) (arista.preprocess.SensorRecord attribute) SensorRecord (class in arista.preprocess) (class in arista.preprocess.io) SessionOverview (class in arista.viz) (class in arista.viz.recording_overview) sex (arista.ingest.AnimalLabel attribute), [1] (arista.ingest.IngestRecord attribute) (arista.ingest.metadata.AnimalLabel attribute), [1] (arista.ingest.parsers.alex.IngestRecord attribute) show_sensor (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.SessionOverview attribute)

show_target (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.SessionOverview attribute) SigmoidFit (class in arista.processing) (class in arista.processing.sigmoid) SigmoidFits (class in arista.viz) (class in arista.viz.sigmoid_fits) skipped_already_done (arista.processing.orchestrator.ProcessingStats attribute) (arista.processing.ProcessingStats attribute) skipped_duplicates (arista.ingest.IngestStats attribute) (arista.ingest.orchestrator.IngestStats attribute) slope (arista.processing.gain.RecordingGain attribute) (arista.processing.RecordingGain attribute) (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute) source_csv (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) step_duration_s (arista.constants.StimulusProtocol attribute) step_index (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute) stimulus_name (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) stimulus_names (arista.viz.nompc_dosage.NompCDosage attribute) (arista.viz.NompCDosage attribute) STIMULUS_RESPONSE_WINDOW_C (in module arista.constants) STIMULUS_SYNONYMS (in module arista.constants) StimulusProtocol (class in arista.constants) StimulusResponseRow (class in arista.processing) (class in arista.processing.stimulus_response) strain_name (arista.ingest.IngestRecord attribute) (arista.ingest.parsers.alex.IngestRecord attribute) strain_prefix (arista.ingest.AnimalLabel attribute), [1] (arista.ingest.metadata.AnimalLabel attribute), [1] strains (arista.viz.adaptation_taus.AdaptationTaus attribute) (arista.viz.AdaptationTaus attribute) (arista.viz.gain_comparison.GainComparison attribute) (arista.viz.GainComparison attribute) (arista.viz.response_curves.ResponseCurves attribute) (arista.viz.ResponseCurves attribute) (arista.viz.sigmoid_fits.SigmoidFits attribute) (arista.viz.SigmoidFits attribute)

T

target_sequence (arista.constants.StimulusProtocol attribute) target_t_c (arista.preprocess.io.Recording attribute) (arista.preprocess.io.SensorRecord attribute) (arista.preprocess.Recording attribute) (arista.preprocess.SensorRecord attribute) target_temp_c (arista.processing.stimulus_response.StimulusResponseRow attribute) (arista.processing.StimulusResponseRow attribute)

tau_s (arista.processing.adaptation.AdaptationFit attribute) (arista.processing.AdaptationFit attribute) time_s (arista.preprocess.io.Recording attribute) (arista.preprocess.Recording attribute) to_dataframe() (arista.preprocess.io.Recording method) (arista.preprocess.Recording method) top (arista.processing.sigmoid.SigmoidFit attribute) (arista.processing.SigmoidFit attribute)

U

use_drift_corrected (arista.viz.recording_overview.SessionOverview attribute) (arista.viz.SessionOverview attribute)

W

write_recording_csv() (in module arista.preprocess) (in module arista.preprocess.io)