Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | W | X | Z _ __post_init__() (fluopy.fluorophores.Fluorophore method) (fluopy.fluorophores.FluorophoreSystem method) (fluopy.transitions.Transition method) A abbreviation (fluopy.transitions.Transition attribute) absorbing_chain (fluopy.prediction.Prediction attribute) acceptor (fluopy.transitions.PairedState property) add_emccd_gain() (fluopy.emissions.Emissions method) add_gaussian_noise() (fluopy.emissions.Emissions method) add_photon_collection_objective() (fluopy.emissions.Emissions method) add_poisson_noise() (fluopy.emissions.Emissions method) add_quantum_efficiency() (fluopy.emissions.Emissions method) add_transmittance() (fluopy.emissions.Emissions method) adjust_rates() (fluopy.transitions.TransitionSet method) Analysis (class in fluopy.analysis) apply_threshold() (fluopy.emissions.Emissions method) approximate() (fluopy.simulation.Simulation method) atto643 (in module fluopy.fluo_data) autocorrelate_time_points() (fluopy.fcs.FCS method) autocorrelate_time_series() (fluopy.fcs.FCS method) autocorrelation (fluopy.fcs.FCS attribute) B B (fluopy.transitions.SingleState attribute) BACK_REACTION (fluopy.fluo_data.FluorophoreData attribute) BISO_CROSS_SECTION (fluopy.fluo_data.FluorophoreData attribute) BISO_EFFICIENCY (fluopy.fluo_data.FluorophoreData attribute) BISO_THERMAL_RATE (fluopy.fluo_data.FluorophoreData attribute) Blinking (class in fluopy.blinking) C calculate_emission_rate() (in module fluopy.formulas) calculate_excitation_rate() (in module fluopy.formulas) calculate_fret_efficiency() (in module fluopy.formulas) calculate_fret_rate() (in module fluopy.formulas) calculate_internal_conversion_rate() (in module fluopy.formulas) calculate_pet_rate() (in module fluopy.formulas) calculate_photon_collection_rate() (in module fluopy.formulas) calculate_photon_flux() (in module fluopy.formulas) calculate_spectral_overlap_integral() (in module fluopy.formulas) cdf() (fluopy.distributions.ExponentialMixtureMarginalModel method) (fluopy.distributions.ExponentialMixtureModel method) (fluopy.distributions.Photoswitching_fingerprint_model method) cdf_grid (fluopy.distributions.ExponentialMixtureMarginalModel attribute) cdf_part() (fluopy.distributions.Photoswitching_fingerprint_model method) check_graph_suitable() (in module fluopy.network) cis (fluopy.transitions.SingleState attribute) combined_state_transitions_df (fluopy.transitions.TransitionSet property) constants (fluopy.fluorophores.Fluorophore attribute) construct_event_time_series() (fluopy.emissions.Emissions method) construct_state_graphs() (in module fluopy.network) construct_transition_graph() (in module fluopy.network) convert_wavenumber_wavelength_frequency() (in module fluopy.formulas) count (fluopy.fluorophores.FluorophoreSystem attribute) cy5_dna (in module fluopy.fluo_data) D data_files (fluopy.fluo_data.FluorophoreData attribute) ddpdf() (fluopy.distributions.Photoswitching_fingerprint_model method) delete_memmaps() (fluopy.simulation.Simulation method) determine_node_order() (in module fluopy.network) distances (fluopy.fluorophores.FluorophoreSystem attribute) domain (fluopy.distributions.ExponentialMixtureModel attribute) (fluopy.distributions.Photoswitching_fingerprint_model attribute) donor (fluopy.transitions.PairedState property) dpdf() (fluopy.distributions.Photoswitching_fingerprint_model method) draw_networkx_curved_edge_labels() (in module fluopy.network) dSTORM DSTORM_P_EL_CROSS_SECTION (fluopy.fluo_data.FluorophoreData attribute) DSTORM_PET_S_RATE_MOL (fluopy.fluo_data.FluorophoreData attribute) DSTORM_PET_SUCCESS_RATE (fluopy.fluo_data.FluorophoreData attribute) DSTORM_PET_T_RATE_MOL (fluopy.fluo_data.FluorophoreData attribute) DSTORM_TH_EL_RATE_1 (fluopy.fluo_data.FluorophoreData attribute) DSTORM_TH_EL_RATE_2 (fluopy.fluo_data.FluorophoreData attribute) E Emissions (class in fluopy.emissions) emissions (fluopy.blinking.Blinking attribute) (fluopy.fcs.FCS attribute) energy_transfer (fluopy.prediction.Prediction attribute) event_time_points (fluopy.emissions.Emissions attribute) event_time_series (fluopy.emissions.Emissions attribute) ExponentialMixtureMarginalModel (class in fluopy.distributions) ExponentialMixtureModel (class in fluopy.distributions) extract() (fluopy.emissions.Emissions method) F FCS (class in fluopy.fcs) filter_by_identity() (fluopy.transitions.TransitionSet method) final_state (fluopy.transitions.Transition attribute) finalize() (fluopy.transitions.TransitionSet method) fluopy module fluopy.analysis module fluopy.blinking module fluopy.distributions module fluopy.emissions module fluopy.fcs module fluopy.figure module fluopy.fitting module fluopy.fluo_data module fluopy.fluopy_types module fluopy.fluorophores module fluopy.formulas module fluopy.kappa_squared module fluopy.miscellaneous module fluopy.network module fluopy.prediction module fluopy.routines module fluopy.simulation module fluopy.simulation_tcspc module fluopy.transitions module FLUORESCENCE_LIFETIME (fluopy.fluo_data.FluorophoreData attribute) Fluorophore (class in fluopy.fluorophores) fluorophore_ids (fluopy.transitions.Transition attribute) fluorophore_system (fluopy.transitions.TransitionSet attribute) FluorophoreData (class in fluopy.fluo_data) fluorophores (fluopy.fluorophores.FluorophoreSystem attribute) FluorophoreSystem (class in fluopy.fluorophores) frequency_states (fluopy.analysis.Analysis attribute) (fluopy.prediction.Prediction attribute) frequency_transitions (fluopy.analysis.Analysis attribute) G generate_combinations() (in module fluopy.distributions) get_emission_indices() (fluopy.emissions.Emissions method) get_emitting_transition_lifetimes() (fluopy.analysis.Analysis method) get_fluorescence_lifetimes() (fluopy.analysis.Analysis method) get_lifetimes() (fluopy.analysis.Analysis method) get_pis() (in module fluopy.distributions) get_state_occurrences() (fluopy.analysis.Analysis method) get_transition_occurrences() (fluopy.analysis.Analysis method) H H2O_ATTACK_S (fluopy.fluo_data.FluorophoreData attribute) H2O_ATTACK_T (fluopy.fluo_data.FluorophoreData attribute) henderson_hasselbalch_equation() (in module fluopy.formulas) hypoexponential_distribution_cdf() (in module fluopy.distributions) hypoexponential_distribution_pdf() (in module fluopy.distributions) hypoexponential_distribution_pdf_1st_order_derivative() (in module fluopy.distributions) hypoexponential_distribution_pdf_2nd_order_derivative() (in module fluopy.distributions) I identity (fluopy.fluorophores.Fluorophore attribute) (fluopy.transitions.Transition attribute) infer_stats() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) initial_state (fluopy.transitions.Transition attribute) integral_kappa_squared() (in module fluopy.kappa_squared) is_absorbing() (fluopy.analysis.Analysis method) ISC_ST_RATE (fluopy.fluo_data.FluorophoreData attribute) ISC_TS_RATE (fluopy.fluo_data.FluorophoreData attribute) ISO_RATE (fluopy.fluo_data.FluorophoreData attribute) K kappa_squared() (in module fluopy.kappa_squared) L load() (fluopy.emissions.Emissions class method) load_transitions() (fluopy.fluorophores.FluorophoreSystem method) logp() (fluopy.distributions.Photoswitching_fingerprint_model method) M map_to_lambdas() (in module fluopy.distributions) mean_transition_times (fluopy.analysis.Analysis attribute) memmap_path (fluopy.simulation.Simulation attribute) module fluopy fluopy.analysis fluopy.blinking fluopy.distributions fluopy.emissions fluopy.fcs fluopy.figure fluopy.fitting fluopy.fluo_data fluopy.fluopy_types fluopy.fluorophores fluopy.formulas fluopy.kappa_squared fluopy.miscellaneous fluopy.network fluopy.prediction fluopy.routines fluopy.simulation fluopy.simulation_tcspc fluopy.transitions multi_type (fluopy.fluorophores.FluorophoreSystem attribute) N name (fluopy.fluorophores.Fluorophore attribute) O OFF (fluopy.transitions.SingleState attribute) OFF2 (fluopy.transitions.SingleState attribute) OFRET_EFFICIENCY (fluopy.fluo_data.FluorophoreData attribute) P P_obs (fluopy.distributions.ExponentialMixtureMarginalModel attribute) PairedState (class in fluopy.transitions) PALM parameters (fluopy.emissions.Emissions attribute) params (fluopy.distributions.ExponentialMixtureModel attribute) (fluopy.distributions.Photoswitching_fingerprint_model attribute) pdf() (fluopy.distributions.ExponentialMixtureMarginalModel method) (fluopy.distributions.ExponentialMixtureModel method) (fluopy.distributions.Photoswitching_fingerprint_model method) pdf_grid (fluopy.distributions.ExponentialMixtureMarginalModel attribute) pdf_part() (fluopy.distributions.Photoswitching_fingerprint_model method) PHOTOBLEACH_T1_RATE (fluopy.fluo_data.FluorophoreData attribute) PHOTOBLEACH_T2_RATE (fluopy.fluo_data.FluorophoreData attribute) photon (fluopy.transitions.Transition attribute) Photoswitching_fingerprint_model (class in fluopy.distributions) photoswitching_fingerprint_prepare() (in module fluopy.distributions) plot() (fluopy.blinking.Blinking method) (fluopy.fcs.FCS method) (fluopy.fluorophores.FluorophoreSystem method) (fluopy.transitions.TransitionSet method) plot_cumulative_events() (fluopy.emissions.Emissions method) plot_frequency_states() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_frequency_transitions() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_graph() (in module fluopy.network) plot_histogram() (fluopy.emissions.Emissions method) plot_lifetime_distributions() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_matplotlib() (fluopy.fcs.FCS method) plot_mean_lifetimes() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_mean_transition_times() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_state_occupations() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) plot_time_series() (fluopy.emissions.Emissions method) plot_transition_time_distributions() (fluopy.analysis.Analysis method) (fluopy.prediction.Prediction method) position (fluopy.fluorophores.Fluorophore attribute) predict_lifetimes() (fluopy.prediction.Prediction method) predict_state_occurrences() (fluopy.prediction.Prediction method) predict_transition_occurrences() (fluopy.prediction.Prediction method) predict_transition_occurrences_abs() (fluopy.prediction.Prediction method) Prediction (class in fluopy.prediction) Q quantile_function() (fluopy.distributions.Photoswitching_fingerprint_model method) QUANTUM_YIELD (fluopy.fluo_data.FluorophoreData attribute) R R (fluopy.transitions.SingleState attribute) RAD_ESCAPE_EFFICIENCY (fluopy.fluo_data.FluorophoreData attribute) RAD_RELAX_RATE (fluopy.fluo_data.FluorophoreData attribute) RandomGeneratorSeed (in module fluopy.fluopy_types) rate (fluopy.transitions.Transition attribute) remove_absorbing_states() (fluopy.transitions.TransitionSet method) remove_energy_transfers() (fluopy.transitions.TransitionSet method) remove_zero_rates() (fluopy.transitions.TransitionSet method) RISC_RATE (fluopy.fluo_data.FluorophoreData attribute) row_sums (fluopy.transitions.TransitionSet property) run() (fluopy.simulation.Simulation method) S S0 (fluopy.transitions.SingleState attribute) S0_B (fluopy.transitions.PairedState attribute) S0_Cis (fluopy.transitions.PairedState attribute) S0_OFF (fluopy.transitions.PairedState attribute) S0_OFF2 (fluopy.transitions.PairedState attribute) S0_R (fluopy.transitions.PairedState attribute) S0_S0 (fluopy.transitions.PairedState attribute) S0_S1 (fluopy.transitions.PairedState attribute) S0_T1 (fluopy.transitions.PairedState attribute) S0_T2 (fluopy.transitions.PairedState attribute) S1 (fluopy.transitions.SingleState attribute) S1_Cis (fluopy.transitions.PairedState attribute) S1_OFF (fluopy.transitions.PairedState attribute) S1_QUENCH_RATE (fluopy.fluo_data.FluorophoreData attribute) S1_R (fluopy.transitions.PairedState attribute) S1_S0 (fluopy.transitions.PairedState attribute) S1_S1 (fluopy.transitions.PairedState attribute) S1_T1 (fluopy.transitions.PairedState attribute) S2 (fluopy.transitions.SingleState attribute) sample_kappa_squared_distribution() (in module fluopy.kappa_squared) save() (fluopy.emissions.Emissions method) simulate() (fluopy.emissions.Emissions method) simulate_rotational_motion() (in module fluopy.kappa_squared) Simulation (class in fluopy.simulation) simulation (fluopy.analysis.Analysis attribute) single_state_values (fluopy.transitions.PairedState property) single_states (fluopy.transitions.TransitionSet attribute) SingleState (class in fluopy.transitions) SMLM STA_EFFICIENCY (fluopy.fluo_data.FluorophoreData attribute) state_series (fluopy.simulation.Simulation attribute) super-resolution microscopy T T1 (fluopy.transitions.SingleState attribute) T2 (fluopy.transitions.SingleState attribute) tau (fluopy.fcs.FCS attribute) tcspc() (fluopy.emissions.Emissions method) time_series (fluopy.simulation.Simulation attribute) Transition (class in fluopy.transitions) transition_df (fluopy.transitions.TransitionSet attribute) transition_matrix (fluopy.transitions.TransitionSet property) transition_series (fluopy.simulation.Simulation attribute) transition_set (fluopy.prediction.Prediction attribute) (fluopy.simulation.Simulation attribute) transition_type (fluopy.transitions.Transition attribute) transitions (fluopy.transitions.TransitionSet attribute) TransitionSet (class in fluopy.transitions) U universal_figure() (in module fluopy.figure) W weights (fluopy.distributions.Photoswitching_fingerprint_model attribute) X x_grid (fluopy.distributions.ExponentialMixtureMarginalModel attribute) Z z (fluopy.distributions.Photoswitching_fingerprint_model attribute)