FRETBursts Reference Manual

Contents:

• Loader functions
  • List of loader functions
  • Load data manually
• The “Data()” class
  • “Data()” class: description and attributes
  • Summary information
  • Analysis methods
  • Burst corrections
  • Burst selection methods
  • Fitting methods
  • Timestamp access methods
• Photon selections
  • Ph_sel
• Background estimation
  • background.py
  • Low-level background fit functions
• Burst selection
  • Selection functions
• Fit framework
  • MultiFitter reference documentation
  • Overview
  • Fitting E or S histograms
  • Lmfit introduction
  • Legacy Fit functions
• Direct FRET fitting
  • fit_E_E_size()
  • fit_E_binom()
  • fit_E_cdf()
  • fit_E_hist()
  • fit_E_m()
  • fit_E_poisson_na()
  • fit_E_poisson_nd()
  • fit_E_poisson_nt()
  • fit_E_slope()
  • get_dist_euclid()
  • get_weights()
  • log_likelihood_binom()
  • log_likelihood_poisson_na()
  • log_likelihood_poisson_nd()
  • log_likelihood_poisson_nt()
  • sim_nd_na()
• Plotting Data
  • Timetrace and ratetrace plots
  • 1D Histograms
  • ALEX plots
  • Scatter plots
• Burst Search in FRETBursts
  • Defining the rate estimator
  • Conventions in burst search
  • The Core Algorithm
  • Burst Fusion
  • Low-level burst search functions
• Photon rates functions
  • kde_gaussian()
  • kde_laplace()
  • kde_rect()
  • mtuple_delays()
  • mtuple_delays_min()
  • mtuple_rates()
  • mtuple_rates_max()
  • mtuple_rates_t()
• FRETBursts plugins
  • asymmetry()
  • burst_data()
  • burst_data_period_mean()
  • burst_photons()
  • burst_search_and_gate()
  • bursts_fitter()
  • calc_bg_brute()
  • calc_bg_brute_cache()
  • calc_mdelays_hist()
  • calc_mean_lifetime()
  • fit_bursts_kde_peak()
  • get_burst_photons()
  • group_data()
  • histogram_mdelays()
  • join_data()
  • moving_window_chunks()
  • moving_window_dataframe()
  • moving_window_startstop()
  • ph_burst_stats()
• Why an HDF5-based smFRET file format
  • What is HDF5?
  • The HDF5 ecosystem
  • Why HDF5 and smFRET?
  • HDF5 in FRETBursts
• FRET Correction Formulas
  • correct_E_gamma_leak_dir()
  • correct_S()
  • dir_ex_correct_E()
  • dir_ex_uncorrect_E()
  • gamma_correct_E()
  • gamma_uncorrect_E()
  • leakage_correct_E()
  • leakage_uncorrect_E()
  • test_fretmath()
  • uncorrect_E_gamma_leak_dir()
  • uncorrect_S()
• Description of the files
  • burstlib.py
  • loader.py
  • select_bursts.py
  • burst_plot.py
  • background.py
  • phtools (folder)
  • dataload (folder)
  • fit (folder)
• FRETBursts Cython extensions