FRETBursts
0.7.1+0.gc51b
Tutorial
Reference Manual
Site
Introducing FRETBursts
Getting started
Getting started for the absolute python beginner
Installing FRETBursts
Running FRETBursts tutorial notebook
FRETBursts Installation
Installing latest stable version
Alternative methods: using PIP
Install FRETBursts in a stand-alone environment
Install latest development version
Running FRETBursts
Why a notebook-based workflow
FRETBursts Dependencies
What's New?
Version 0.7.1
Version 0.7 (Jul. 2018)
Version 0.6.5 (Aug. 2017)
Version 0.6.4 (Jul. 2017)
Version 0.6.3 (Apr. 2017)
Version 0.6.2 (Apr. 2017)
Version 0.6.1 (Apr. 2017)
Version 0.6 (Jan. 2017)
Backward-incompatible changes
Effect on burst search
Details of auto-threshold changes
Background attributes
Compatibility layer
Details of changed attributes
Version 0.5.9 (Sep. 2016)
Version 0.5.7 (Sep. 2016)
Data Class
Plot functions
Burst selection
Burst Weights
Installation via conda-forge
Version 0.5.6
μs-ALEX Tutorial
List of Jupyter Notebooks
Reference manual
Loader functions
List of loader functions
Load data manually
The “Data()” class
“Data()” class: description and attributes
Summary information
Analysis methods
Burst corrections
Correction factors
Correction methods
Burst selection methods
Fitting methods
Timestamp access methods
Photon selections
Background estimation
background.py
Low-level background fit functions
Burst selection
Selection functions
Fit framework
MultiFitter reference documentation
The MultiFitter class
Model factory functions
Utility functions
Overview
Fitting E or S histograms
Lmfit introduction
Legacy Fit functions
Gaussian fitting
Exponential fitting
Direct FRET fitting
Plotting Data
Timetrace and ratetrace plots
1D Histograms
Bursts: ratiometric quantities
Bursts: tail distributions
Others
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
FRETBursts plugins
Why an HDF5-based smFRET file format
What is HDF5?
The HDF5 ecosystem
Why HDF5 and smFRET?
HDF5 in FRETBursts
HDF5-based smFRET file format
Read and write HDF5 smFRET files
FRET Correction Formulas
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
FRETBursts Paper
Burst Search Algorithm
Defining the rate estimator
Conventions in burst search
The Core Algorithm
Burst Fusion
Low-level burst search functions
BVA
2CDE
Exporting burst data
Report an issue
Page
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
U
|
W
A
A_em (fretbursts.burstlib.Data attribute)
alex_apply_period() (in module fretbursts.loader)
alex_jointplot() (in module fretbursts.burst_plot)
alex_period (fretbursts.burstlib.Data attribute)
and_gate() (fretbursts.phtools.burstsearch.Bursts method)
asym_gaussian() (in module fretbursts.mfit)
asymmetry() (in module fretbursts.burstlib_ext)
B
background_correction() (fretbursts.burstlib.Data method)
bg (fretbursts.burstlib.Data attribute)
bg_bs (fretbursts.burstlib.Data attribute)
bg_fun (fretbursts.burstlib.Data attribute)
bg_mean (fretbursts.burstlib.Data attribute)
bg_ph_sel (fretbursts.burstlib.Data attribute)
bound_check() (in module fretbursts.fit.gaussian_fitting)
bp (fretbursts.burstlib.Data attribute)
bridge_function() (in module fretbursts.mfit)
brightness() (in module fretbursts.select_bursts)
bsearch_py() (in module fretbursts.phtools.burstsearch)
Burst (class in fretbursts.phtools.burstsearch)
burst_data() (in module fretbursts.burstlib_ext)
burst_data_period_mean() (in module fretbursts.burstlib_ext)
burst_photons() (in module fretbursts.burstlib_ext)
burst_search() (fretbursts.burstlib.Data method)
burst_search_and_gate() (in module fretbursts.burstlib_ext)
burst_sizes() (fretbursts.burstlib.Data method)
burst_sizes_ich() (fretbursts.burstlib.Data method)
burst_sizes_pax_ich() (fretbursts.burstlib.Data method)
burst_widths (fretbursts.burstlib.Data attribute)
BurstGap (class in fretbursts.phtools.burstsearch)
Bursts (class in fretbursts.phtools.burstsearch)
bursts_fitter() (in module fretbursts.burstlib_ext)
BurstsGap (class in fretbursts.phtools.burstsearch)
C
calc_bg() (fretbursts.burstlib.Data method)
calc_bg_brute() (in module fretbursts.burstlib_ext)
calc_bg_brute_cache() (in module fretbursts.burstlib_ext)
calc_fret() (fretbursts.burstlib.Data method)
calc_kde() (fretbursts.mfit.MultiFitter method)
calc_max_rate() (fretbursts.burstlib.Data method)
calc_mdelays_hist() (in module fretbursts.burstlib_ext)
calc_mean_lifetime() (in module fretbursts.burstlib_ext)
calc_ph_num() (fretbursts.burstlib.Data method)
calc_sbr() (fretbursts.burstlib.Data method)
chi_ch (fretbursts.burstlib.Data attribute)
clk_p (fretbursts.burstlib.Data attribute)
consecutive() (in module fretbursts.select_bursts)
copy() (fretbursts.burstlib.Data method)
(fretbursts.phtools.burstsearch.Bursts method)
correct_E_gamma_leak_dir() (in module fretbursts.fretmath)
correct_S() (in module fretbursts.fretmath)
count_ph_in_bursts() (in module fretbursts.phtools.burstsearch)
counts (fretbursts.phtools.burstsearch.Burst property)
(fretbursts.phtools.burstsearch.BurstGap property)
(fretbursts.phtools.burstsearch.Bursts property)
(fretbursts.phtools.burstsearch.BurstsGap property)
D
D_em (fretbursts.burstlib.Data attribute)
Data (class in fretbursts.burstlib)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
dataframe (fretbursts.phtools.burstsearch.Bursts property)
(fretbursts.phtools.burstsearch.BurstsGap property)
dir_ex (fretbursts.burstlib.Data attribute)
dir_ex_correct_E() (in module fretbursts.fretmath)
dir_ex_uncorrect_E() (in module fretbursts.fretmath)
dither() (fretbursts.burstlib.Data method)
E
E (fretbursts.burstlib.Data attribute)
E() (in module fretbursts.select_bursts)
empty() (fretbursts.phtools.burstsearch.Bursts class method)
ES() (in module fretbursts.select_bursts)
ES_ellips() (in module fretbursts.select_bursts)
ES_rect() (in module fretbursts.select_bursts)
exp_cdf_fit() (in module fretbursts.background)
exp_fit() (in module fretbursts.background)
exp_hist_fit() (in module fretbursts.background)
expand() (fretbursts.burstlib.Data method)
expon_fit() (in module fretbursts.fit.exp_fitting)
,
[1]
expon_fit_cdf() (in module fretbursts.fit.exp_fitting)
,
[1]
expon_fit_hist() (in module fretbursts.fit.exp_fitting)
,
[1]
F
F (fretbursts.burstlib.Data attribute)
factory_asym_gaussian() (in module fretbursts.mfit)
factory_gaussian() (in module fretbursts.mfit)
factory_three_gaussians() (in module fretbursts.mfit)
factory_two_asym_gaussians() (in module fretbursts.mfit)
factory_two_gaussians() (in module fretbursts.mfit)
find_kde_max() (fretbursts.mfit.MultiFitter method)
fit_bursts_kde_peak() (in module fretbursts.burstlib_ext)
fit_E_binom() (in module fretbursts.fret_fit)
fit_E_cdf() (in module fretbursts.fret_fit)
fit_E_E_size() (in module fretbursts.fret_fit)
fit_E_generic() (fretbursts.burstlib.Data method)
fit_E_hist() (in module fretbursts.fret_fit)
fit_E_m() (fretbursts.burstlib.Data method)
(in module fretbursts.fret_fit)
fit_E_minimize() (fretbursts.burstlib.Data method)
fit_E_ML_poiss() (fretbursts.burstlib.Data method)
fit_E_poisson_na() (in module fretbursts.fret_fit)
fit_E_poisson_nd() (in module fretbursts.fret_fit)
fit_E_poisson_nt() (in module fretbursts.fret_fit)
fit_E_slope() (in module fretbursts.fret_fit)
fit_E_two_gauss_EM() (fretbursts.burstlib.Data method)
fit_histogram() (fretbursts.mfit.MultiFitter method)
fname (fretbursts.burstlib.Data attribute)
fretbursts
module
fretbursts.background
module
,
[1]
fretbursts.burst_plot
module
,
[1]
fretbursts.burstlib
module
,
[1]
,
[2]
fretbursts.burstlib_ext
module
fretbursts.dataload
module
fretbursts.fit
module
fretbursts.fit.exp_fitting
module
,
[1]
fretbursts.fit.gaussian_fitting
module
fretbursts.fret_fit
module
fretbursts.fretmath
module
fretbursts.loader
module
,
[1]
fretbursts.mfit
module
fretbursts.ph_sel
module
fretbursts.phtools
module
fretbursts.phtools.burstsearch
module
fretbursts.phtools.phrates
module
fretbursts.select_bursts
module
from_burst() (fretbursts.phtools.burstsearch.BurstGap static method)
from_list() (fretbursts.phtools.burstsearch.Bursts class method)
(fretbursts.phtools.burstsearch.BurstsGap class method)
fuse (fretbursts.burstlib.Data attribute)
fuse_bursts() (fretbursts.burstlib.Data method)
G
gamma (fretbursts.burstlib.Data attribute)
,
[1]
gamma_correct_E() (in module fretbursts.fretmath)
gamma_uncorrect_E() (in module fretbursts.fretmath)
gap (fretbursts.phtools.burstsearch.BurstsGap property)
gap_counts (fretbursts.phtools.burstsearch.BurstsGap property)
gaussian2d_fit() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_cdf() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_curve() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_hist() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_ml() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_pdf() (in module fretbursts.fit.gaussian_fitting)
get_burst_photons() (in module fretbursts.burstlib_ext)
get_dist_euclid() (in module fretbursts.fret_fit)
get_ecdf() (in module fretbursts.fit.exp_fitting)
,
[1]
get_epdf() (in module fretbursts.fit.gaussian_fitting)
get_ph_mask() (fretbursts.burstlib.Data method)
get_ph_times() (fretbursts.burstlib.Data method)
get_residuals() (in module fretbursts.fit.exp_fitting)
,
[1]
get_weights() (in module fretbursts.fret_fit)
group_data() (in module fretbursts.burstlib_ext)
H
hexbin_alex() (in module fretbursts.burst_plot)
hist2d_alex() (in module fretbursts.burst_plot)
hist_asymmetry() (in module fretbursts.burst_plot)
hist_bg() (in module fretbursts.burst_plot)
hist_bg_single() (in module fretbursts.burst_plot)
hist_brightness() (in module fretbursts.burst_plot)
hist_burst_data() (in module fretbursts.burst_plot)
hist_burst_delays() (in module fretbursts.burst_plot)
hist_burst_phrate() (in module fretbursts.burst_plot)
hist_fret() (in module fretbursts.burst_plot)
hist_interphoton() (in module fretbursts.burst_plot)
hist_interphoton_single() (in module fretbursts.burst_plot)
hist_S() (in module fretbursts.burst_plot)
hist_sbr() (in module fretbursts.burst_plot)
hist_size() (in module fretbursts.burst_plot)
hist_size_all() (in module fretbursts.burst_plot)
hist_width() (in module fretbursts.burst_plot)
histogram() (fretbursts.mfit.MultiFitter method)
histogram_mdelays() (in module fretbursts.burstlib_ext)
I
istart (fretbursts.phtools.burstsearch.Bursts property)
istop (fretbursts.phtools.burstsearch.Bursts property)
iter_bursts_ph() (fretbursts.burstlib.Data method)
iter_ph_masks() (fretbursts.burstlib.Data method)
iter_ph_times() (fretbursts.burstlib.Data method)
J
join() (fretbursts.phtools.burstsearch.Bursts method)
join_data() (in module fretbursts.burstlib_ext)
K
kde_gaussian() (in module fretbursts.phtools.phrates)
kde_laplace() (in module fretbursts.phtools.phrates)
kde_rect() (in module fretbursts.phtools.phrates)
L
L (fretbursts.burstlib.Data attribute)
leakage (fretbursts.burstlib.Data attribute)
,
[1]
leakage_correct_E() (in module fretbursts.fretmath)
leakage_correction() (fretbursts.burstlib.Data method)
leakage_uncorrect_E() (in module fretbursts.fretmath)
Lim (fretbursts.burstlib.Data attribute)
log_likelihood_binom() (in module fretbursts.fret_fit)
log_likelihood_poisson_na() (in module fretbursts.fret_fit)
log_likelihood_poisson_nd() (in module fretbursts.fret_fit)
log_likelihood_poisson_nt() (in module fretbursts.fret_fit)
M
m (fretbursts.burstlib.Data attribute)
mburst (fretbursts.burstlib.Data attribute)
mch_count_ph_in_bursts_py() (in module fretbursts.phtools.burstsearch)
merge() (fretbursts.phtools.burstsearch.Bursts class method)
module
fretbursts
fretbursts.background
,
[1]
fretbursts.burst_plot
,
[1]
fretbursts.burstlib
,
[1]
,
[2]
fretbursts.burstlib_ext
fretbursts.dataload
fretbursts.fit
fretbursts.fit.exp_fitting
,
[1]
fretbursts.fit.gaussian_fitting
fretbursts.fret_fit
fretbursts.fretmath
fretbursts.loader
,
[1]
fretbursts.mfit
fretbursts.ph_sel
fretbursts.phtools
fretbursts.phtools.burstsearch
fretbursts.phtools.phrates
fretbursts.select_bursts
moving_window_chunks() (in module fretbursts.burstlib_ext)
moving_window_dataframe() (in module fretbursts.burstlib_ext)
moving_window_startstop() (in module fretbursts.burstlib_ext)
mtuple_delays() (in module fretbursts.phtools.phrates)
mtuple_delays_min() (in module fretbursts.phtools.phrates)
mtuple_rates() (in module fretbursts.phtools.phrates)
mtuple_rates_max() (in module fretbursts.phtools.phrates)
mtuple_rates_t() (in module fretbursts.phtools.phrates)
MultiFitter (class in fretbursts.mfit)
N
na() (in module fretbursts.select_bursts)
na_bg() (in module fretbursts.select_bursts)
na_bg_p() (in module fretbursts.select_bursts)
naa (fretbursts.burstlib.Data attribute)
naa() (in module fretbursts.select_bursts)
naa_bg() (in module fretbursts.select_bursts)
naa_bg_p() (in module fretbursts.select_bursts)
name (fretbursts.burstlib.Data attribute)
Name() (fretbursts.burstlib.Data method)
nar (fretbursts.burstlib.Data attribute)
nch (fretbursts.burstlib.Data attribute)
nd() (in module fretbursts.select_bursts)
nd_bg() (in module fretbursts.select_bursts)
nd_bg_p() (in module fretbursts.select_bursts)
nda_percentile() (in module fretbursts.select_bursts)
normpdf() (in module fretbursts.fit.gaussian_fitting)
nperiods (fretbursts.burstlib.Data attribute)
nsalex() (in module fretbursts.loader)
nsalex_apply_period() (in module fretbursts.loader)
nt (fretbursts.burstlib.Data attribute)
nt_bg() (in module fretbursts.select_bursts)
nt_bg_p() (in module fretbursts.select_bursts)
num_bursts (fretbursts.burstlib.Data attribute)
(fretbursts.phtools.burstsearch.Bursts property)
P
P (fretbursts.burstlib.Data attribute)
peak_phrate() (in module fretbursts.select_bursts)
period() (in module fretbursts.select_bursts)
ph_burst_stats() (in module fretbursts.burstlib_ext)
ph_data_sizes (fretbursts.burstlib.Data attribute)
ph_in_bursts_ich() (fretbursts.burstlib.Data method)
,
[1]
ph_in_bursts_mask_ich() (fretbursts.burstlib.Data method)
,
[1]
Ph_p (fretbursts.burstlib.Data attribute)
ph_rate (fretbursts.phtools.burstsearch.Burst property)
(fretbursts.phtools.burstsearch.Bursts property)
Ph_sel (class in fretbursts.ph_sel)
ph_sel (fretbursts.burstlib.Data attribute)
ph_times_m (fretbursts.burstlib.Data attribute)
photon_hdf5() (in module fretbursts.loader)
plot_alternation_hist() (in module fretbursts.burst_plot)
plot_alternation_hist_nsalex() (in module fretbursts.burst_plot)
plot_ES_selection() (in module fretbursts.burst_plot)
R
ratetrace() (in module fretbursts.burst_plot)
ratetrace_single() (in module fretbursts.burst_plot)
recompute_index_expand() (fretbursts.phtools.burstsearch.Bursts method)
recompute_index_reduce() (fretbursts.phtools.burstsearch.Bursts method)
recompute_times() (fretbursts.phtools.burstsearch.Bursts method)
reorder_parameters() (in module fretbursts.fit.gaussian_fitting)
reorder_parameters_ab() (in module fretbursts.fit.gaussian_fitting)
S
S (fretbursts.burstlib.Data attribute)
sbr() (in module fretbursts.select_bursts)
scatter_alex() (in module fretbursts.burst_plot)
scatter_da() (in module fretbursts.burst_plot)
scatter_fret_nd_na() (in module fretbursts.burst_plot)
scatter_fret_size() (in module fretbursts.burst_plot)
scatter_fret_width() (in module fretbursts.burst_plot)
scatter_naa_nt() (in module fretbursts.burst_plot)
scatter_rate_da() (in module fretbursts.burst_plot)
scatter_width_size() (in module fretbursts.burst_plot)
select_bursts() (fretbursts.burstlib.Data method)
select_bursts_mask() (fretbursts.burstlib.Data method)
select_bursts_mask_apply() (fretbursts.burstlib.Data method)
separation (fretbursts.phtools.burstsearch.Bursts property)
set_weights_func() (fretbursts.mfit.MultiFitter method)
sim_nd_na() (in module fretbursts.fret_fit)
single() (in module fretbursts.select_bursts)
size (fretbursts.phtools.burstsearch.Bursts property)
size() (in module fretbursts.select_bursts)
slice_ph() (fretbursts.burstlib.Data method)
sm_single_laser() (in module fretbursts.loader)
start (fretbursts.phtools.burstsearch.Bursts property)
status() (fretbursts.burstlib.Data method)
stop (fretbursts.phtools.burstsearch.Bursts property)
str_G() (in module fretbursts.select_bursts)
T
T (fretbursts.burstlib.Data attribute)
test_fretmath() (in module fretbursts.fretmath)
Th_us (fretbursts.burstlib.Data attribute)
time() (in module fretbursts.select_bursts)
time_max (fretbursts.burstlib.Data attribute)
time_min (fretbursts.burstlib.Data attribute)
timetrace() (in module fretbursts.burst_plot)
timetrace_b_rate() (in module fretbursts.burst_plot)
timetrace_bg() (in module fretbursts.burst_plot)
timetrace_single() (in module fretbursts.burst_plot)
topN_max_rate() (in module fretbursts.select_bursts)
topN_nda() (in module fretbursts.select_bursts)
topN_sbr() (in module fretbursts.select_bursts)
TT (fretbursts.burstlib.Data attribute)
two_gauss_mix_ab() (in module fretbursts.fit.gaussian_fitting)
two_gauss_mix_pdf() (in module fretbursts.fit.gaussian_fitting)
two_gaussian2d_fit() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_cdf() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_curve() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_EM() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_EM_b() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist_min() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist_min_ab() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_KDE_curve() (in module fretbursts.fit.gaussian_fitting)
U
uncorrect_E_gamma_leak_dir() (in module fretbursts.fretmath)
uncorrect_S() (in module fretbursts.fretmath)
usalex() (in module fretbursts.loader)
usalex_apply_period() (in module fretbursts.loader)
W
width (fretbursts.phtools.burstsearch.Burst property)
(fretbursts.phtools.burstsearch.BurstGap property)
(fretbursts.phtools.burstsearch.Bursts property)
(fretbursts.phtools.burstsearch.BurstsGap property)
width() (in module fretbursts.select_bursts)