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
Getting started
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