Antonino Ingargiola edited Introduction.tex  over 9 years ago

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FRETBursts is a python package for burst analysis of confocal single-molecule  FRET (smFRET) data.  In this paper we provide an broad  overview of the FRETBursts software. The paper is structured as follows. In section~\ref{sec:concepts} we  introduce some basic concepts and terminology related to burst analysis.  In section~\ref{sec:analysis} we illustrate how to execute the several steps involved  in the burst analysis (background correction, analysis: background correction (section~\ref{sec:bg_calc}),  burst search, search  (section~\ref{sec:burstsearch}),  burst filtering, filtering (section~\ref{sec:burstsel}),  FRET fitting).  \textit{Expand abstract fitting (section~\ref{sec:fretfit}). For each step different approached and options are  discussed.  In addition  to introduce smFRET this paper, we refer the interested readers to the   \href{http://nbviewer.ipython.org/github/tritemio/FRETBursts_notebooks/blob/master/notebooks/FRETBursts%20-%20us-ALEX%20smFRET%20burst%20analysis.ipynb}{FRETBursts µs-ALEX tutorial}   for a single complete example of µs-ALEX data analysis  and what is burst analysis}. to the  \href{http://fretbursts.readthedocs.org/}{FRETBursts Reference Documentation}  for a detailed description of each function.  \subsection{Installing FRETBursts}  FRETBursts is a standard python package that requires the "scipy stack", a set