Antonino Ingargiola edited background-estimation.tex  about 8 years ago

Commit id: e953559b3ce724b02587cc3d8a6d2039552aba20

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The first argument (\verb|bg.exp_fit|) is the function used to fit the  background rate for each photon stream (see section~\ref{sec:bg_intro}).  %we used to define a photon stream by its excitation period and channel.   The function  \verb|bg.exp_fit| estimates the background using a maximum likelihood estimation  (MLE) of the delays distribution.  %where is the fitting method specified? Is it implicit in the choice of method?  Additional fitting functions are available in  \verb|bg| namespace   (i.e. the \verb|background| module, \href{http://fretbursts.readthedocs.org/en/latest/background.html}  {link}). The second argument, \verb|time_s|, is the duration of the  \textit{background period} (section~\ref{sec:bg_intro}) and the third, \verb|tail_min_us|,  is the minimum inter-photon delay to use when fitting the distribution to the specified model function.  %so there is only an exponential model then?  It is possible to use different thresholds for each photon stream, passing a  tuple (i.e. a comma-separated list of values, \href{https://docs.python.org/3.5/tutorial/datastructures.html#tuples-and-sequences}{link}) instead of a scalar.  Finally, it is possible to use a heuristic estimation of the threshold using  \verb|tail_min_us='auto'|. For more details refer to \textit{Background estimation}   section of  the \verb|Data.calc_bg| documentation  (\href{http://fretbursts.readthedocs.org/en/latest/data_class.html#fretbursts.burstlib.Data.calc_bg}{link}). μs-ALEX tutorial   (\href{http://nbviewer.jupyter.org/github/tritemio/FRETBursts_notebooks/blob/master/notebooks/FRETBursts%20-%20us-ALEX%20smFRET%20burst%20analysis.ipynb#Background-estimation}{link}).  FRETBursts provides two kinds of plots to represent the background. One is the histograms  of inter-photon delays compared to the fitted exponential distribution, shown in