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