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Antonino Ingargiola edited Concepts.tex
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$$n_t = n_a + \gamma\,n_d $$
The former includes all photons, while the latter only photons during
donor
execitation excitation periods.
The inclusion of $\gamma$ factor allows to correct
bias when comparing the number of bursts
accross across several sub-populations.
The results of burst search is a distribution of burst sizes that approximately
follows an exponential distribution.
Bursts with large size (which contain most of the information)
are much less frequent than bursts with smaller sizes. For this reason, it is
important to select burst sizes larger than a threshold in order
to properly characterize FRET
populations(see populations (see section~\ref{sec:burstsel}).
Selecting bursts by size is a critically important step.
A too low threshold will broaden the FRET populations and introduce
artifacts (spurious peaks and patterns) due to the majority of bursts
having E and S computed from ratios of small integers.
Conversely Conversely, a too high threshold will result in a lower number of bursts
and possibly poor statistics in representing FRET populations.
When Additionally, when selecting bursts (see
section~~\ref{sec:burstsel}), section~\ref{sec:burstsel}),
it is important to use $\gamma$-corrected burst sizes,
in order to avoid under-representing some FRET sub-populations
due to different quantum yields between donor and acceptor dyes and/or
...
The weighting can be used to build weighted histograms and Kernel Density
Estimation (KDE) plots. When using weights, the choice of a particular
burst size threshold affects less the shape of the burst distribution,
so lower thresholds can be used (better statistics)
wihtout without broadening
the peaks of sub-populations (better population identification).
\subsubsection{Python details}
FRETBursts has the option to weight bursts using $\gamma$-corrected
burst sizes and to include the acceptor excitation photons \verb|naa|.
Passing A weight proportional to the burst size is applied by passing the argument
\verb|weights='size'| to
histogram or KDE plot
functions. The \verb|weights|
keyword can be also passed to fitting functions
a weight proportional in order to
fit
the
burst size is applied. Other weighted E or S distributions (see section~\ref{sec:fretfit}).
Several other weighting functions (for example quadratical) are listed in the
\href{http://fretbursts.readthedocs.org/en/latest/fret_fit.html#fretbursts.fret_fit.get_weights}{\texttt{fret\_fit.get\_weights} documentation}.
\subsection{Plotting "Data"}