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\subsection{Burst selection}
\label{sec:burstsel}
After burst
search search, it is common to select bursts according to different
criteria, among which one criteria. One of the most common is the burst size.
For
example, instance, to select bursts with more than 100 photons
(after (as computed
after background correction) detected during the donor excitation periods
one can write: the following command is used:
\begin{verbatim}
ds = d.select_bursts(select_bursts.size, th1=100)
\end{verbatim}
In the previous
command command, a new \textit{Data} variable (\verb|ds|) containing
the selected bursts is created.
As mentioned before the new object will share the photon data
arrays with the original object (\verb|d|) in order to minimize the RAM
consumption. use.
The
\href{http://fretbursts.readthedocs.org/en/latest/data_class.html#burst-selection-methods}{\texttt{select\_bursts()} method}
requires, as first argument, requires a function implementing the "selection criterion"
as its first argument
(\verb|select_bursts.size| in this example);
all the remaining arguments
(here only \verb|th1|) are passed to the selection
function. function (in this case
the only additional argument is \verb|th1|).
The \href{http://fretbursts.readthedocs.org/en/latest/burst_selection.html}{\texttt{select\_bursts} module}
contains numerous
\href{http://fretbursts.readthedocs.org/en/latest/burst_selection.html#module-fretbursts.select_bursts}{built-in selection
functions},
for example in order functions}.
For example,
\verb|select_bursts.ES|
is used to select a region on the E-S ALEX
histogram (\verb|select_bursts.ES|), histogram,
\verb|select_bursts.width|
to select bursts based on their
duration (\verb|select_bursts.width|) and so on. duration.
New criteria can be easily implemented by defining a new selection function,
usually not longer than a couple of lines (see the
\href{https://github.com/tritemio/FRETBursts/blob/master/fretbursts/select\_bursts.py}{\texttt{select\_bursts} module} for several examples).
Finally note that Finally, different criteria can be combined by applying them sequentially.
For
example with example, after the following commands
\begin{verbatim}
ds = d.select_bursts(select_bursts.size,
th1=50, th2=200)
dsw = ds.select_bursts(select_bursts.width,
th1=0.5e-3, th2=3e-3)
\end{verbatim}
the variable \verb|dsw| will contain all
the bursts with sizes between 50 and
200 photons,
with and duration between 0.5 and 3~ms.
\subsubsection{Burst size selection}
In the previous
section we used a section, the definition of "burst size"
as was implicitly referring
to the total number of detected counts in the donor and in the acceptor channel
during donor
excitation periods. excitation.
We can modify the The selection command
can be provided with an additional parameter in order to
also include photons detected in the acceptor channels during acceptor
excitation periods. excitation.
This is achieved
by passing the flag \verb|add_naa=True| to the selection function
as follows:
\begin{verbatim}
ds = d.select_bursts(select_bursts.size,
th1=100, add_naa=True)
\end{verbatim}
Another important parameter
in for defining the burst size is the gamma-factor, i.e.
the imbalance between the donor and the acceptor channels. The gamma-factor is
used to correct for the different fluorescence quantum yields of the D and A
fluorophores as well as the different photon-detection efficiencies of the D and A channels.
Neglecting the effect of gamma-factor on the burst size leads to a biased burst
selection,
especially if $\gamma$
significantly differs is different from
a value of one. 1.
To include the effect of $\gamma$ on
the burst size and obtain a
"fair" burst
selection
(i.e. a selection that which does not favor high or low FRET
states) we
need to pass states,
the argument \verb|gamma| (or \verb|gamma1|)
like needs to be provided,
as shown in
the following this example:
\begin{verbatim}
ds = d.select_bursts(select_bursts.size,
th1=100, gamma=0.65)
\end{verbatim}
