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Antonino Ingargiola edited background-estimation.tex
about 8 years ago
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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 the \verb|calc_bg| documentation
(\href{http://fretbursts.readthedocs.org/en/latest/data\_class.html#fretbursts.burstlib.Data.calc_bg}{link}). (\href{http://fretbursts.readthedocs.org/en/latest/data_class.html#fretbursts.burstlib.Data.calc_bg}{link}).
FRETBursts provides are two kind of plots to represent the background. One is the histograms
of inter-photon delays compared to the fitted exponential distribution reported in
...
Figure~\ref{fig:bg_dist_all} allows to quickly identify pathological cases when the
background fitting procedure returns unreasonable values.
The second background-related plot is
a the timetrace of
the estimated background rates,
as shown in figure~\ref{fig:bg_timetrace}. This plot allows to monitor background changes
taking place during the
measurement and measurement. This plot is obtained with the
command: commans:
\begin{lstlisting}
dplot(d, timetrace_bg)
\end{lstlisting}
Normally, samples should have a constant background as a function of time
like in figure~\ref{fig:bg_timetrace}(a). However, oftentimes, non-ideal
experimental conditions can yield a time-varying background, as shown in
figure~\ref{fig:bg_timetrace}(b).
For example, when the sample is not sealed in an observation chamber,
evaporation can induce background variations (typically increasing)
as a function of time. Additionally,
cover-glass Coverglass impurities can contribute to the background even when focusing
deep into the sample (10μm or
more). more),
These impurities tend to bleach on timescales of minutes resulting in
background variations during the course of the
measurement. measurement, such as
the one shown in figure~\ref{fig:bg_timetrace}a.
Additionally, when the sample in not sealed in an observation chamber,
evaporation can contribute to background variations, similar to the
one shown in figure~\ref{fig:bg_timetrace}b.
\paragraph{Python details} For an ALEX measurement, the tuple passed to
\verb|tail_min_us| to define the thresholds, is required to have have