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threshold and the number of photons $m$ and as therefore it has become a common
practice to manually tweak those parameters for each specific measurement.
A more general approach
consist in consists taking into account the background rate of
the specific measurements and in choosing a rate threshold that is $F$ times
larger than the background rate. This approach assures
that all the resulting bursts
all
have a
single-to-background Signal-To-Background ratio (SBR) larger than
$(F-1)$~\cite{Michalet_2012}. A consistent criterion to choose the threshold is
very important when comparing different measurements with different background
rates, when the background significantly
changes varies during
the measurements or in
multi-spot measurements where each spot has a different background rate.
A second important aspect of burst search is which photon stream is processed.
...
the appropriate \verb|Ph_sel| object to the burst search method (see
section~\ref{sec:ph_streams} for more info on photon stream definitions).
Finally, Nir~\textit{et al.}~\cite{Nir_2006} proposed a
dual-channel burst
search Dual-Channel Burst
Search (DCBS) that allows
to mitigate the mitigation (to some extent)
of artifacts due to
photo-physical effects such as
blinking. photo-blinking. In this case a search is performed
independently on two photon streams and bursts are marked only when both photon
streams exhibit a rate higher than the threshold,
implementing a kind of an AND-gate logic.
Usually, the term DCBS
is refers to a burst search where the two photon streams
are all the photons
during donor excitation (\verb|Ph_sel(Dex='DAem')|) and acceptor channel photons
during acceptor
...
(i.e. the minimum bursts size is $m$).
An additional parameter $L$ can be passed to apply a threshold on the raw burst
size (before any correction).
We however suggest to perform a more accurate We, however, strongly encourage performing an accurater burst size selection as shown in
the next section~\ref{sec:burstsel}.
In µs-ALEX there are 3 important correction parameters: gamma factor,
donor spectral
leakage
into acceptorchannel and
acceptor direct excitation~\cite{Lee_2005}. These corrections can be applied by
simply setting the respective
Data attributes:
...
save RAM, FRETBursts shares the timestamps and detectors arrays between
different copies of a \verb|Data| object (for example \verb|d| and
\verb|d_dcbs|), while all the other data (including background and burst data)
is are copied.
The function \verb|burst_search_and_gate| accepts additional arguments
\verb|ph_sel1| and \verb|ph_sel2|
used to specify different
photons photon streams. The default values
(\verb|ph_sel1 = Ph_sel(Dex='DAem')| and \verb|ph_sel2 = Ph_sel(Aex='Aem')|)
correspond to the classical DCBS
(see section~\ref{sec:burstsearch_intro}).