Eitan Lerner edited burst-search.tex  over 9 years ago

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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 burstsall  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  duringthe  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 DCBSis  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}).