deletions | additions       diff --git a/Burst search.tex b/Burst search.tex  index 34fc666..884d0a1 100644  --- a/Burst search.tex  +++ b/Burst search.tex 
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\subsubsection{Introduction to burst search}  After background estimation, the burst search is the next fundamental step of the analysis. The core "sliding window" algorithm, proposed by Eggeling~\textit{et al.} in 1998~\cite{Eggeling_1998}, involves searching for bursts of photons  in which $m$ consecutive photons are within a minimum time lag $\Delta t$. In other words, the bursts are thethe  portions of the photon stream where the local a rate (computed using $m$ photons) is above a minimum rate choosen chosen  as a threshold. Eggeling did not provide any criteria on how to chose choose  the rate 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 taking into accout 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 the resulting bursts all have a single-to-background ratio (SBR) larger than $(F-1)$~\cite{Michalet_2012}. A consisten consistent  criterium to choose the threshold is very important when comparing different measurements with different background rates, when the background significantly changes during the measurements or in multi-spot measurements where each spot has a different background rates. A second important aspect of burst search is which photon stream is processed. Usually, when indentifying identifying  FRET populations, we want to apply the burst search to all the photons. Other times, when focusing on donor-only or acceptor only population population,  is better to use only the donor or acceptor signal. In general we want to be able to apply the burst search to an arbitrary selection of photons. In FRETBursts this can be achieved passing 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~\text{et Nir~\textit{et  al.} proposed a refined burst search (AND-gate burst search) that is able to avoid artifacts due to photophysical photo-physical  effects such as blinking. In this case a search is perfomer performer  independently on two photon streams and bursts are marked only when both photon streams exibit exhibit  a rate higher then than  the threshold. \subsubsection{Burst search in FRETBursts}  \label{sec:burstsearch-intro} 
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\end{verbatim}  The previous command perfoms a burst search on all photons (\verb|ph_sel=Ph_sel('all')|), with a minimum rate 6 times larger than the background rate (\verb|F=6|) and using 10 consecutive photons to compute the local rate (\verb|m=10|).  These parameters are generally a good starting point for smFRET analisys analysis  but can be tweaked in specific cases. When there is a need to perform a burst-search using a fixed threshold (independent from the background rate),   the \verb|min_rate| argument can be used as follows (considering a minimun minimum  rate threshold of 50~kHz): \begin{verbatim}  d.burst_search_t(rate_min=50e3, m=10, ph_sel=Ph_sel('all'))  \end{verbatim}  Finally, to perfom perform  an AND-gate burst search (see section~\ref{sec:burstsearch-intro}) the plugin function \href{http://fretbursts.readthedocs.org/en/latest/plugins.html#fretbursts.burstlib_ext.burst_search_and_gate}{\verb|burst_search_and_gate|} can be used. \subsection{Burst selection}