deletions | additions       diff --git a/smFRET data analysis.tex b/smFRET data analysis.tex  index f48fe07..6586d21 100644  --- a/smFRET data analysis.tex  +++ b/smFRET data analysis.tex 
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The fundamental data at the core of smFRET experiments is the array of photon timestamps. In single-spot measurements, all the timestamps are stored in a single array. In multi-spot measurements we have as many timestamps arrays as the number of excitation spots.  Each timestamps array contains timestamps from both the donor (D) and the acceptor channel (A). In ALEX measurements, we can further differentiate between photons emitted during D and A excitation periods. In FRETBursts the different selections of photons/timestamps are called "photon streams" and they are specified with a \href{http://fretbursts.readthedocs.org/en/latest/data_class.html#module-fretbursts.ph_sel}{\texttt{Ph\_sel} \href{http://fretbursts.readthedocs.org/en/latest/ph_sel.html}{\texttt{Ph\_sel}  object} . In non-ALEX smFRET data we have 3 base photon streams (table~\ref{tab:ph_sel_smfret}), while in ALEX data we have 5 base photon streams (table~\ref{tab:ph_sel_alex}).  The \href{http://fretbursts.readthedocs.org/en/latest/data_class.html#module-fretbursts.ph_sel}{\texttt{Ph\_sel} \href{http://fretbursts.readthedocs.org/en/latest/ph_sel.html}{\texttt{Ph\_sel}  class} allows to express any combination of photon streams. For example, in ALEX measurements, the D-emission during A-excitation stream is usually excluded because it does not contain any useful signal\cite{Lee_2005}. To indicate all but the photons in this photon stream we write \verb|Ph_sel(Dex='DAem', Aex='Aem')|, that litteraly means \textit{select donor and acceptor photons (DAem) during donor excitation (Dex) and only acceptor photons (Aem) during acceptor excitation (Aex)}.  \begin{table}