Antonino Ingargiola edited Concepts.tex  about 8 years ago

Commit id: 11f590df484f2c0f64a23a799d4af0afd567987b

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Each array contains timestamps from both donor (D) and acceptor (A) channels.  In ALEX measurements~\cite{Lee_2005}, 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" ``photon streams''  and they are specified with a  \href{http://fretbursts.readthedocs.org/en/latest/ph_sel.html}{\texttt{Ph\_sel}  object} . In non-ALEX smFRET data there are 3 photon streams 

\begin{itemize}  \item \verb|nd|: number of photons detected by the donor channel  (during donor excitation period, if ALEX) period in ALEX case)  \item \verb|na|: number of photons detected by the acceptor channel  (during donor excitation period, if ALEX) period in ALEX case)  \item \verb|naa|: number of photons detected by the acceptor channel  during acceptor excitation period (present only in ALEX measurements)  \end{itemize}  These fields are background-corrected by default. Furthermore,  \verb|na| is corrected for leakage and direct excitation (section~\ref{sec:corrcoeff})  if the relative coefficients are specified (by default they are 0). There is also a field named \verb|nda| containing donor photon during   acceptor excitation, which is only due to background.  \paragraph{Python details}  Most arrays in \texttt{Data} are contained in lists with lengths equal to the  number of excitation spots. This means that, in  single-spot measurements, to access an array of burst-data