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Antonino Ingargiola edited Concepts.tex
about 8 years ago
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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