Antonino Ingargiola edited Concepts.tex  about 8 years ago

Commit id: fd89a46b2d24e93662c223f938ea880ff6fb548d

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The recorded stream of timestamps is the result of two processes: one characterized  by a high count rate, due to fluorescence photons of single molecules crossing the  excitation volume, and another characterized by a lower count rate, due to “background  counts” "background  counts"  originating from detector dark counts, afterpulsing, out-of-focus molecules and sample scattering and/or impurities~\cite{Gopich_2008}.  % Gopich provides a theoretical expression for out-of-focus counts, but ignores scattering, impurities, dcr and afterpulsing (which you do not mention). For this reason, I would rather cite an original experimental paper going back to the early FCS works (dealing with exactly the same issues.   The signature of these two types of processes can be 

Experimentally, we found that when the background is not constant,  it usually varies  on time scales of tens of seconds (see figure~\ref{fig:bg_timetrace}).  FRETBursts divides the data set acquisition  in constant duration constant-duration  time windows called \textit{background periods} and computes the background rates for  each of these windows (see section~\ref{sec:bg_calc}).  Note that FRETBursts uses the same definitions of constant these local  background period windows rates also  during burst search, in order to compute time-dependent burst detection thresholds   and for background correction of burst data (see section~\ref{sec:burstsearch}).