Antonino Ingargiola edited dataload.tex  about 8 years ago

Commit id: 3e6613daf365b79ed35aa6d193d76f2038431036

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\label{sec:dataload}  While FRETBursts can load several data files formats,  we encourage users to adopt the recently introduced Photon-HDF5 file format~\cite{Ingargiola2016}.  Photon-HDF5 is an HDF5-based, open format, specifically designed for freely-diffusing smFRET and other timestamp-based experiments. Photon-HDF5 is a self-documented, platform- and language-independent binary format,  which supports compression and allows saving photon data (e.g. timestamps) and measurement-specific metadata  (e.g. setup and sample information, authors, provenance, etc.). 

\subsection{Alternation Parameters}  \label{sec:alternation}  For µs-ALEX and ns-ALEX data, it is necessary to specify the Photon-HDF5 normally stores parameters defining  alternation periods corresponding to donor and acceptor laser excitation.  % maybe mention that At load time,  a Photon-HDF5 file may already provide this information. What happens then?  - user can plot these parameters and change them if deemed necessary.  In µs-ALEX measurements,  %insert ref measurements~\cite{Kapanidis_2004},  CW laser lines are alternated on timescales of the order of 10 to 100~µs.  Plotting an histogram of timestamps modulo the alternation period, it  is possible to identify the donor and acceptor excitation periods (see figure~\ref{fig:altern_hist_double}a).  - In ns-ALEX measurements,%insert refs  pulsed lasers with equal repetition rates are delayed with respect to one another with typical delays of 10 to 100~ns. In this case, forming an histogram of nanotimes  %which haven't been defined so far TCSPC times (nanotimes)  will allow   the definition of the period of fluorescence after excitation of either the donor or the acceptor  (see figure~\ref{fig:altern_hist_double}b).