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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).