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tritemio committed May 14, 2015
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Expand Up @@ -10,27 +10,33 @@ Photon-HDF5 file format documentation
:Contact: tritemio@gmail.com
:Version: 0.3

.. note ::
This document describes **Photon-HDF5 version 0.3**, the third iteration of the *Photon-HDF5 file format*.
The latest version of this document can be found at
`http://photon-hdf5.readthedocs.org <http://photon-hdf5.readthedocs.org/>`__.
Photon-HDF5 is a file format single-molecule experiments
that requires storing photon stream data (e.g. photon timestamps).
Typical examples are freely-diffusing single-molecule FRET (smFRET)
(with or without lifetime), Fluorescence Correlation Spectroscopy (FCS)
and related techniques.

Photon-HDF5 is a file format for a class of single-molecule spectroscopy
experiments that requires storing photon stream data.
Any dataset containing a photon timestamp and other per-photon information
can be stored using the Photon-HDF5 format.
Additionally, for some predefined types of measurements, it is possible to
store all associated metadata needed for a complete interpretation
of the dataset. For example, a dataset created in a single confocal spot,
diffusing single-molecule FRET (smFRET) experiment,
will contain a description of the relation between detector IDs and donor/acceptor channels
(called ``spectral_ch1`` and ``spectral_ch2`` respectively) allowing for
a correct interpretation of the dataset by a burst analysis program.
freely-diffusing smFRET experiment,
will contain a description of the relation between detector IDs and
donor/acceptor channels (called ``spectral_ch1`` and ``spectral_ch2``
respectively) allowing for a correct interpretation of the dataset
by a burst analysis program.

For a brief introduction on the HDF5 format and its
use for single-molecule spectroscopy, see
`Why an HDF5-based smFRET file format <http://fretbursts.readthedocs.org/en/latest/HDF5_format.html>`__.


.. note ::
This document describes **Photon-HDF5 version 0.3**, the third iteration of the *Photon-HDF5 file format*.
The latest version of this document can be found at
`http://photon-hdf5.readthedocs.org <http://photon-hdf5.readthedocs.org/>`__.
.. warning::

Although this specification is still a draft, it is the third complete
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