.. Photon-HDF5 documentation master file, created by
   sphinx-quickstart on Tue Dec 09 10:48:26 2014.
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Photon-HDF5 file format documentation
======================================

:Authors: Antonino Ingargiola, Xavier Michalet, Ted Laurence
:Contact: `Photon-HDF5 Google Group <https://groups.google.com/forum/#!forum/photon-hdf5>`_
:Format Version: 0.5rc1


This is the reference documentation for **Photon-HDF5** (`homepage <http://photon-hdf5.org/>`__),
a file format for timestamp-based single-molecule spectroscopy
experiments such as single-molecule FRET (smFRET) (with or without lifetime),
Fluorescence Correlation Spectroscopy (FCS) and other related techniques.

Any dataset containing photon timestamps and other per-photon data
can be stored in Photon-HDF5 files.
Photon-HDF5 is designed for long-term preservation and data sharing and
can store experimental details and metadata such as
setup configurations, sample information, authorship and provenance.

The present document contains the reference documentation for the Photon-HDF5 format.

**Other related resources** (see also `Photon-HDF5 Homepage <http://photon-hdf5.org/>`__):

- |example_files|, view them with |hdfview|.
- |read_examples|
- |phconvert|: reference library to create and convert Photon-HDF5 files
- Biophysical Journal (2016), |photon-hdf5_paper_bj| (|photon-hdf5_paper|).
- |photon-hdf5_demo|


.. |example_files| raw:: html

   <a href="http://figshare.com/articles/Example_smFRET_data_files_in_Photon_HDF5_format/1456362" target="_blank">Example Photon-HDF5 data files</a>

.. |hdfview| raw:: html

   <a href="https://www.hdfgroup.org/products/java/hdfview/" target="_blank">HDFView</a>

.. |read_examples| raw:: html

   <a href="https://github.com/Photon-Data/photon_hdf5_reading_examples" target="_blank">Code examples of reading Photon-HDF5 files in multiple languages</a>

.. |phconvert| raw:: html

   <a href="http://photon-hdf5.github.io/phconvert/" target="_blank">phconvert</a>

.. |photon-hdf5_paper| raw:: html

   <a href="http://dx.doi.org/10.1101/026484" target="_blank">BioRxiv manuscript</a>

.. |photon-hdf5_paper_bj| raw:: html

   <a href="http://dx.doi.org/10.1016/j.bpj.2015.11.013" target="_blank">Photon-HDF5: an open file format for timestamp-based single-molecule fluorescence experiments</a>

.. |photon-hdf5_demo| raw:: html

   <a href="http://photon-hdf5.github.io/Photon-HDF5-Converter" target="_blank">Photon-HDF5 Online Converter</a>


Table of Contents
-----------------

.. toctree::
    :maxdepth: 2
    :numbered:

    intro
    phdata
    whats_new_ver05
    reading
    writing
    new_measurement_specs
    limitations
    contributing