In this post I introduce Photon-HDF5,
a format I co-authored during the past year.
For a more complete overview you can read the recently published paper
(get the biorRxiv preprint or
the version just published by Biophysical Journal).
Briefly, Photon-HDF5 is a file format for storing single-molecule
fluorescence data based on photon timestamps and other per-photon data.
It is, in essence, a conventional structure to save this class of data
in HDF5 files, therefore facilitating
data sharing and long-term archival.
The format was initially designed to store freely-diffusing single-molecule
FRET data, but it has evolved to store any measurement
which consists of streams of “photon-data” (e.g. timestamps, detectors,
TCSPC nanotimes, etc.).
Design and Features
Since Photon-HDF5 is based on HDF5 files, it inherits all its advantages.
In particular it is open standard, multi-platform and multi-language.
It is also an efficient binary format supporting compression transparently.
In designing Photon-HDF5, we followed a set of generic principles
that may be useful also for other scientific formats:
- self-describing: each data field embeds a description explaining
the purpose of the field;
- self-contained: it contains all the information necessary to analyze the data;
- suitable for long-term archival: rich metadata records experimental details,
provenance, author and software version;
- supports arbitrary user data;
- all support software is open source (under MIT license).
Finally, the following features make Photon-HDF5 suitable for a wide range
of single-molecule fluorescence data:
- supports any number of spectral, polarization or beam-split channels.
- supports single- and multi-spot data.
- extensible: the bulk “photon-data” (present in all types of measurements)
is logically separated from data specific of a single measurement type.
Thanks to this extensible structure, new measurement-types can be defined
in backward-compatible manner. In fact, we encourage users to propose
new measurement types (use the
Photon-HDF5 mailing list).
All Photon-HDF5 development (both specification documents and software)
takes place publicly on GitHub.
We encourage users to join the effort, providing feedback and/or submitting Issues or
By providing feedback and ideas, you can shape the future development
of Photon-HDF5. Plus we acknowledge all contributions.
Photon-HDF5 files can be opened in HDFView
and read exactly in the same way you read other HDF5 files. To help newcomers,
in Python, MATLAB and LabVIEW.
To write valid Photon-HDF5 files from scratch, we provide
a small open source python library called phconvert.
includes, additionally, Jupyter notebooks to convert common file formats to Photon-HDF5.
For all the other languages, the easiest and most robust way of writing
Photon-HD5 files is using an ad-hoc script called phforge.
Try it Online!
To get a the taste of it, you can use the
online conversion service
to convert an existing data file (Becker Hickl SPC or PicoQuant HT3)
to Photon-HDF5. This service uses MyBinder.org to provide access to
the Jupyter Notebooks implementing the file conversion.
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