Photon-HDF5 file format documentation

Authors:Antonino Ingargiola, Xavier Michalet, Ted Laurence


This document describes the version “0.2-Draft” of the Photon-HDF5 file format. The latest version of this document can be found at

Photon-HDF5 is a file format for a class of single-molecule spectroscopy experiments that requires storing photon stream data. A noteworthy example is represented by confocal single-molecule FRET (smFRET) experiments.

For a brief introduction on what the HDF5 format is about and why it is important for single-molecule data see Why an HDF5-based smFRET file format.


This specification is still a draft. Comments and suggestions (including typos fixes) are encouraged.