Photon-HDF5 file format documentation

Authors:Antonino Ingargiola, Xavier Michalet, Ted Laurence

Photon-HDF5 is a file format for freely diffusing single-molecule spectroscopy experiments such as single-molecule FRET (smFRET) (with or without lifetime), Fluorescence Correlation Spectroscopy (FCS) and 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 therefore 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 are:


This document describes Photon-HDF5 version 0.3. The latest version of this document can be found at To send correction or getting involved in the file format development please see the contributing section.