1. Quick-start: View Files

To open and export data from example Photon-HDF5 files install the HDF5 viewer HDFView and download the example Photon-HDF5 data files.

2. Quick-start: Convert Files

To convert files from other formats (HT3, SPC) to Photon-HDF5 use phconvert.

Welcome to Photon-HDF5 Project

Latest News

We are currently working on the next Photon-HDF5 version (0.5) which will support many more measurement types. This is a good time for proposing new features. You are more than welcome to partecipate or follow us using GitHub Issues:


Photon-HDF5 is a file format designed to store data from freely-diffusing single-molecule spectroscopy experiments, single-molecule FRET (smFRET) (with or without lifetime), Fluorescence Correlation Spectroscopy (FCS) and related photon-counting techniques.

Photon-HDF5 is not limited to fluorescence-based techinues. Any dataset containing photon timestamps and other per-photon data can be stored using the Photon-HDF5 format. Photon-HDF5 can store important experimental details and metadata (setup configurations, sample information, authorship and provenance) to make the file suitable for long-term preservation and data sharing.

The Photon-HDF5 format defines a conventional structure in HDF5 files for a wide variety of timestamp-based spectroscopy data (single-molecule techniques being the initial focus). We provide detailed format description, examples to read Photon-HDF5 in multiple languages and a reference python library to create and convert Photon-HDF5 files.

Project Resources

Documentation & Papers


Contacts and Troubleshooting

For questions about the Photon-HDF5 format please use the Photon-HDF5 google group.

For bug reports or enhancements to the supporting software please open a GitHub Issue at the following links:

GitHub issues for phconvert (software to write and convert Photon-HDF5 files). GitHub issues for code examples on reading Photon-HDF5 files.

Software supporting Photon-HDF5

Software supporting Photon-HDF5 for reading or writing:

If you would like to add other software to this list please contact us.


This work was supported by NIH Grant R01-GM95904.