Welcome to Photon-HDF5 Project
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 support for new types of setups or measurements. You can partecipate or follow us using the GitHub Issues:
What is Photon-HDF5?
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 techniques.
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 single-molecule spectroscopy data. 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.
Documentation & Papers:
- Photon-HDF5 Reference Documentation
- Photon-HDF5: an open file format for timestamp-based single-molecule fluorescence experiments. Biophysical Journal 110-1 (2016) or bioRxiv preprint.
- Reading Photon-HDF5 in multiple languages
- phconvert: library to create and convert Photon-HDF5 files
- phforge: script to create Photon-HDF5 files in any language
- Writing Photon-HDF5 in Python
- Writing Photon-HDF5 in LabVIEW
- Writing Photon-HDF5 in MATLAB
- Photon-HDF5 Project on GitHub
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:
- FRETBursts: burst analysis software for confocal smFRET (read support).
- PyBroMo: confocal smFRET simulator (write support).
If you would like to add other software to this list please contact us.
This work was supported by NIH Grant R01-GM95904.