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:
Description
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 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 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
- 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.
Software
- Reading Photon-HDF5 in multiple languages
- phconvert: a library to create and convert Photon-HDF5 files
- phforge: a 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 diffusion-based smFRET (read support).
- PyBroMo confocal smFRET simulator (write support).
- ALiX: smFRET analysis and more (read support).
If you would like to add other software to this list please contact us.
Acknowledgements
This work was supported by NIH Grant R01-GM95904.