Photon-HDF5 file format documentation¶
|Authors:||Antonino Ingargiola, Xavier Michalet, Ted Laurence|
|Contact:||Photon-HDF5 Google Group|
This is the reference documentation for Photon-HDF5 (homepage), a file format for timestamp-based single-molecule spectroscopy experiments such as single-molecule FRET (smFRET) (with or without lifetime), Fluorescence Correlation Spectroscopy (FCS) and other 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 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 (see also Photon-HDF5 Homepage):
- Example Photon-HDF5 data files, view them with HDFView.
- Code examples of reading Photon-HDF5 files in multiple languages
- phconvert: reference library to create and convert Photon-HDF5 files
- Biophysical Journal (2016), Photon-HDF5: an open file format for timestamp-based single-molecule fluorescence experiments (BioRxiv manuscript).
- Photon-HDF5 Online Converter
Table of Contents¶
- 1. Introduction
- 2. Photon-HDF5 format definition
- 3. What will change in version 0.5
- 4. Reading Photon-HDF5 files
- 5. Writing Photon-HDF5 files
- 6. Defining new measurement types
- 7. Known Limitations
- 8. Collaborating