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:
- Examples of reading Photon-HDF5 files in multiple languages
- phconvert: reference library to create and convert Photon-HDF5 files
- Why an HDF5-based smFRET file format
- Photon-HDF5: an open format for single-molecule spectroscopy using photon-counting devices (coming soon).
This document describes Photon-HDF5 version 0.3. The latest version of this document can be found at http://photon-hdf5.readthedocs.org. To send correction or getting involved in the file format development please see the contributing section.
Table of contents¶
- 1. Introduction
- 2. Photon-HDF5 format definition
- 2.1. Overview
- 2.2. Root-level parameters
- 2.3. Photon-data group
- 2.4. Setup group
- 2.5. Identity group
- 2.6. Provenance group
- 2.7. Sample group
- 2.8. Additional notes and definitions
- 3. Known Limitations
- 4. Collaborating