Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Data

Abstract

During the past 20 years, an ever-growing number of techniques for single-molecule fluorescence experiments have emerged. While camera-based experiments use tiff or raw binary formats for data storage, photon-counting-based experiments uses a plethora of setup-dependent custom file formats.This situation hinders the ability to reproduce published results, creates barriers to data sharing and collaborations between different groups.Moreover, in light of the recent push by most funding agencies and scientific journals toward mandatory data sharing, the need for a common, general-purpose file format for publication and long term archival becomes even more pressing.Enters Photon-HDF5, an open file format for the diverse pool of timestamp-based single-molecule fluorescence experiments. Photon-HDF5 (www.photon-hdf5.org) is open, language- and platform-independent and based on the highly successful HDF5 format. Each data field in a Photon-HDF5 file has a self-contained description that can be accessed with user-friendly HDF5 viewers such as HDFView, making the format self-describing. A growing number of custom file formats can be converted to Photon-HDF5 using the accompanying utility phconvert (http://photon-hdf5.github.io/phconvert). Photon-HDF5 allows minimizing the efforts needed to support data from different setups and lowers the barriers for sharing data between different software and research groups. At the same time, the rich set of metadata makes Photon-HDF5 ideal for sharing and long-term archival.Both Photon-HDF5 specifications and supporting tools are openly developed on GitHub and available for review and contributions from everyone. We publish detailed format specifications together with examples for reading Photon-HDF5 in all the major programming languages. Moreover, we provide a reference library, phconvert, to help writing compliant Photon-HDF5 files. We encourage interested scientists to join the effort of making Photon-HDF5 a useful tool for the single-molecule community at large.