Photon-HDF5: Open data format and computational tools for timestamp-based single-molecule experiments

Antonino Ingargiola, Ted Laurence, Robert Boutelle, Shimon Weiss, Xavier Michalet

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

5 Scopus citations


Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (, an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon- HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon- HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon- HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Original languageEnglish
Title of host publicationSingle Molecule Spectroscopy and Superresolution Imaging IX
EditorsJorg Enderlein, Ingo Gregor, Zygmunt Karol Gryczynski, Rainer Erdmann, Felix Koberling
ISBN (Electronic)9781628419481
StatePublished - 13 Feb 2016
Externally publishedYes
EventSingle Molecule Spectroscopy and Superresolution Imaging IX - San Francisco, United States
Duration: 13 Feb 201614 Feb 2016

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceSingle Molecule Spectroscopy and Superresolution Imaging IX
Country/TerritoryUnited States
CitySan Francisco

Bibliographical note

Funding Information:
We thank Dr. Sangyoon Chung and Dr. Eitan Lerner for providing experimental data files. This work was supported in part by NIH Grant R01-GM95904 and by DOE Grant DE-FC02-02ER63421-00. Dr. Weiss discloses equity in Nesher Technologies and intellectual property used in the research reported here. The work at UCLA was conducted in Dr. Weiss's Laboratory. Dr. Laurence's work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Publisher Copyright:
© 2016 SPIE.


  • FCS
  • FRET
  • File format
  • HDF5
  • SPAD
  • open data
  • single-molecule
  • uorescence


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