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1 March 2016 Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments
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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.
Conference Presentation
© (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Antonino Ingargiola, Ted Laurence, Robert Boutelle, Shimon Weiss, and Xavier Michalet "Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments", Proc. SPIE 9714, Single Molecule Spectroscopy and Superresolution Imaging IX, 971405 (1 March 2016);

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