Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

Journal Article · Wed Dec 23 00:00:00 EST 2015 · Biophysical Journal

DOI:https://doi.org/10.1101/026484· OSTI ID:1399723

Ingargiola, A. ^[1]; Laurence, T. A. ^[2]; Boutelle, R. ^[1]; Weiss, S. ^[1]; Michalet, X. ^[1]

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1. Univ. of California, Los Angeles, CA (United States)
2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

• Research Organization: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE
• Grant/Contract Number: AC52-07NA27344
• OSTI ID: 1399723
• Report Number(s): LLNL-JRNL-736685
• Journal Information: Biophysical Journal, Vol. 110, Issue 1; ISSN 0006-3495
• Publisher: Elsevier
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES