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

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.
Authors:
 [1] ;  [2] ;  [1] ;  [1] ;  [1]
  1. Univ. of California, Los Angeles, CA (United States)
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Report Number(s):
LLNL-JRNL-736685
Journal ID: ISSN 0006-3495
Grant/Contract Number:
AC52-07NA27344
Type:
Accepted Manuscript
Journal Name:
Biophysical Journal
Additional Journal Information:
Journal Volume: 110; Journal Issue: 1; Journal ID: ISSN 0006-3495
Publisher:
Elsevier
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1399723