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

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

doi:10.1016/j.bpj.2015.11.013

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

Full Record
Other Related Research

Authors:: Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

Publication Date:: Fri Jan 01 00:00:00 EST 2016

Sponsoring Org.:: USDOE

OSTI Identifier:: 1338258

Alternate Identifier(s):: OSTI ID: 1325276

Grant/Contract Number:: FC02-02ER63421-00; AC52-07NA27344

Resource Type:: Published Article

Journal Name:: Biophysical Journal

Additional Journal Information:: Journal Name: Biophysical Journal Journal Volume: 110 Journal Issue: 1; Journal ID: ISSN 0006-3495

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Ingargiola, Antonino, Laurence, Ted, Boutelle, Robert, Weiss, Shimon, and Michalet, Xavier. Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.  United States: N. p., 2016. 
Web.  doi:10.1016/j.bpj.2015.11.013.

Copy to clipboard


                    Ingargiola, Antonino, Laurence, Ted, Boutelle, Robert, Weiss, Shimon, & Michalet, Xavier. Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.  United States.  https://doi.org/10.1016/j.bpj.2015.11.013

Copy to clipboard


                    Ingargiola, Antonino, Laurence, Ted, Boutelle, Robert, Weiss, Shimon, and Michalet, Xavier. Fri .  
"Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments".  United States.  https://doi.org/10.1016/j.bpj.2015.11.013.

Copy to clipboard


                    
@article{osti_1338258,

  title        = {Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments},

  author       = {Ingargiola, Antonino and Laurence, Ted and Boutelle, Robert and Weiss, Shimon and Michalet, Xavier},

  abstractNote = {},

  doi          = {10.1016/j.bpj.2015.11.013},

  journal      = {Biophysical Journal},

  number       = 1,

  volume       = 110,

  place        = {United States},

  year         = {Fri Jan 01 00:00:00 EST 2016},

  month        = {Fri Jan 01 00:00:00 EST 2016}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1016/j.bpj.2015.11.013

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 24 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

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

Journal Article Ingargiola, A. ; Laurence, T. A. ; Boutelle, R. ; ... - Biophysical Journal

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. Themore »« less
https://doi.org/10.1101/026484

Full Text Available
Single-Photon Source for Quantum Information Based on Single Dye Molecule Fluorescence in Liquid Crystal Host

Conference Lukishova, S G ; Knox, R P ; Freivald, P ; ... - Molecular Crystals and Liquid Crystals

This paper describes a new application for liquid crystals: quantum information technology. A deterministically polarized single-photon source that efficiently produces photons exhibiting antibunching is a pivotal hardware element in absolutely secure quantum communication. Planar-aligned nematic liquid crystal hosts deterministically align the single dye molecules which produce deterministically polarized single (antibunched) photons. In addition, 1-D photonic bandgap cholesteric liquid crystals will increase single-photon source efficiency. The experiments and challenges in the observation of deterministically polarized fluorescence from single dye molecules in planar-aligned glassy nematic-liquid-crystal oligomer as well as photon antibunching in glassy cholesteric oligomer are described for the first time.
Multiple Independent File Parallel I/O with HDF5

Program Document Miller, M. C.

The HDF5 library has supported the I/O requirements of HPC codes at Lawrence Livermore National Labs (LLNL) since the late 90’s. In particular, HDF5 used in the Multiple Independent File (MIF) parallel I/O paradigm has supported LLNL code’s scalable I/O requirements and has recently been gainfully used at scales as large as O(10⁶) parallel tasks.
Influence of conformational changes in complex molecules on photon statistics of single molecule fluorescence

Journal Article Osad'ko, I S ; Moscow Pedagogical State University, 119991 Moscow ; Fedyanin, V V - Physical Review. A

A single complex molecule with conformational changes (conformations 0 and 2) is considered. When such a molecule is irradiated by cw-laser light it can randomly change the intensity or polarization of its fluorescence due to jumps from one conformation to another. In fact, the molecule manifests itself either like the 0-type or the 2-type emitter. An expression for the matrix s{sub {alpha}{beta}}(t) called the start-stop correlator (waiting time distribution) in which {alpha}=0,2 and {beta}=0,2 is derived. An expression for the matrix p{sub {alpha}{beta}}(t) called the full correlator is derived as well. It determines the density of the probability of findingmore »« less
https://doi.org/10.1103/PHYSREVA.83.063841
Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

Journal Article Hoffmann, A ; Kane, A ; Nettels, D ; ... - Proceedings of the National Academy of Sciences of the United States of America, na, na, December 21, 2006, pp. 105 - 110
Full Text Available

Similar Records