ArticleBiophysical journal2016
Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed.
- Benchmarking dynamic analysis methods in diffusion-based single-molecule FRET.Cell reports methods · 2026Article
- BLeaching In-cell Single-molecule burstS (BLISS) reveals a small dynamic fraction of HP1α clusters in undifferentiated embryonic stem cells.bioRxiv : the preprint server for biology · 2026Article
- Single-Molecule Forster Resonance Energy Transfer With a Minimalistic 3D-Printed Setup and Dyes in the Blue-Green Spectral Region.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- How SecB maintains clients in a translocation competent state.Communications biology · 2025Article
- Single-molecule visualization of ATP-induced dynamics of the subunit composition of an ECF transporter complex under turnover conditions.Nature communications · 2025Article
- tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.Bioinformatics (Oxford, England) · 2025Article
- The Research Progress of Single-Molecule Sequencing and Its Significance in Nucleic Acid Metrology.Biosensors · 2024Review
- The substrate-binding domains of the osmoregulatory ABC importer OpuA transiently interact.eLife · 2024Article
- Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores.eLife · 2024Article
- Structural and dynamic insights into α-synuclein dimer conformations.Structure (London, England : 1993) · 2023Article
- Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy.The journal of physical chemistry. B · 2022Article
- Multi-parameter photon-by-photon hidden Markov modeling.Nature communications · 2022Article
- The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds.Structure (London, England : 1993) · 2021Article
- FRETboard: Semisupervised classification of FRET traces.Biophysical journal · 2021Article
- Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One α-Synuclein Monomer at a Time.Journal of visualized experiments : JoVE · 2021Article
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs.Communications biology · 2020Article
- Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients.Nature communications · 2020Article
- High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins.Methods (San Diego, Calif.) · 2019Article
- Systematic Assessment of Burst Impurity in Confocal-Based Single-Molecule Fluorescence Detection Using Brownian Motion Simulations.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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, photomultiplier tube, 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. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.