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

2015 ◽  
Author(s):  
Antonino Ingargiola ◽  
Ted Laurence ◽  
Robert Boutelle ◽  
Shimon Weiss ◽  
Xavier Michalet
Keyword(s):  
Programming Languages ◽  
Single Molecule ◽  
Single Photon ◽  
Photon Counting ◽  
File Format ◽  
Single Molecule Fluorescence ◽  
File Formats ◽  
Photon Counting Detectors ◽  
User Friendly

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. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

scholarly journals Development of new photon-counting detectors for single-molecule fluorescence microscopy

2013 ◽  
Vol 368 (1611) ◽  
pp. 20120035 ◽  
Author(s):  
X. Michalet ◽  
R. A. Colyer ◽  
G. Scalia ◽  
A. Ingargiola ◽  
R. Lin ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Single Molecule ◽  
Single Photon ◽  
Photon Counting ◽  
Wide Field ◽  
Fluorescence Lifetime Imaging ◽  
Large Area ◽  
Single Molecule Fluorescence ◽  
Single Photon Counting ◽  
Single Molecule Fluorescence Microscopy

Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level.

scholarly journals Low-Light Photodetectors for Fluorescence Microscopy

2021 ◽  
Vol 11 (6) ◽  
pp. 2773
Author(s):  
Hiroaki Yokota ◽  
Atsuhito Fukasawa ◽  
Minako Hirano ◽  
Toru Ide
Keyword(s):  
Fluorescence Microscopy ◽  
Fluorescence Imaging ◽  
Single Molecule ◽  
Science Studies ◽  
Single Photon ◽  
Laser Scanning Microscopy ◽  
Oxide Semiconductor ◽  
Wide Field ◽  
Single Molecule Fluorescence ◽  
Low Light

Over the years, fluorescence microscopy has evolved and has become a necessary element of life science studies. Microscopy has elucidated biological processes in live cells and organisms, and also enabled tracking of biomolecules in real time. Development of highly sensitive photodetectors and light sources, in addition to the evolution of various illumination methods and fluorophores, has helped microscopy acquire single-molecule fluorescence sensitivity, enabling single-molecule fluorescence imaging and detection. Low-light photodetectors used in microscopy are classified into two categories: point photodetectors and wide-field photodetectors. Although point photodetectors, notably photomultiplier tubes (PMTs), have been commonly used in laser scanning microscopy (LSM) with a confocal illumination setup, wide-field photodetectors, such as electron-multiplying charge-coupled devices (EMCCDs) and scientific complementary metal-oxide-semiconductor (sCMOS) cameras have been used in fluorescence imaging. This review focuses on the former low-light point photodetectors and presents their fluorescence microscopy applications and recent progress. These photodetectors include conventional PMTs, single photon avalanche diodes (SPADs), hybrid photodetectors (HPDs), in addition to newly emerging photodetectors, such as silicon photomultipliers (SiPMs) (also known as multi-pixel photon counters (MPPCs)) and superconducting nanowire single photon detectors (SSPDs). In particular, this review shows distinctive features of HPD and application of HPD to wide-field single-molecule fluorescence detection.

Digital File Formats for Digital Preservation

2018 ◽  
pp. 218-233
Author(s):  
Mayank Yuvaraj
Keyword(s):  
Digital Libraries ◽  
Digital Preservation ◽  
Institutional Repository ◽  
File Format ◽  
Institutional Repositories ◽  
File Formats ◽  
Digital File ◽  
The Common ◽  
Common Understanding

During the course of planning an institutional repository, digital library collections or digital preservation service it is inevitable to draft file format policies in order to ensure long term digital preservation, its accessibility and compatibility. Sincere efforts have been made to encourage the adoption of standard formats yet the digital preservation policies vary from library to library. The present paper is based against this background to present the digital preservation community with a common understanding of the common file formats used in the digital libraries or institutional repositories. The paper discusses both open and proprietary file formats for several media.

scholarly journals Photonic Readout of Superconducting Nanowire Single Photon Counting Detectors

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marc de Cea ◽  
Emma E. Wollman ◽  
Amir H. Atabaki ◽  
Dodd J. Gray ◽  
Matthew D. Shaw ◽  
...  
Keyword(s):  
Single Photon ◽  
Photon Counting ◽  
Single Photon Counting ◽  
Photon Counting Detectors ◽  
Superconducting Nanowire
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