Ingargiola Antonino, Laurence Ted, Boutelle Robert, Weiss Shimon, Michalet Xavier
Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California.
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
Biophys J. 2016 Jan 5;110(1):26-33. doi: 10.1016/j.bpj.2015.11.013.
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.
我们引入了Photon-HDF5，这是一种开放且高效的文件格式，用于简化基于单光子雪崩二极管、光电倍增管或此类探测器阵列等光子计数探测器的单分子荧光实验数据的交换和长期可访问性。该格式基于HDF5，这是一种广泛使用的与平台和语言无关的分层文件格式，有用户友好的查看器可用。Photon-HDF5可以存储来自任何采集硬件的原始光子数据（时间戳、通道号等），还可以存储设置和样本描述、出处、作者信息及其他元数据，并且足够灵活以包含任何类型的自定义数据。格式规范托管在一个公共网站上，该网站向生物物理学界开放以供贡献。作为初始资源，该网站提供了用几种编程语言读取Photon-HDF5文件的代码示例以及一个参考Python库（phconvert），用于创建新的Photon-HDF5文件并将几种现有文件格式转换为Photon-HDF5。为鼓励学术界和商业界采用，所有软件均根据麻省理工学院开源许可发布。
