A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format
A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format
复制标题
一个用户友好的工具，可将光子计数数据转换为开源 Photon-HDF5 文件格式
DOI：
10.1117/12.2608487
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Michalet, Xavier
中科院分区：
文献类型：
--
作者：
Ferschweiler, Donald;Segal, Maya;Weiss, Shimon;Michalet, Xavier
Photon-HDF5是一种开源和开放的文件格式，用于存储来自单分子显微镜实验的光子计数数据，旨在简化数据交换并提高数据分析的可重复性。phconvert是Photon-HDF5生态系统的一部分，它是一个可扩展的python库，允许将专有格式转换为Photon-HDF5文件。但是，使用它需要对命令行指令、python编程语言和YAML标记格式有一定的熟练程度。这给那些没有专业知识，但又想从以开放格式发布文件的优势中获益的潜在用户造成了很大的障碍。在这项工作中，我们提出了一个GUI，降低了这个障碍，从而简化了Photon-HDF5的使用。该工具使用phconvert python库将原来以专有数据格式保存的数据文件转换为Photon-HDF5文件，而无需用户编写一行代码。由于可重复分析依赖于基本的实验信息，例如激光功率或样本描述，因此GUI还包括（目前有限的）将有效元数据与转换文件关联起来的功能，而无需编写任何YAML。最后，GUI包括几个提高生产力的特性，例如全目录批处理转换和重新运行失败的批处理的能力，只转换在前一次运行中无法转换的文件。
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5 ecosystem, is phconvert, an extensible python library that allows converting proprietary formats into Photon-HDF5 files. However, its use requires some proficiency with command line instructions, the python programming language, and the YAML markup format. This creates a significant barrier for potential users without that expertise, but who want to benefit from the advantages of releasing their files in an open format. In this work, we present a GUI that lowers this barrier, thus simplifying the use of Photon-HDF5. This tool uses the phconvert python library to convert data files originally saved in proprietary data formats to Photon-HDF5 files, without users having to write a single line of code. Because reproducible analyses depend on essential experimental information, such as laser power or sample description, the GUI also includes (currently limited) functionality to associate valid metadata with the converted file, without having to write any YAML. Finally, the GUI includes several productivity-enhancing features such as whole-directory batch conversion and the ability to re-run a failed batch, only converting the files that could not be converted in the previous run.
FRETBursts：用于分析自由扩散单分子 FRET 的开源工具包
影响因子：
3.7
作者：
Antonino Ingargiola;E. Lerner;SangYoon Chung;S. Weiss;X. Michalet
通讯作者：
X. Michalet