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arXiv · 2203.10179

A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format

Donald Ferschweiler·Maya Segal·Shimon Weiss·Xavier Michalet
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Abstract

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.

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Donald Ferschweiler, Maya Segal, Shimon Weiss, Xavier Michalet. 2022-03-18. A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format. https://doi.org/10.1117/12.2608487

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