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Sherjeel Shabih
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Adds text to summary about usage
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# Summary
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Scientific data across physics, materials science, and materials engineering often lacks adherence to FAIR principles [@Wilkinson:2016; @Jacobsen:2020; @Barker:2022; @Wilkinson:2025] due to incompatible instrument-specific formats and diverse standardization practices. `pynxtools` is a Python software development framework with a command line interface (CLI) that standardizes data conversion for scientific experiments in materials science to the NeXus format [@Koennecke:2015; @Koennecke:2006; @Klosowski:1997] across diverse scientific domains. NeXus defines data storage specifications for different experimental techniques through application definitions. `pynxtools` provides a fixed, versioned set of NeXus application definitions that ensures convergence and alignment in data specifications across, among others, atom probe tomography, electron microscopy, optical spectroscopy, photoemission spectroscopy, scanning probe microscopy, and X-ray diffraction. Through its modular plugin architecture `pynxtools` provides conversion of data and metadata from instruments and electronic lab notebooks to these unified definitions, while performing validation to ensure data correctness and NeXus compliance. `pynxtools` can be integrated directly into Research Data Management Systems (RDMS) to facilitate parsing and normalization. We detail one example for the RDM system NOMAD. By simplifying the adoption of NeXus, the framework enables true data interoperability and FAIR data management across multiple experimental techniques.
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Scientific data across physics, materials science, and materials engineering often lacks adherence to FAIR principles [@Wilkinson:2016; @Jacobsen:2020; @Barker:2022; @Wilkinson:2025] due to incompatible instrument-specific formats and diverse standardization practices. `pynxtools` is a Python software development framework with a command line interface (CLI) that standardizes data conversion for scientific experiments in materials science to the NeXus format [@Koennecke:2015; @Koennecke:2006; @Klosowski:1997] across diverse scientific domains. NeXus defines data storage specifications for different experimental techniques through application definitions. `pynxtools` provides a fixed, versioned set of NeXus application definitions that ensures convergence and alignment in data specifications across, among others, atom probe tomography, electron microscopy, optical spectroscopy, photoemission spectroscopy, scanning probe microscopy, and X-ray diffraction. Through its modular plugin architecture `pynxtools` provides conversion of data and metadata from instruments and electronic lab notebooks to these unified definitions, while performing validation to ensure data correctness and NeXus compliance. `pynxtools` can be integrated directly into Research Data Management Systems (RDMS) to facilitate parsing and normalization. We detail one example for the RDM system NOMAD. By simplifying the adoption of NeXus, the framework enables true data interoperability and FAIR data management across multiple experimental techniques. `pynxtools` is deployed in production as part of the NOMAD research data management platform and is used across multiple NOMAD Oasis installations operated locally in experimental laboratories. It is also used by external Python packages for NeXus conversion and validation and has been applied in the publication of datasets on Zenodo.
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# Statement of need
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