pynxtools: A Python framework for generating and validating NeXus files in experimental data workflows
Shabih S, Pielsticker L, Dobener F, Albino A, Chang T, Emminger C, Ginzburg L, Hildebrandt R, Kühbach M, Mozumder R, Pincelli T, Aeschlimann M, Grundmann M, Hetaba W, Palma CA, Rettig L, Scheidgen M, Brockhauser S, Márquez Prieto JA, Draxl C, Koch CT, Weber HB (2026)
Publication Type: Journal article
Publication year: 2026
Journal
Original Authors: Sherjeel Shabih, Lukas Pielsticker, Florian Dobener, Andrea Albino, Theodore Chang, Carola Emminger, Lev Ginzburg, Ron Hildebrandt, Markus Kühbach, Rubel Mozumder, Tommaso Pincelli, Martin Aeschlimann, Marius Grundmann, Walid Hetaba, Carlos-Andres Palma, Laurenz Rettig, Markus Scheidgen, Sandor Brockhauser, José Antonio Márquez Prieto, Claudia Draxl, Christoph T. Koch, Heiko B. Weber
Book Volume: 11
Issue: 126
DOI: 10.21105/joss.10691
Abstract
Scientific data across physics, materials science, and materials engineering often lacks adherence to FAIR principles (Barker et al., 2022; Jacobsen et al., 2020; M. D. Wilkinson et al., 2016; S. R. Wilkinson et al., 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 to the NeXus format (Klosowski et al., 1997; Könnecke, 2006; Könnecke et al., 2015) across diverse scientific domains including atom probe tomography, electron microscopy, optical spectroscopy, photoemission spectroscopy, scanning probe microscopy, and X-ray diffraction. Through its modular plugin architecture, pynxtools converts data and metadata from instruments and electronic lab notebooks to unified NeXus application definitions, which are standardized schemas that specify how data and metadata for a particular type of experiment are organized within NeXus, while performing automated validation to ensure compliance. The framework is deployed in production as part of the NOMAD (Draxl & Scheffler, 2019; Scheidgen et al., 2023) research data management platform and is used across multiple NOMAD Oasis installations in experimental laboratories, by external Python packages, and in dataset publications on Zenodo.
Authors with CRIS profile
Involved external institutions
Universität Leipzig
Germany (DE)
Humboldt-Universität zu Berlin
Germany (DE)
Max-Planck-Institut für Eisenforschung GmbH (MPIE) / Max Planck Institute for Iron Research
Germany (DE)
Chinese Academy of Sciences (CAS) / 中国科学院
China (CN)
Fritz-Haber-Institut der Max-Planck-Gesellschaft (FHI)
Germany (DE)
Germany (DE)
Humboldt-Universität zu Berlin
Germany (DE)
Max-Planck-Institut für Eisenforschung GmbH (MPIE) / Max Planck Institute for Iron Research
Germany (DE)
Chinese Academy of Sciences (CAS) / 中国科学院
China (CN)
Fritz-Haber-Institut der Max-Planck-Gesellschaft (FHI)
Germany (DE)
How to cite
APA:
Shabih, S., Pielsticker, L., Dobener, F., Albino, A., Chang, .T., Emminger, C.,... Weber, H.B. (2026). pynxtools: A Python framework for generating and validating NeXus files in experimental data workflows. Journal of Open Source Software, 11. https://doi.org/10.21105/joss.10691
MLA:
Shabih, Sherjeel, et al. "pynxtools: A Python framework for generating and validating NeXus files in experimental data workflows." Journal of Open Source Software 11 (2026).
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