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You're reading the documentation for a development version (master). For the latest released version, please have a look at v1.7.

Citing NL-BIOMERO and BIOMERO

Thank you for citing the work that made NL-BIOMERO and BIOMERO possible. The appropriate paper depends on which part of the ecosystem your work uses.

Which paper should I cite?

  • NL-BIOMERO, BIOMERO 2.0, or the complete platform: cite the 2026 Journal of Microscopy paper. This paper describes the end-to-end infrastructure, including data import and preprocessing with BIOMERO.importer, analysis, provenance, and the integrated OMERO experience.

  • The BIOMERO Python library or HPC analysis framework: cite the 2024 Patterns paper. This paper describes the scalable workflow-execution framework connecting OMERO, FAIR workflows, and Slurm/HPC resources.

  • Work that relies substantially on both layers: citing both papers gives readers the clearest account of the complete system and its core analysis framework.

BIOMERO 2.0 / NL-BIOMERO

Luik, T. T., de Folter, J., Rosas-Bertolini, R., Reits, E. A. J., Hoebe, R. A., & Krawczyk, P. M. (2026). BIOMERO 2.0: End-to-end FAIR infrastructure for bioimaging data import, analysis, and provenance. Journal of Microscopy. https://doi.org/10.1111/jmi.70114

@article{Luik2026BIOMERO2,
  author  = {Luik, Torec T. and de Folter, Joost and Rosas-Bertolini, Rodrigo and Reits, Eric A. J. and Hoebe, Ron A. and Krawczyk, Przemek M.},
  title   = {BIOMERO 2.0: End-to-end FAIR infrastructure for bioimaging data import, analysis, and provenance},
  journal = {Journal of Microscopy},
  year    = {2026},
  doi     = {10.1111/jmi.70114},
  url     = {https://doi.org/10.1111/jmi.70114}
}

BIOMERO analysis framework

Luik, T. T., Rosas-Bertolini, R., Reits, E. A. J., Hoebe, R. A., & Krawczyk, P. M. (2024). BIOMERO: A scalable and extensible image analysis framework. Patterns, 5(8), 101024. https://doi.org/10.1016/j.patter.2024.101024

@article{Luik2024BIOMERO,
  author  = {Luik, Torec T. and Rosas-Bertolini, Rodrigo and Reits, Eric A. J. and Hoebe, Ron A. and Krawczyk, Przemek M.},
  title   = {BIOMERO: A scalable and extensible image analysis framework},
  journal = {Patterns},
  volume  = {5},
  number  = {8},
  pages   = {101024},
  year    = {2024},
  doi     = {10.1016/j.patter.2024.101024},
  url     = {https://doi.org/10.1016/j.patter.2024.101024}
}

Software citation metadata

The repository also provides machine-readable citation metadata in CITATION.cff. Please report the NL-BIOMERO version and the relevant workflow and container versions in methods and data-provenance records.