Citing BIOMERO

Thank you for citing BIOMERO. This repository contains the BIOMERO Python library, also known as BIOMERO.analyzer. Its primary citation is the 2024 Patterns paper.

BIOMERO Python library and analysis framework

Use this citation for the Python library, BIOMERO.scripts integration, or the Slurm/HPC workflow-execution 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}
}

BIOMERO 2.0 and NL-BIOMERO

If your work uses the complete BIOMERO 2.0 platform—particularly NL-BIOMERO, BIOMERO.importer, integrated data import and preprocessing, or end-to-end provenance—cite the 2026 Journal of Microscopy paper. Work that relies substantially on both the full platform and the core analysis framework may cite both papers.

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}
}

Software citation metadata

Machine-readable metadata for the library’s preferred citation is available in CITATION.cff. For reproducibility, also report the BIOMERO version used. The software archive DOI for all BIOMERO versions is 10.5281/zenodo.8108214.