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 <https://doi.org/10.1016/j.patter.2024.101024>`_

.. code-block:: bibtex

   @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 <https://doi.org/10.1111/jmi.70114>`_

.. code-block:: bibtex

   @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 <https://github.com/NL-BioImaging/biomero/blob/main/CITATION.cff>`_.
For reproducibility, also report the BIOMERO version used. The software archive
DOI for all BIOMERO versions is
`10.5281/zenodo.8108214 <https://doi.org/10.5281/zenodo.8108214>`_.