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CITATION.cff
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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'BIOMERO: BioImage analysis in OMERO'
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Torec Tom
family-names: Luik
email: t.t.luik@amsterdamumc.nl
affiliation: Amsterdam UMC
orcid: 'https://orcid.org/0009-0007-9361-0586'
- given-names: Rodrigo
family-names: Rosas-Bertolini
affiliation: Amsterdam UMC
- given-names: Eric A.J.
family-names: Reits
affiliation: Amsterdam UMC
- given-names: Ron A.
family-names: Hoebe
affiliation: Amsterdam UMC
- given-names: Przemek M.
family-names: Krawczyk
affiliation: Amsterdam UMC
identifiers:
- type: url
value: 'https://arxiv.org/abs/2402.00734'
description: Preprint on arxiv
- type: doi
value: 10.5281/zenodo.8108214
description: ZENODO DOI for all versions
repository-code: 'https://github.com/NL-BioImaging/biomero'
url: 'https://nl-bioimaging.github.io/biomero/'
repository: 'https://github.com/NL-BioImaging/biomero-scripts'
repository-artifact: 'https://pypi.org/project/biomero/'
abstract: >-
In the rapidly evolving field of bioimaging, the
integration and orchestration of Findable, Accessible,
Interoperable, and Reusable (FAIR) image analysis
workflows remains a challenge. We introduce BIOMERO, a
bridge connecting OMERO, a renowned bioimaging data
management platform, FAIR workflows and high-performance
computing (HPC) environments. BIOMERO, featuring our
opensource Python library "OMERO Slurm Client",
facilitates seamless execution of FAIR workflows,
particularly for large datasets from High Content or High
Throughput Screening. BIOMERO empowers researchers by
eliminating the need for specialized knowledge, enabling
scalable image processing directly from OMERO. BIOMERO
notably supports the sharing and utilization of FAIR
workflows between OMERO, Cytomine/BIAFLOWS, and other
bioimaging communities. BIOMERO will promote the
widespread adoption of FAIR workflows, emphasizing
reusability, across the realm of bioimaging research. Its
user-friendly interface will empower users, including
those without technical expertise, to seamlessly apply
these workflows to their datasets, democratizing the
utilization of AI by the broader research community.
keywords:
- python
- omero
- slurm
- high-performance-computing
- fair
- image-analysis
- bioimaging
- cytomine
- biomero
- biaflows
- high-throughput-screening
- high-content-screening
license: Apache-2.0