ArticlePatterns (New York, N.Y.)2020
BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
Article in Patterns (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Artificial intelligence-powered microscopy: Transforming the landscape of parasitology.Journal of microscopy · 2026Review
- The crucial role of bioimage analysts in scientific research and publication.Journal of cell science · 2024Article
- BIOMERO: A scalable and extensible image analysis framework.Patterns (New York, N.Y.) · 2024Article
- Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research.Microscopy (Oxford, England) · 2024Review
- Defining the boundaries: challenges and advances in identifying cells in microscopy images.Current opinion in biotechnology · 2024Review
- SciJava Ops: an improved algorithms framework for Fiji and beyond.Frontiers in bioinformatics · 2024Article
- Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species.Biomolecules · 2023Review
- ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification.Computer methods and programs in biomedicine · 2023Article
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- Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research.Frontiers in cellular and infection microbiology · 2022Review
- Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data.Nature communications · 2021Article
- Advances and opportunities in image analysis of bacterial cells and communities.FEMS microbiology reviews · 2021Article
- New Extensibility and Scripting Tools in the ImageJ Ecosystem.Current protocols · 2021Article
- Reproducible image handling and analysis.The EMBO journal · 2021Article
- Bioimage analysis workflows: community resources to navigate through a complex ecosystem.F1000Research · 2021Article
- SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells.GigaScience · 2020Article
- Open Practices and Resources for Collaborative Digital Pathology.Frontiers in medicine · 2019Review
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Image analysis is key to extracting quantitative information from scientific microscopy images, but the methods involved are now often so refined that they can no longer be unambiguously described by written protocols. We introduce BIAFLOWS, an open-source web tool enabling to reproducibly deploy and benchmark bioimage analysis workflows coming from any software ecosystem. A curated instance of BIAFLOWS populated with 34 image analysis workflows and 15 microscopy image datasets recapitulating common bioimage analysis problems is available online. The workflows can be launched and assessed remotely by comparing their performance visually and according to standard benchmark metrics. We illustrated these features by comparing seven nuclei segmentation workflows, including deep-learning methods. BIAFLOWS enables to benchmark and share bioimage analysis workflows, hence safeguarding research results and promoting high-quality standards in image analysis. The platform is thoroughly documented and ready to gather annotated microscopy datasets and workflows contributed by the bioimaging community.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.