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BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows

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 an...

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Autores principales: Rubens, Ulysse, Mormont, Romain, Paavolainen, Lassi, Bäcker, Volker, Pavie, Benjamin, Scholz, Leandro A., Michiels, Gino, Maška, Martin, Ünay, Devrim, Ball, Graeme, Hoyoux, Renaud, Vandaele, Rémy, Golani, Ofra, Stanciu, Stefan G., Sladoje, Natasa, Paul-Gilloteaux, Perrine, Marée, Raphaël, Tosi, Sébastien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660398/
https://www.ncbi.nlm.nih.gov/pubmed/33205108
http://dx.doi.org/10.1016/j.patter.2020.100040
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author Rubens, Ulysse
Mormont, Romain
Paavolainen, Lassi
Bäcker, Volker
Pavie, Benjamin
Scholz, Leandro A.
Michiels, Gino
Maška, Martin
Ünay, Devrim
Ball, Graeme
Hoyoux, Renaud
Vandaele, Rémy
Golani, Ofra
Stanciu, Stefan G.
Sladoje, Natasa
Paul-Gilloteaux, Perrine
Marée, Raphaël
Tosi, Sébastien
author_facet Rubens, Ulysse
Mormont, Romain
Paavolainen, Lassi
Bäcker, Volker
Pavie, Benjamin
Scholz, Leandro A.
Michiels, Gino
Maška, Martin
Ünay, Devrim
Ball, Graeme
Hoyoux, Renaud
Vandaele, Rémy
Golani, Ofra
Stanciu, Stefan G.
Sladoje, Natasa
Paul-Gilloteaux, Perrine
Marée, Raphaël
Tosi, Sébastien
author_sort Rubens, Ulysse
collection PubMed
description 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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spelling pubmed-76603982020-11-16 BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows Rubens, Ulysse Mormont, Romain Paavolainen, Lassi Bäcker, Volker Pavie, Benjamin Scholz, Leandro A. Michiels, Gino Maška, Martin Ünay, Devrim Ball, Graeme Hoyoux, Renaud Vandaele, Rémy Golani, Ofra Stanciu, Stefan G. Sladoje, Natasa Paul-Gilloteaux, Perrine Marée, Raphaël Tosi, Sébastien Patterns (N Y) Descriptor 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. Elsevier 2020-06-03 /pmc/articles/PMC7660398/ /pubmed/33205108 http://dx.doi.org/10.1016/j.patter.2020.100040 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Descriptor
Rubens, Ulysse
Mormont, Romain
Paavolainen, Lassi
Bäcker, Volker
Pavie, Benjamin
Scholz, Leandro A.
Michiels, Gino
Maška, Martin
Ünay, Devrim
Ball, Graeme
Hoyoux, Renaud
Vandaele, Rémy
Golani, Ofra
Stanciu, Stefan G.
Sladoje, Natasa
Paul-Gilloteaux, Perrine
Marée, Raphaël
Tosi, Sébastien
BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title_full BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title_fullStr BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title_full_unstemmed BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title_short BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
title_sort biaflows: a collaborative framework to reproducibly deploy and benchmark bioimage analysis workflows
topic Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660398/
https://www.ncbi.nlm.nih.gov/pubmed/33205108
http://dx.doi.org/10.1016/j.patter.2020.100040
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