Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1783608997562023936 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7660398 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT rubensulysse biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT mormontromain biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT paavolainenlassi biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT backervolker biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT paviebenjamin biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT scholzleandroa biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT michielsgino biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT maskamartin biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT unaydevrim biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT ballgraeme biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT hoyouxrenaud biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT vandaeleremy biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT golaniofra biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT stanciustefang biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT sladojenatasa biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT paulgilloteauxperrine biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT mareeraphael biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows AT tosisebastien biaflowsacollaborativeframeworktoreproduciblydeployandbenchmarkbioimageanalysisworkflows |