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BIAFLOWS :
BIAFLOWS : A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
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Rubens, Ulysse (author)
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Mormont, Romain (author)
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Paavolainen, Lassi (author)
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Bäcker, Volker (author)
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Pavie, Benjamin (author)
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Scholz, Leandro A (author)
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Michiels, Gino (author)
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Maška, Martin (author)
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Ünay, Devrim (author)
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Ball, Graeme (author)
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Hoyoux, Renaud (author)
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Vandaele, Rémy (author)
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Golani, Ofra (author)
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Stanciu, Stefan G (author)
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- Sladoje, Natasa (author)
- Uppsala universitet,Avdelningen för visuell information och interaktion,Bildanalys och människa-datorinteraktion
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Paul-Gilloteaux, Perrine (author)
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Marée, Raphaël (author)
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Tosi, Sébastien (author)
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(creator_code:org_t)
- Elsevier BV, 2020
- 2020
- English.
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In: Patterns (New York, N.Y.). - : Elsevier BV. - 2666-3899. ; 1:3
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https://uu.diva-port... (primary) (Raw object)
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Abstract
Subject headings
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- 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.
Subject headings
- TEKNIK OCH TEKNOLOGIER -- Medicinteknik -- Medicinsk bildbehandling (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Medical Engineering -- Medical Image Processing (hsv//eng)
Keyword
- benchmarking
- bioimaging
- community
- deep learning
- deployment
- image analysis
- reproducibility
- software
- web application
- Computerized Image Processing
- Datoriserad bildbehandling
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Rubens, Ulysse
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Mormont, Romain
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Paavolainen, Las ...
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Bäcker, Volker
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Pavie, Benjamin
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Scholz, Leandro ...
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show more...
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Michiels, Gino
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Maška, Martin
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Ünay, Devrim
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Ball, Graeme
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Hoyoux, Renaud
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Vandaele, Rémy
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Golani, Ofra
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Stanciu, Stefan ...
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Sladoje, Natasa
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Paul-Gilloteaux, ...
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Marée, Raphaël
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Tosi, Sébastien
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show less...
- About the subject
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Medical Engineer ...
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and Medical Image Pr ...
- Articles in the publication
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Patterns (New Yo ...
- By the university
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Uppsala University