BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
Ulysse Rubens,
Romain Mormont,
Lassi Paavolainen,
Volker Bäcker,
Benjamin Pavie,
Leandro A. Scholz,
Gino Michiels,
Martin Maška,
Devrim Ünay,
Graeme Ball,
Renaud Hoyoux,
Rémy Vandaele,
Ofra Golani,
Stefan G. Stanciu,
Natasa Sladoje,
Perrine Paul-Gilloteaux,
Raphaël Marée,
Sébastien Tosi
Affiliations
Ulysse Rubens
Montefiore Institute, University of Liège, 4000 Liège, Belgium
Romain Mormont
Montefiore Institute, University of Liège, 4000 Liège, Belgium
Lassi Paavolainen
FIMM, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
Volker Bäcker
MRI, BioCampus Montpellier, Montpellier 34094, France
Benjamin Pavie
VIB BioImaging Core, 3000 Leuven, Belgium
Leandro A. Scholz
Universidade Federal do Paraná, Curitiba 80060-000, Brazil
Gino Michiels
HEPL, University of Liège, 4000 Liège, Belgium
Martin Maška
Masaryk University, 601 77 Brno, Czech Republic
Devrim Ünay
Faculty of Engineering İzmir, Demokrasi University, 35330 Balçova, Turkey
Graeme Ball
Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
Renaud Hoyoux
Cytomine SCRL FS, 4000 Liège, Belgium
Rémy Vandaele
Montefiore Institute, University of Liège, 4000 Liège, Belgium
Ofra Golani
Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
Stefan G. Stanciu
Politehnica Bucarest, Bucarest 060042, Romania
Natasa Sladoje
Uppsala University, P.O. Box 256, 751 05 Uppsala, Sweden
Perrine Paul-Gilloteaux
Structure Fédérative de Recherche François Bonamy, Université de Nantes, CNRS, INSERM, Nantes Cedex 1 13522 44035, France
Raphaël Marée
Montefiore Institute, University of Liège, 4000 Liège, Belgium
Sébastien Tosi
Institute for Research in Biomedicine, IRB Barcelona, Barcelona Institute of Science and Technology, BIST, 08028 Barcelona, Spain; Corresponding author
Summary: 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. The Bigger Picture: Image analysis is currently one of the major hurdles in the bioimaging chain, especially for large datasets. BIAFLOWS seeds the ground for virtual access to image analysis workflows running in high-performance computing environments. Providing a broader access to state-of-the-art image analysis is expected to have a strong impact on research in biology, and in other fields where image analysis is a critical step in extracting scientific results from images. BIAFLOWS could also be adopted as a federated platform to publish microscopy images together with the workflows that were used to extract scientific data from these images. This is a milestone of open science that will help to accelerate scientific progress by fostering collaborative practices.
