BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows

Ulysse Rubens° , Romain Mormont° , Volker Baecker , Gino Michiels , Lassi Paavolainen , Graeme Ball , Devrim Ünay (1) , Benjamin Pavie , Anatole Chessel (2) , Leandro A Scholz , Martin Maška (3) , Renaud Hoyoux , Rémy Vandaele (4) , Stefan G Stanciu , Ofra Golani , Natasa Sladoje , Perrine Paul-Gilloteaux (5) , Raphaël Marée (6) , Sébastien Tosi

1 Biomedical Engineering [Istanbul]
2 PICT-IBiSA - BioImaging Cell and Tissue Core Facility
3 MUNI - Masaryk University [Brno]
4 Institut Montefiore - Département d'Electricité, Electronique et Informatique (Liège)
5 SFR François Bonamy - Structure fédérative de recherche François Bonamy
6 Institut Montefiore - Department of Electrical Engineering and Computer Science

Automated image analysis has become key to extract quantitative information from microscopy images, however the methods involved are now often so complex that they can no longer be unambiguously described using written protocols. We introduce BIAFLOWS, a web based framework to encapsulate, reproducibly deploy, and benchmark automated bioimage analysis workflows. BIAFLOWS helps diffusing and fairly comparing image analysis methods, hence safeguarding research based on their results by enforcing highest quality standards. All rights reserved. No reuse allowed without permission. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the praeprint in perpetuity.

Domaines: Traitement des images [eess.IV]; Vision par ordinateur et reconnaissance de formes [cs.CV]; Imagerie; Performance et fiabilité [cs.PF]; Base de données [cs.DB]

Ulysse Rubens°, Romain Mormont°, Volker Baecker, Gino Michiels, Lassi Paavolainen, et al.. BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows. 2019. ⟨hal-02267577⟩