Skip to Main content Skip to Navigation
Journal articles

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

Abstract : Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows. The emergence of "big data” in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.
Complete list of metadata

http://hal.univ-nantes.fr/hal-03208600
Contributor : Perrine Paul-Gilloteaux <>
Submitted on : Monday, April 26, 2021 - 4:34:40 PM
Last modification on : Tuesday, April 27, 2021 - 3:34:55 AM

Links full text

Identifiers

Collections

Citation

Perrine Paul-Gilloteaux, Sébastien Tosi, Jean-Karim Hériché, Alban Gaignard, Hervé Ménager, et al.. Bioimage analysis workflows: community resources to navigate through a complex ecosystem. F1000Research, Faculty of 1000, 2021, 10, pp.320. ⟨10.12688/f1000research.52569.1⟩. ⟨hal-03208600⟩

Share

Metrics

Record views

14