F-BIAS: Towards a distributed national core facility for bioimage analysis

Abstract

We discuss in this article the creation and organization of a national core facility for bioimage analysis, based on a distributed team. F-BIAS federates bioimage analysts across France and relies on them to deliver services to the researchers of this territory. The main challenge in implementing this structure is to ensure significant scientific value to the analysts, thereby encouraging their active participation and persuading their respective host teams to support their involvement. F-BIAS accomplished this by creating a professional network that mitigates the negative effects of isolation experienced by its members, who are often the sole bioimage analyst within their local teams, and fosters the development of their technical skills. In a second phase we capitalized on F-BIAS to create a virtual, remotely-operating core facility for bioimage analysis, offering consultations and collaborative project services to the scientific community of France. The services are organized so that they also contribute to the technical proficiency of the analysts. To promote the creation of similar structures, we present and discuss here the organization of this nationally distributed bioimage analysis service core, highlighting successes and challenges.

Fig 1. The geographical repartition of F-BIAS members and their host structure (here in 2024).

F-BIAS federates willing FBI research engineers whose main mission is to provide bioimage analysis services to the scientific community. With few exceptions, the main model is for bioimage analysis services to be provided by 1-2 analysts embedded within a larger structure dedicated to imaging. Numbers above the analysts’ icons correspond to their respective affiliations listed in the preamble of this article. Base layer from https://fr.m.wikipedia.org/wiki/Fichier:Blank_France_map,_no_Departments.svg.

Fig 2. Overview of the bioimage analysis services provided by F-BIAS.

(A) The consultations services take the shape of open desk sessions of one hour organized regularly. A user can book such a session in an online form, providing a description of the image analysis problem they want to discuss, and uploading a few example images. During the preparation phase, the requests are each allocated to an open desk session, with a panel of 2 to 3 analysts selected according to their expertise. All the sessions happen the same day, with 2 to 3 running in parallel. The analysts join the user in an online meeting of 1 hour and work on the user’s problem during this time, actively prototyping the solutions they propose. The output of a session can be advice on how to address the problem, small analysis pipeline or small macros. (B) When a question cannot be addressed in one hour and / or requires some development, a user can request a collaborative project, during an open desk session or by direct contact. Project requests are then evaluated by the F-BIAS team, which estimates the project cost, start delay, and duration. Upon acceptance, an analyst is assigned based on availability and expertise. As a potential opportunity. a senior analyst from another site will provide mentoring to the project’s analyst. The user and analyst collaborate asynchronously, with regular analyst reports, using various communication media (emails, online/onsite meetings). Project outputs may include analysis pipelines, results, and reports. This figure uses icons that are derived from the work of Hilmy Abiyyu Asad (the Noun Project) and released under CC BY-3.0.