Biological imaging technologies generates a great amount of data that are very demanding in terms of image processing and data management. The FBI.data project, one of the key missions of France-BioImaging, addresses the questions related to the computational analysis and handling of image data. New methodological approaches to extract information from massive amounts of image data are definitively required. If not developed concomitantly, the lack of accurate methods in this field can become the real bottleneck of innovative bioimaging approaches. Several lines of research and development can be delineated:
1. image processing and analysis solutions for bioimaging data quantification and modeling;
2. intelligent image data archival and retrieval;
3. high performance computing infrastructures dedicated to massive computational demands.
Quantitative Bioimage Informatics – Image Processing
All technologies offered or developed inside FBI generate BIG DATA, comparable to the volume produced by NGS. This sub Work Package focuses on their processing and analysis and perform intensive development of innovative algorithms, software and automation of image treatment workflows.
BioImage Analysis and Data Management
Facing the deluge of Massive Data produced by new technologies requires intelligent image data management, archival and retrieval. Consequently the use of high performance computing infrastructures dedicated to massive computation is mandatory. Knowing the nodes and sites needs in this matter and making a precise survey of strength and weaknesses inside FBI, is its first mission. Then, integration to a common and dedicated infrastructure or association to existing ones in other national INBS or International Networks will be decided.
FAIRisation of Data
The FAIRisation of data for Open Science is an initiative fully endorsed by France-BioImaging. Meaning that data are Findable, Accessible, Interoperable and Reusable, the benefits for the bioimaging community are numerous. It improves transparency and reproducibility, enhances quality of results, accelerates scientific progress and method development and finally boosts collaboration within the scientific community.
Several experts are involved in this FBI.data working group:
- Perrine Paul-Gilloteaux, research engineer at MicroPICell core facility and FBI.data mission officer
- Emmanuel Faure, researcher at LIRMM (Laboratoire d’informatique, de robotique et de microélectronique de Montpellier) and FBI.data mission officer
- Guillaume Gay, research engineer at LIRMM, working full time for the FBI.data project
- Marc Mongy, research engineer at MicroPIcell, working full time for the FBI.data project
- Guillaume Maucort, research engineer in image analysis at Bordeaux Imaging Center (BIC)
- Jean-François Guillaume, research Engineer on the BIRD facility, Nantes and Pays de La Loire mesocenter (shared IT system engineer between FBI and Institut Français de Bioinformatique)
- Thierry Pecot, research engineer in image analysis at Rennes (Bretagne Loire Node)
- Dorian Kauffmann, engineer for FBI.data challenges at LIRMM
Example of work in progress
OMERO, developed by the University of Dundee & Open Microscopy Environment teams, on which the FBI.data group is working, is one of the software making user data FAIR. Being a microscopy image data management decentralised platform, it helps organise, access and archive data. Besides, it combines image and metadata storage, a viewer and data analysis resources. Furthermore, OMERO is linked to the most valuable tools for bioimaging experts (ImageJ, Napari, QPath, etc.). And users can access their data from anywhere and keep them safe.