Microscopy (meta)data management at France BioImaging

Guillaume Gay — guillaume.gay@umontpellier.fr —

ImageIA 2025 - Aix, 13 / 05 / 2025

France BioImaging Data project

France BioImaging: 10 regional nodes, ~ 6 000 users.

FBI.data

  • Mission officers :
    • Perrine Paul-Gilloteaux
    • Emmanuel Faure
  • Engineers :
    • Théo Barnouin,
    • Guillaume Gay
    • Dorian Kauffmann
    • Guillaume Maucort
    • Marc Mongy

The microscopy community

  • National structure: RTmfm & France BioImaging
  • International : EMBL, Euro / Global BioImaging
  • Standardization body: QUAREP-LiMi
  • Openmicroscopy: open formats, converters

BioImage data management

Challenges with microscopy images

  • Data diversity:
    • Different image sizes and shapes:
      • 1024x1024x1
      • 8000x8000x10
      • 2000x2000x600x600x3
    • Too many propriertary formats

  • Data complexity:

    • Different microscope modalities
    • Not really images? Single Molecule Localisation, Fluorescence Life Time imaging
    • Complex sample preparation

Metadata for microscopy

REMBI

What is “good enough” metadata for Biological Images?

Recommended Metadata for BioImages:

REMBI metadata categories

QUAREP-LiMi

Exhaustive instrumental metadata - NBO-Q

ISA Framework

The Investigation Study Assay Framework is a spectification to organize research data hierarchically

Public Archives for Bioimages

Image Data Resource
BioImage Archive

Data Mangement at France BioImaging

BioImage Town

Bio Image Town Utopia
Bio Image Town

Services architecture

  • Core services in the datacenter (Montpellier or Nantes)
  • Facility buffer / regional storage

Implementation at France BioImaging

bioimage-tube

bioimage-tube

bioimage-tube

bioimage-tube

New destinations !

Learn Microscopy Data Management!

RDMKit
Guide des Bonnes Pratiques
Naming Files

Remerciements

  • The whole MiFoBio team
  • Les référents data
  • Les béta-testeurs à Nantes et Montpellier
  • Nos interlocuteurs SI & RSSI
  • Les communautés microscopie, bioimage et science ouverte