Data management at France BioImaging

July 5th 2023

Some context

Objectives

  • Bring microscopy data to the ☁️
  • Together with bioimage analysis
  • Switch to an Open Science culture 🌍

Constrains

Infra

  • IaaS
  • Pluggable at the facility
  • Minimal local IT involvement

Data

  • FAIR
  • Close to compute

User

  • Keep raw data access
  • Opt in
  • Ease collaborations
  • Don’t repeat user inputs
  • Ease analysis worflows

BioImage Town

Utiopia

Current

Goal

iRODS and OMERO

Implemented architecture

irods / omero imaging working group

Data Layers

User experience

0. At training

  • 📖 learn
  • 👤 create account
  • 🔑 authenticate

1. Instrument ➡️ User space

  • 🔬 acquire
  • 🔑 mount network share
  • 🚌 transfer to user layer
  • 🔍 pre-analysis & curation
  • user download (user can get out here)

2. User space ➡️ Cooperative

  • 🎫 plan data “metro ride”
  • 🔗 link to context
  • 🚋 import into coop

3. Cooperative ↔︎️ Cooperative

  • 🔄 share
  • 👁️ Visualise
  • 🖊️ Annotate
  • 📊 Analyse (in place)

4. Cooperative ➡️ Commons

  • Easy if we agree on metadata 😉

Current Actions and Deployment agenda

Present

  • Test instances in Montpellier and Nantes
  • Many test omero deployments (Rennes, Bordeaux, Marseille)
  • Training sessions here (ANF OMERO-Fairly), deployment at MiFoBio

Next months

  • September: early production deployment in Montpellier, beta test research groups
  • October: Coding sprint in Bordeaux: documentation and consolidation
  • Next: users onboarding

Collaborations

  • GT-GeDeM RTmfmf
  • Openmicroscopy Working groups (QA, data transfer): Dundee, Glencoe, BINA, GerBi
  • Quarep-Limi (Metadata specification)

Thank yous

  • FBI.data team
    • Perrine Paul Guilloteaux
    • Emmanuel Faure
    • Marc Mongy
    • Jean-François Guillaume
    • Guillaume Maucort
    • Raphaël Braud Mussi
    • Thierry Pécot
    • Dorian Kauffmann
  • Montpellier
    • Julio Mateo-Langerak
    • Virginie Georget
    • Patrick Lemaire (& team)
    • Olivier Miquel
    • Anne Laurent
    • Alexandre Dehne Garcia
    • Jean-Luc Olms
  • French Community
    • Frédéric Brau
    • Faisal Bekkouche
    • Paulette Lieby
    • Oana Vigy
    • Nadia Goué
    • Christophe Blanchet
    • Thomas Guilbert
    • Sophie Abelanet
    • All the members of GT GeDeM
    • Sophie Allart & the RTmfm
  • Marseille
    • Cédric Matthews
    • Sotiris Papapdiamantis
    • the centuri enginneering team
    • Magali Requin
    • Mathieu Fallet
  • The openmicroscopy community
    • Jason Swedlow
    • Josh Moore
    • Suzanne Kunis
    • Stefanie Weidkamp Peters
  • FBI
    • Caroline Thiriet
    • Alban Belloir
    • Alexandre Philips
    • Édouard Bertrand
    • Fabrice Cordelières
  • IFB
    • Julien Seiler
    • Frédérick de Lamotte
    • Alban Gaignard
    • Jean-François Dufayard
  • EuBI
    • Aashta Mathur
  • iRODS
    • Terrell Russell
  • The openmicroscopy community (cnt)
    • Caterina Strambio De Castilla
    • Sebastien Besson
    • Judith Lacoste (et al.)
    • Jean-Marie Burel
    • Keneth Ho
    • Damir Sudar
    • Matthew Hartley
    • Erick Ratamero
    • Rodrigo Rosas
    • Roland Nietschke

✨ Every one is super helpful! ✨

Thank you for your attention !

Rich thumbnail

RO-Crate has an html preview page for each crate, could play well with Arnim Jenett’s data “abstract” presented here

Opened issues