Point d’étape OMERO / iRODS

11 octobre 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

iRODS, OMERO, Madbot

madbot

  • manage ISA architecture
  • manage metadata and data links

iRODS

Services architecture

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

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 😉

Roadmap