Train the trainer workshop

OME 2024 Community meeting

May 2024
OME Team

Aims of this workshop

Training landscape

Key questions

  • What is important for a workshop?
  • What can I get from the OME Team for my workshop?
  • How does the OME Team run workshops?
  • What does the community have and want? (Discussions)

What do I need for an OMERO training?

  • Guides for participants
  • Server
  • Server setup
  • 3rd party software setup
  • Analysis environments
  • Server cleanup or re-deployment strategy

What can I get from OME Team?

  • Data and DB in a zip? ✓
  • OMERO.guides? ✓
  • Servers? 🌓 ⚠
  • Blueprint for setting up your training server? ✓
  • Image data? ✓
  • The setup scripts for
    • Users/Groups ✓
    • Image imports ✓
    • Metadata import and handling ✓
    • Creation of annotations ✓
  • Scripts for cleanup of the server? ✓
  • Analysis and 3rd party tools environments? ✓

OME Team: Public walkthroughs, presentations, guides

OMERO guides

  • Walkthroughs, not a description of all functionalities
  • Each guide is a separate project, bundled with code

OME: Main training servers

Training servers - alternative for you: #1

Training servers - alternative for you: #2

Setup #1 - public repositories

  • No server setup required.✓
  • Limited audience, read-only server, only API workflows ⚠

Setup #2 - empty server

  • Very little setup required, larger audience ✓
  • Very limited workflows, low user satisfaction ⚠

Setup #3 - server with few images

  • No IDR data import needed ✓
  • Little setup, large audience, crucial workflows covered ✓
  • Basic analysis, limited scripting, no OMERO.parade ⚠

Setup #4 - OME server copy

  • Start with provided DB and data.✓
  • Full audience, workflows and analysis ✓
  • Need to import IDR data to match workflows ⚠
  • Setup needs planning, space, maintenance ⚠

Training servers - for discussion

  • A docker, possibly based on OME deployment examples
  • A docker-compose with all the data included (a wish from community)
    • Import of data (costly)
    • Transfer of data between OMERO servers (not solved)
    • Size of data and complexity (accrued value vs. lightweight setup)
    • Keep indefinitely up and cleanup or spin up and delete
    • Maintenance and upgrades

What now?

  • General discussion
  • Playful hands-on - prepare a training workflow:
    • 1. OMERO.figure assessment:
      • See overview of images or browse the OMERO.web to find "your" image type.
      • Log in to training server.
      • Using OMERO.guides and YouTube channel (search for OMERO.figure) as a lead, create an OMERO.figure, save and export it as a pdf.
    • 2. Analysis environments:

Thank you