OMERO workshops

University Gadjah Mada

March 2024

OME Team

Outline

  • What is OME?
  • What is OMERO?
  • Workshop overview

OME: Interoperability

OMERO is a server with clients

Image Data - Read by Bio-Formats

  • Support for reading > 160 image formats
  • Read pixel data and metadata
  • Includes 5D images, HCS data, Tiled WSI images
  • Domains: biological, medical, general (tiff, png, etc.)

Metadata

  • Stored in a Relational Database
  • Acquisition Metadata
  • User-added Annotations
  • ROIs / Segmentations

Search

  • Text and Annotations indexed with Lucene
  • Allows keyword searches

OMERO.tables

  • HDF5 tables for analysis results
  • Flexible columns

OMERO API

Python | Java | Matlab | R

Integration

Open with... Web apps

OMERO setups - community

idr.openmicroscopy.org

IDR is based on OMERO

Integrate IDR with other repositories

Your own trainings on OMERO

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?

  • 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? ✓

OMERO guide

What should OME user know ?

Support on image.sc - community

Read-annotate setup example

  • Group Owner (PI) can always see all data in every setup

    • Teaching setup example

    • Courses highlighted on a "landing page"
    • Images and ROIs are read-only for students

    Import: Desktop Application

    Read the import guide or watch the import video

    Import: Advanced options

    Read the import guides

    Thank you