OMERO workshop

ELMI, Heidelberg

June 2025

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

Implementation of OMERO at the Münster Imaging Network, setup from Zobel et al. 2022:

idr.openmicroscopy.org

IDR is based on OMERO

Integrate IDR with other repositories

https://workflowhub.eu/workflows/242

OMERO guide

Workshop content is in OMERO guides

https://omero-guides.readthedocs.io

Support on image.sc - community

Import: Desktop Application

Read the import guide or watch the import video

Data management

Annotations

OMERO.figure

A plugin for OMERO.web for creation of figures
Search for OMERO.figure in omero-guides
Recommended video OMERO.figure

Thank you