Introduction to Omero. Using the Helmholtz Omero Instance

Thursday 17 Jul 2025, 10:00 → 18:00 Europe/Berlin

Online

Christian Schmidt, Riccardo Massei, Michele Bortolomeazzi

Workshop on the Helmholtz OMERO Instance

Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. Image processing and analysis is a standard procedure to retrieve quantitative information from biological imaging. Due to the complex nature of bioimaging files that often come in proprietary formats, it can be challenging to organize, structure, and annotate bioimaging data throughout a project. Data often needs to be moved between collaboration partners, transformed into open formats, processed with a variety of software tools, and exported to smaller-sized images for presentation. The path from image acquisition to final publication figures with quantitative results must be documented and reproducible.

In this workshop, participants learn how to use OMERO to organize their data and enrich the bioimage data with structured metadata annotations. We also focus on image analysis workflows in combination with OMERO based on the Fiji/ImageJ software and using Jupyter Notebooks. In the last part, we explore how OMERO can be used to create publication figures and prepare bioimage data for publication in a suitable repository such as the Bioimage Archive.

Required Knowledge: For Module 2 and 3 a basic knoledge of Fiji / QuPath and Python is required.

10:00 → 11:30 Module 1: Introduction to imaging Research Data Management (RDM) with OMERO

· Introduction to (bio)imaging RDM
· Introduction to OMERO
· Connection to OMERO in the HMGU Instance via HIFIS
· Technical considerations
· Data organization with folders and Tags
· Figure creation with OMERO.figure
· Outlook to the next modules

Conveners: Christian Schmidt (Deutsches Krebsforschungszentrum, Abt. Enabling Technology), Michele Bortolomeazzi, Riccardo Massei

11:30 → 12:30 Lunch Break

12:30 → 14:00 Module 2: OMERO and Fiji / QuPath

· Image Analysis on the basis of well-structured image data
· Using the OMERO Fiji plugin
· Accessing OMERO through Fiji macros
· Using the QuPath OMERO plugin
· Collaborative workflow with OMERO and QuPath

Conveners: Michele Bortolomeazzi, Riccardo Massei

14:00 → 14:30 Coffee Break

14:30 → 16:00 Module 3: Image analysis in OMERO with Python and Galaxy

· Python connection to OMERO through the API
· A simple python workflow with OMERO
· Galaxy workflows and loading data from OMERO

Conveners: Michele Bortolomeazzi, Riccardo Massei

16:00 → 16:30 Coffee Break

16:30 → 18:00 Module 4: Annotating data with ontology- and REMBI compliant metadata

· Introduction to ontologies
· Introduction to REMBI
· Using Key-Value Pairs in OMERO to annotate data
· Outlook: Publishing your data in BioImage Archive
· Outlook: Find help from NFDI4BIOIMAGE Help Desk / HI Help Desk

Conveners: Christian Schmidt (Deutsches Krebsforschungszentrum, Abt. Enabling Technology), Michele Bortolomeazzi, Riccardo Massei