[Workshop] Bioimage data management and analysis with OMERO

Here we share the material used in a workshop held on May 13th, 2024, at the German Cancer Research Center in Heidelberg (on-premise)

Description:
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.

Module 1 (9 am - 10.15 am): 
Basics of OMERO, data structuring and annotation

Module 2 (10.45 am - 12.45 pm): 
OMERO and Fiji

Module 3 (1.45 pm - 3.45 pm): 
OMERO and Jupyter Notebooks

Module 4 (4.15 pm - 6. pm): 
Publication-ready figures and data with OMERO

The target group for this workshop
This workshop is directed at researchers at all career levels who plan to or have started to use OMERO for their microscopy research data management. 
We encourage the workshop participants to bring example data from their research to discuss suitable metadata annotation for their everyday practice.

Prerequisites:
Users should bring their laptops and have access to the internet through one of the following options:
- eduroam
- institutional WiFi
- VPN connection to their institutional networks to access OMERO

Who are the trainers?

Dr. Riccardo Massei (Helmholtz-Center for Environmental Research, UFZ, Leipzig) - Data Steward for Bioimaging Data in NFDI4BIOIMAGE

Dr. Michele Bortolomeazzi (DKFZ, Single cell Open Lab, bioimage data specialist, bioinformatician, staff scientist in the NFDI4BIOIMAGE project)

Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)