[OME2026] Workshop: EuBI-Bridge: A Toolkit for OME-Zarr Conversion, Visualisation and Metadata Editing

Abstract: As bioimaging datasets grow in size and complexity, converting proprietary microscopy formats into OME-Zarr is rarely straightforward. This workshop surveys the practical challenges that arise in real conversion workflows and presents strategies to address them.

In the hands-on demo session, we will introduce EuBI-Bridge, a Python-based tool for conversion, visualisation, and metadata editing. Available as both a CLI and GUI application requiring no programming experience, it supports parallelised conversion of bioimage collections from diverse microscopy formats into OME-Zarr. Participants will learn how to perform standard one-to-one conversions as well as “aggregative conversion,” enabling concatenation of multiple images along user-defined dimensions. We will also demonstrate how conversion parameters such as chunking, sharding and compression schemes can be configured in EuBI-Bridge.

Finally, we will showcase data visualisation and metadata inspection/editing workflows, enabling efficient exploration and preparation of OME-Zarr datasets for downstream analysis, sharing or archive submission pipelines.