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Presentation . 2026
License: CC BY
Data sources: Datacite
ZENODO
Presentation . 2026
License: CC BY
Data sources: Datacite
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[OME2026] Workshop: EuBI-Bridge: A Toolkit for OME-Zarr Conversion, Visualisation and Metadata Editing

Authors: Özdemir, Bugra;

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

Abstract

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.

Keywords

OMEmeeting2026

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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