3C-CoDash EMBL Event & Hackathon 2026
When
January 28–30, 2025
Euro-BioImaging is delighted to participate in the Data Science 3C-CoDash from January 28-30 alongside EMBL & other partners. It takes place from January 28-30. This event is free and open for all participants and takes place at EMBL Heidelberg or online. Day 1 includes presentations & training on new tools developed for biological data science. Day 2 is a Hackathon, where participants will have the opportunity to contribute to the development of some of the tools presented on Day 1. The third day is dedicated to wrap up and conclusions. With this event, we hope to share information, bring people together and build cool things. Everyone is invited to attend!
Euro-BIoImaging Hub team Image Data Specialist Bugra Oezdemir will contribute to the Training session on “FAIR imaging data management with OME-Zarr, REMBI and LabID - from image conversion to visualisation, processing and publication,” where you can learn about next generation file formats.
Participants will have the opportunity to experiment with this new format, and see how they can integrate it in their data management practices. Workshop participants are encouraged to bring a small image dataset of their own, that they would like to convert to OME-Zarr. The workshop will be performed on two cloud-based desktop environments for image analysis developed at the EMBL, BARD (for internal users) and BAND (for external users). We will start by providing a brief introduction to this platform and the OME-Zarr specification. Then we will introduce conversion tools such asEuBI-Bridge to convert image datasets to OME-Zarr. Participants will be assist to convert their datasets using these tools. We will also show how to visualize images saved in this format, and demonstrate a small example of analysis workflow / programmatic access to the data. We will discuss how to make the imaging data FAIR (Findable Accessible Interoperable Reusable) by providing REMBI (REcommended Metadata for Biological Imaging) compliant metadata. Finally we will see how the conversion workflow and the associated data can be registered in LabID, the on-site data management system available at the EMBL, and how to make it ready for submission to BioImage Archive. Click to see the BioImage Archive submission will be used as a show case.
On Day 2, we will build a simple point and click user interface for the EuBI-Bridge conversion tool. Options for this include a “terminal-based user interface” (TUI), or a plug-in for the python based Napari image viewer. Such a UI should increase accessibility of the conversion tool to non-expert users, and facilitate adoption of the OME-Zarr format.
We hope you will join us!
Register by December 12