Image Data Community Days

Time: Monday, April 7 2025, 9:00-10:00 CEST

Euro-BioImaging Hub staff introduce the diversity of data services that are offered through the Euro-BioImaging Nodes and at the Hub. Join us for an insightful overview of current opportunities and expert guidance on all things data.

Time: Monday, April 7 2025, 10:00-11:30 CEST

Growing size and complexity of image data has brought forward many challenges for researchers to efficiently analyse their image data to gain biological insights. To support researchers in their endeavours, various Euro-BioImaging Nodes have stepped up to provide image analysis services, including as a standalone service on data acquired already. In this session you will hear about the cutting edge data services that some of our Nodes offer, and how you can access them.

Time: Monday, April 7 2025, 13:00-14:00 CEST

BioImaging core facilities are vital for providing services to departments and stakeholders. Typically, they provide support to users for experimental design, acquisition, and analysis. In bioimage analysis and data management, infrastructure comes in various forms, starting with advanced microscopy facilities, computational resources, and collaborative networks. When it comes to scalability, there are practical bottlenecks and limits to buying bigger workstations, and the question of high-performance computing infrastructure arises. Overall, creating scalable and reproducible bioimage analysis workflows should be dear to all our hearts to ensure FAIR data provision. Consequently, we feel that high-performance computing is an underused opportunity for bioimage analysis and to make modern data management and analysis that is committed to FAIR principles and improved reproducibility a reality at our place, Flanders BioImaging has been teaming up with the Flemish supercomputing center (Vlaams Supercomputer Centrum, VSC) and KU Leuven’s central IT infrastructure.

Here, we will explore the interaction possibilities with high-performance computing centers and discuss the use of OpenOnDemand, Easybuild, and containers and their potential use as a user service. In addition, we aim to demonstrate some of these possibilities and talk about the data journey from the devices via storage to deposition in public repositories.

Time: Monday, April 7 2025, 14:00-16:00 CEST

Tired of staring at segmented blobs all day? Need a break from debugging? Feeling all alone in a world where there are supposed to be other bioimage analysts? Or are you just starting out in image analysis and want to find out more? Join us in the image.sc Gather instance for a relaxed networking session designed for bioimage analysts of all stripes!

Whether you want to swap stories about career adventures, discuss the art of getting acknowledged, or just engage in some free-range chat, this is the space for you. No analysis required—just bring yourself, your curiosity, and maybe a virtual beverage of choice.

Time: Tuesday, April 8 2025, 9:00-11:00 CEST

The foundingGIDE session will showcase the project's ongoing efforts to enhance interoperability for biological and preclinical image data resources. Key topics will include metadata and ontologies for biological and preclinical imaging, as well as the critical role of persistent identifiers in improving data findability, accessibility, and reusability.

Time: Tuesday, April 8 2025, 11:00-15:00 CEST

This workshop aims to bridge the gap between FAIR data principles and their practical implementation in imaging core facilities to ensure that user project data comply with FAIR guidelines. Through showcases from Euro-BioImaging Nodes, bioimaging repositories and collaborative discussions, participants will explore practical approaches and actionable steps for integrating FAIR principles into facility workflows and user interactions, thereby enhancing the reproducibility and impact of the research conducted.

Time: Wednesday, April 9 2025, 9:00-12:00 CEST

This session provides an overview for the emerging ecosystem around the Next Generation File Format (NGFF), a file format optimized for access to large-scale image data (possibly stored in the cloud). A range of existing open-source tools will be introduced, including those for reading, writing, visualizing and modifying big image datasets.

Time: Wednesday, April 9 2025, 13:00-15:00 CEST

The FAIR Image Data Workflows Expert Group at Euro-BioImaging is a collaborative community dedicated to enhancing the accessibility, interoperability, and reproducibility of bioimage analysis workflows. Bringing together researchers, developers, and trainers, the group promotes knowledge exchange, best practices, and the implementation of FAIR principles in image data analysis.  Key objectives include reducing redundancy in tools and workflows, fostering collaboration, and expanding training resources. Through monthly online meetings and participation in scientific conferences, members engage in discussions on workflow development, grant writing, and community-driven initiatives.  Joining the group provides opportunities to contribute to FAIR-compliant workflows, collaborate on projects, gain early access to new tools, and expand professional networks. Researchers, developers, and trainers are encouraged to participate to enhance bioimage analysis and ensure sustainability in data workflows.

Time: Wednesday, April 9 2025, 15:00-16:00 CEST

This session will provide an overview of the challenges and opportunities involved in constructing multi-omics brain atlases from 3D imaging, sequencing, brain network, and anatomical data. The nature of omics data will be outlined and the process of integrating and providing it in a useful way will be described. The talk will be concluded with a showcase of the publicly available multi-omics brain data exploration tool BrainTrawler.

Time: Thursday, April 10 2025, 9:00-12:00 CEST

This session will introduce data management, quality control, and image processing tools such as segmentation, developed by Euro-BioImaging nodes and external researchers. These tools are designed to improve workflow and accuracy in the preclinical imaging community. Attendees will learn how these solutions can improve data processing and analysis in their research.

Time: Thursday, April 10 2025, 13:00-16:00 CEST

This session will explore advanced tools for analyzing clinical datasets, with a focus on data processing, quality control, and cutting-edge solutions to enhance clinical research workflows. This session is ideal for researchers, analysts, and clinicians looking to improve their research and improve predictability of clinical outcomes.

Time: Friday, April 11 2025, 9:00-10:00 CEST

This session provides an introduction to the European Open Science Cloud (EOSC), a multi-disciplinary environment designed to facilitate the sharing, reuse, and analysis of research data across Europe. Participants will gain insights into Euro-BioImaging's strategies for enhancing open access to imaging technologies, data services, and providing collaborative spaces for biological and medical research within the EOSC framework.

Time: Friday, April 11 2025, 10:00-12:00 CEST

Artificial Intelligence (AI) has revolutionized research in the life sciences, yet access to these powerful methods remains limited. AI4Life, a Horizon Europe-funded project, addresses this challenge by providing life scientists access to FAIR AI models and AI-ready image-analysis datasets. To ensure that life science communities can benefit from AI-powered image analysis methods, AI4Life builds bridges by integrating services on the common European research infrastructures. The project is developing an open, accessible, community-driven repository of FAIR pre-trained AI models and services to deliver these models to life scientists, including those without substantial extensive computational expertise. Additionally, AI4Life is curating a collection of AI-ready datasets, enabling scientists to leverage AI techniques more effectively while promoting data reuse and reducing redundant computations. The project provides state-of-the-art solutions to unsolved image analysis problems in the life sciences through open calls and public challenges.

Time: Friday, April 11 2025, 13:00-14:00 CEST

In our special edition virtual pub on image data we will welcome Pete Bankhead from the University of Edinburgh to talk about 'QuPath for bioimage analysis'.

Time: Friday, April 11 2025, 14:00-15:00 CEST

This session features flash talks showcasing innovative image analysis and data tools. Discover new solutions, engage with experts, and foster collaboration within the imaging community.