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28 October 2022

Stakeholder meeting: Digital platforms

Join us at this Stakeholder Meeting to share experiences and views on how we can work together for better science and innovation in the field of bioimage analysis.


New opportunities with image analysis

Image analysis has become a bottleneck in image-based life science. Since 2015 the field of image analysis has achieved considerable breakthroughs with artificial intelligence offering the ability to segment and track objects in images for high-level modeling.

At the same time, the Danish Imaging Core Facilities are expanding rapidly offering better image resolutions, new modalities, and automatic sampling, and life-scientists today have an unprecedented opportunity to see their world in new ways and generate enormous amounts of imaging data.

Achieving the best in both imaging and analysis is no simple task since it requires expert knowledge in life sciences, microscope hardware, artificial intelligence, and computing resource management.
At the first Stakeholder Meeting in March, we identified some core challenges as the most prevalent topics to continue discussing:

SOFTWARE TOOLS:There is a knowledge boundary in non-IT professionals for identifying, and followingly, applying the most appropriate software tools.

KNOWLEDGE,  INFORMATION, AND COMMUNICATION: Building and maintaining communication channels between industry, core facilities, and research could improve better usage of the existing analysis possibilities and explore new applications and matching analysis methods and life science hypotheses.

DATA HANDLING AND PROCESSING POWER:Computer power and connecting instruments with analysis computers become bottlenecks in bioimaging analysis.

On https://tinyurl.com/4vzsu3jf you will find our joint notes from the meeting including a feedback summary and a summary of the Miro board discussion.

Agenda Stakeholder Meeting #2

At this second Stakeholder Meeting, we will continue our community discussion on how to shape a software environment, which easily integrates the skills of the programmers, people with image problems, researchers, and companies – in short, how to optimally shape the digital platforms for supporting microscope image analysis.

If you attend physically, please bring your laptop with you.

The agenda includes the following presentations, followed by an open discussion among all participants:

14:15–14:45 European Population Imaging Infrastructure (EPI2) Stefan Klein, Dept. Of Radiology & Nuclear Medicine Erasmus MC, Rotterdam, the Netherlands Stefan will talk about the use of XNAT for image data management and the FASTR and WORC software for image analysis and machine learning.

14:45–15:00 Image processing pipelines at Center for Quantification of Imaging Data from MAX IV Hans Martin Kjer, QIM and Dept. of Applied Mathematics and Computer Science, DTU

15:00–15:15 BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows Sébastien Tosi, Head of the Danish Bioimaging Network (DBI) Image Analysis Core Facility, Faculty of Health and Medical Sciences, University of Copenhagen

15:15–15:30 Development and application of image processing pipelines in biomedical research Daniel Wüstner, Dept. of Biochemistry and Molecular Biology (BMB), SDUA

15:30–15:45 Experience from building digital platforms at the Alexandra Institute Michael Christensen, Alexandra Institute

15:45–16:15 Startup of discussion & break

16:15–17:00 Plenum discussion


Stefan Klein

Associate Professor
Medical Image Analysis
Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands

Daniel Wüstner

Associate Professor
Bioimaging section
Department of Biochemistry and Molecular Biology (BMB)
University of Southern Denmark, Odense

Hans Martin Kjer

Department of Applied Mathematics
and Computer Science
Technical University of Denmark

Sébastien Tosi

Head of the Danish Bioimaging Network (DBI)
Image Analysis Core Facility
Faculty of Health and Medical Sciences, University of Copenhagen

Michael Christensen

Principal Software Architect
Digital Experience
and Solutions (DxS) Lab
Alexandra Institute


Key takeaways

Expected outcomes are:

  • Knowledge exchange
  • Identifying high-level interests and needs
  • Networking
  • Planning future events


Your contacts regarding the Stakeholder Meeting

Professor, PhD

Department of Computer Science
University of Copenhagen

+45 24 25 23 34

Associate Professor, PhD

Faculty of Health and Medical Sciences
University of Copenhagen

+45 24 94 25 22

Associate Professor

Department of Biochemistry and Molecular Biology, University of Southern Denmark

+45 6550 2405


Senior Computer Vision and Graphics Specialist / Assistant Head of Lab

Alexandra Institute

+45 26 28 27 98

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