The Stakeholder Meetings are a series of afternoon meetings, where software producers, microscope facilities, and life scientists discuss common goals and needs.
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 previous meeting, we identified a number of core challenges in bioimage analysis (see below).
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.
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.
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
Daniel Wüstner
Associate Professor
Bioimaging section
Department of Biochemistry and Molecular Biology (BMB)
University of Southern Denmark, Odense
Hans Martin Kjer
Researcher
Department of Applied Mathematics
and Computer Science
Technical University of Denmark
Michael Christensen
Principal Software Architect
Digital Experience
and Solutions (DxS) Lab
Alexandra Institute
Sébastien Tosi
Head of the Danish Bioimaging Network (DBI)
Image Analysis Core Facility
Faculty of Health and Medical Sciences, University of Copenhagen
Stefan Klein
Associate Professor
Medical Image Analysis
Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
Expected outcomes are:
Jon Sporring
Professor, PhD
Department of Computer Science
University of Copenhagen
+45 24 25 23 34
sporring@di.ku.dk
Clara Prats Gavalda
Associate Professor, PhD
Faculty of Health and Medical Sciences
University of Copenhagen
+45 24 94 25 22
cprats@sund.ku.dk
cprats@sund.ku.dk
Daniel Wüstner
Associate Professor
Department of Biochemistry and Molecular Biology
University of Southern Denmark
+45 6550 2405
wuestner@bmb.sdu.dk
wuestner@bmb.sdu.dk
Katrine Hommelhoff Jensen
Senior Computer Vision and Graphics Specialist / Assistant Head of Lab
Alexandra Institute
+45 26 28 27 98
katrine.hommelhoff@alexandra.dk
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