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12 May 2023

Stakeholder Meeting #3

Should life scientists learn to program?

Join us at this Stakeholder Meeting where we wish to discuss whether life scientists using biodata analysis for their research need to learn how to program to quantitatively analyse their data.

Workshop topic

To program or not to program?

The Stakeholder Meetings are a series of afternoon meetings, where software producers, microscope facilities, and life scientists discuss common goals and needs.

At the previous meeting, we discussed digital platforms. In this meeting, we will explore the following questions:

  • Can bioimage analysis tools successfully address the specificities of a wide range of applications (including data analysis) without requiring programming/scripting?
  • How to keep up with the integration of the latest data analysis techniques.
  • How are new developments in machine learning changing the game?
  • Are tools such as Python notebooks the right answer to allow users to customise their analysis workflows and immerse non-experts into programming.
  • For companies: Is your software the solution?

Please help other application developers give their end users the best experience by sharing your views and experiences.

Target audience

Who should participate in the Stakeholder Meeting?

We invite researchers, companies and facilities in the field of biodata analysis to share their experiences and views on how we can work together for better science and innovation in the field.

Please take our survey

During the meeting, a panel discussion will take place to voice the point of view of different actors in the field of image analysis. One topic will be on the perspective of the software user.

If you are a biodata analysis software user, or have been at some point in your career, and would like your experience to be voiced, please help us to fill the survey and help us to have a clearer picture of what is needed to serve the community better.
At our second Stakeholder Meeting in October, we identified a joint need for expliciting how a mutual knowledge-sharing community can be built around biodata analysis tools.

An important question arose: Do life science users need to learn to program?

”It needs a community effort to educate both sides in what is possible, what is easy/hard, and what is important. When programs have been made, then it again requires a community effort to learn and maintain solutions.” (participant in the second Stakeholder Meeting).

On this miroboard you will find our joint notes from the meeting.

Agenda Stakeholder Meeting

If you attend physically, please bring your laptop.

The agenda will include presentations by the speakers below, followed by an open discussion among all participants:

Challenges and Opportunities for Bio-image Analysis Core-facilities

KEYNOTE SPEAKER: Robert Haase, PhD, Group Leader, Bio-image Analysis Technology Development Group, DFG Cluster of Excellence “Physics of Life”, University of Technology, TU Dresden

Image analysis from a microscopist’s viewpoint

Pia Nyeng, PhD, Associate Professor, Pancreas Development Group, Molecular & Medical Biology Research Section, Department of Science and Environment, Roskilde University
Read more here

“To program or not to program”– from a life scientist point of view

Richard De Mets, PhD, Research consultant, CFIM, Biomedicinsk Institut, University of Copenhagen
Read more here

“High throughput image analysis”

Casper Salinas, PhD, Department Manager, AI Technology, Gubra
Read more here

The meeting is organized by the Alexandra Institute in collaboration with Danish BioImaging Network (DBI) and Center for Quantification of Imaging Data from MAX IV (QIM)


Robert Haase

PhD, Group Leader, Bio-image Analysis Technology Development Group
DFG Cluster of Excellence “Physics of Life”
University of Technology, TU Dresden

Pia Nyeng

PhD, Associate Professor
Pancreas Development Group
Molecular & Medical Biology Research Section
Department of Science and Environment
Roskilde University

Very few of my graduate students use Python or R, so when they do image analysis, I get them started with free software that allows them to make small macros on their own.
Read more here

Richard De Mets

PhD, Research consultant
CFIM, Biomedicinsk Institut
University of Copenhagen

I found that the medical doctors don’t want to touch the PC; they would rather have me program everything for them, whereas the physicists enjoy trying to understand how the program works.
Read more here

Casper Salinas

Department Manager, AI Technology

Read more here


Key takeaways

Expected outcomes are:

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


Your contacts regarding the Stakeholder Meeting

John Sporring

Professor, PhD
Department of Computer Science
University of Copenhagen
+45 24 25 23 34

Clara Prats Gavalda

Associate Professor, PhD
Faculty of Health and Medical Sciences
University of Copenhagen
+45 24 94 25 22

Katrine Hommelhoff Jensen

Senior Computer Vision and Graphics Specialist / Assistant Head of Lab
Alexandra Institute
+45 26 28 27 98

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