EVOLVE Job Shadowing Series – How to run an Image Analysis Core Facility and much more – from Denmark to Sweden 

Julia Mertesdorf is an early-career bioimage analyst with a background in computer science, who works at the Image Analysis Core Facility (IACF) at Danish BioImaging Node in Copenhagen. The facility she works for just started offering services to the public in September 2023. To learn more about how image analysis services are run, she reached out to Anna Klemm, Head of the BioImage Informatics Facility (BIIF) in Uppsala,  a well-established imaging analysis core facility which is part of Euro-BioImaging’s Swedish NMI Node. Julia was keen to learn about how the BioImage Informatics Facility manages and organizes their services. She also felt she needed training on image analysis software such as TissUUmaps, developed by BIIF, so she would feel more comfortable teaching others about them as part of our Danish BioImaging node’s workshops and PhD schools in the future.

In November 2024, the Euro-BioImaging/EVOLVE job shadowing programme provided a framework for her to go to Sweden to learn more. Read the article below to learn more about what Julia hoped to gain from her job shadowing experience and watch the short video to learn why this experience was so important for her career. In her video, she also provides important advice to future job shadowing applicants. 

“We can all learn a lot from each other. In bioimage analysis, we have so many different fields coming together. Each person has a different toolset and existing knowledge. By having this exchange we can help each other out and learn from each other. I think shadowing is a very good initiative to support this collaboration.”

• - Julia Mertesdorf, Computer Scientist at DBI-IFRA Image Analysis Core Facility (IACF)

Watch the video on YouTube: https://youtu.be/hlx7pMWZaKc?feature=shared 

Skill building plan 

Julia’s objectives were very clear: she wanted to learn about how the BioImage  Informatics Facility manages and organizes their services and infrastructure and she wanted to learn more about  the software tools commonly used in bioimage analysis. Her visit was co-

organised with a staff member from the MicroPICell facility in Nantes, creating additional opportunities for collaboration and shared learning.

Sharing the knowledge

The six-day visit offered valuable insights into facility management, software tools, and collaboration with image analysis experts at BIIF. Key topics included writing effective user agreements, project management strategies, and methods to improve user outreach. Discussions with the BIIF team highlighted practical approaches to making bioimage analysis tools more accessible, addressing common challenges, and optimizing workflows. The visit also included hands-on training in advanced image analysis software tools, such as TissUUmaps for spatial transcriptomics visualization, Napari for advanced data visualization and analysis, and MagicGUI for creating user-friendly Napari plugins. This knowledge was shared with the whole IACF team. The mastery of image analysis software tools is passed on to researchers the IACF serves via Danish BioImaging workshops, training and PhD courses.

Continuing the relationship

The shadowing experience provided a great opportunity to learn, exchange ideas, and connect with the broader bioimage analysis community. It inspired actionable ideas and offered practical tools and methodologies to enhance operations at the IACF. Furthermore, the visit established a solid foundation for future collaboration, supporting ongoing knowledge exchange and advancing bioimage analysis practices across Euro-BioImaging Nodes.

In conclusion, there have been many great outcomes of this job shadowing visit, on the personal, institutional and intra-Node levels. We’re delighted to have made this experience possible with funding from the EVOLVE project!