Published on 21.03.2024

Helmholtz Imaging Newsletter Issue No. 14

Decorative image to promote HI Newsletter No. 14
Image: Sebastian Dupraz (AG-Bradke, DZNE)

Dear Imaging Enthusiast,

We’re delighted to present the newest edition of our newsletter, bringing you the latest updates and highlights from our endeavors and affiliated platforms. Join us as we explore the world of imaging. Let’s delve into the content together!

Happy reading!

Your Helmholtz Imaging team


Decorative Image to promote the 4th Helmholtz Imaging Conference on 14-15 May 2024
Alina Blume, Avi Putri Pertiwi, Chengfa Benjamin Lee, Spyros Christofilakos and Dimos Traganos from DLR, and Global Seagrass Watch

Helmholtz Imaging Conference 2024: Register & Submit Your Poster Abstract Today

Join us on 14-15 May 2024 for our 4th Helmholtz Imaging Conference in Heidelberg to delve into the world of imaging research & collaboration with colleagues, friends, and like-minded people!

Why should you join us?

  • Get insights from leading experts in the field, including Zeynep Akata from Helmholtz AI, TUM and Helmholtz Munich, Joost Batenburg from Leiden University, and Jan Taucher from GEOMAR.
  • Present and solve imaging challenges in collaborative discussions as part of our new session format “Bring your Own Imaging Challenge”. Submit your imaging challenge to with “BYOIC” as the subject.
  • Connect with peers and explore collaborations within the imaging community. Get in touch with potential cooperation partners for the new Helmholtz Imaging Project Call (that will be published on 1 May).
  • Enjoy a comprehensive program covering topics such as image analysis, data acquisition, and visualization, alongside a poster session with a dedicated area for Helmholtz Imaging Projects.
  • Join the award ceremony for the best image 2024, and explore the exhibit showcasing the unique imaging portfolio of Helmholtz.

Don’t miss this opportunity to connect, learn, and contribute to the world of imaging science. 

Register & submit your poster abstract

Decorative image to promote the Support Hub, formerly known as HelpDesk

Exciting News: The HelpDesk is Evolving

Have imaging-related questions, need guidance, seek collaborations, or encounter technical challenges in the realm of imaging science? Then look no further! Our Support Hub – formerly known as HelpDesk – is here to provide expert assistance and support for your imaging-related inquiry. Regardless of whether you are an experienced researcher or new to the field, our dedicated team is here to provide assistance with a wide array of topics. This includes inquiries related to imaging technologies, data analysis, and visualization, as well as offering targeted support for your specific challenges. Our goal is to support your research endeavors by providing accurate and timely solutions.

Contact us at, or visit our website to learn more about how Helmholtz Imaging can empower  your research:

Decorative image to promote Helmholtz Imaging CONNECT, formerly known as Helmholtz Imaging Modalities

Helmholtz Imaging CONNECT Relaunch

We recently relaunched Helmholtz Imaging CONNECT. CONNECT, formerly known as Modalities, serves as a centralized platform, spotlighting the diverse scientific imaging portfolio within the Helmholtz Association. It simplifies the process of finding collaborators, seeking support for specific imaging modalities, and discovering cutting-edge technologies offered by the Helmholtz Association.
New features include:

  • Personalized Dashboard: tailor your experience with a personalized dashboard
  • Enhanced Network: see your connections at a glance
  • Blogs and Galleries: share your imaging-related stories and showcase your best images
  • Integration of Helmholtz Imaging Album Solutions: explore album solutions
  • Optimized Search: enjoy an enhanced and faster search experience
  • Improved Usability: navigate the platform effortlessly

Don’t miss the chance to CONNECT today! Engage with the community, find collaborators, share insightful blog posts, and stunning scientific images.

Read our article to explore the exciting new features that await you & CONNECT today

Profile photo of Prof. Dr. Dagmar Kainmüller

Welcome Dagmar Kainmüller as New Helmholtz Imaging Spokesperson

Please join us in welcoming Dagmar Kainmüller, Head of Research Unit at MDC, as she steps into her new role as Helmholtz Imaging Spokesperson. Congratulations, Dagmar! We are excited to have you as our new spokesperson and look forward to closely working with you! Dagmar succeeds Christian Schroer. He was the father of the idea of Helmholtz Imaging, developed the platform application to a large extent and accompanied Helmholtz Imaging intensively and tirelessly until the very successful evaluation in 2023 and beyond. We are delighted that he will continue to accompany and support Helmholtz Imaging as Center Coordinator. Thank you, Christian, for all your outstanding commitment!

Learn more about Dagmar and her research

HI team members during the HI roadshow at HZB

Helmholtz Imaging Roadshow at HZB: A Short Recap

The Helmholtz Imaging Roadshow came to the Helmholtz-Zentrum Berlin (HZB). Thanks for hosting us! We had a fantastic time. During our information session on 29 February, we shared insights into our diverse activities, and introduced our extensive support and imaging expertise portfolio. We also showcased the Best Scientific Images of 2023 from the Helmholtz Association as part of our roadshow. Following the information session, we offered a virtual consultation hour on 7 March for anyone who needed help with image analysis.

Silvia Zerbe from HZB interviewed Philipp Heuser, Head of Helmholtz Imaging Engineering and Support Unit at DESY, to explore what is behind a roadshow. Read the interview.

Missed our session but need help with your imaging-related challenge? Contact us at We are happy to assist you.

Interested in bringing the Helmholtz Imaging Roadshow to your Helmholtz Center? Reach out to us at

Decorative image by Igor Omilaev on Unsplash
Igor Omilaev on Unsplash

Foundation Models: The Future of Scientific Discovery

The Helmholtz Association has launched an ambitious initiative to harness the recent advancements in AI and the rise of Foundation Models. Foundation Models are complex AI applications that have the power to transform research data into high-impact tools for scientific discovery.

In this article published by the Helmholtz Association, Dagmar Kainmüller, Head of Research Unit at MDC, and Florian Grötsch, Senior Adviser to Helmholtz AI    and Helmholtz Imaging at Helmholtz Association explain what Foundation Models are, how they can be used and what snow deep below the surface of the water has got to do with it.

Access the full article and discover the intersection of AI and scientific progress

Decorative image to promote new publications on metrics validation

Advancing Image Analysis Validation: A Comprehensive Approach through Two Pioneering Sister Publications

Validating metrics is crucial for bridging the gap between AI research and real-world applications, but often, metrics are chosen poorly. Helmholtz Imaging team members from the Research Unit as well as Engineering and Support Unit at DKFZ together with an international, multidisciplinary expert consortium published two pioneering articles, “Understanding metric-related pitfalls in image analysis validation“ by Annika Reinke, Minu D. Tizabi et al. and “Metrics reloaded: recommendations for image analysis validation” by Lena-Maier-Hein, Annika Reinke et al. These two articles provide a profound insight into the challenges and solutions surrounding validation metrics in image analysis, particularly in the biomedical domain.

Deep dive into the articles

A team of experts from Deutsches Elektronen-Synchrotron DESY, University of Hamburg and CNRS designed and built a mobile tomographic X-ray scanner to scan cuneiform tablets at the Musée du Louvre.

Unlocking Ancient Secrets: ENCI X-ray Scanner at the Louvre

Join us as we journey back thousands of years with ENCI to unlock the mysteries of ancient cuneiform tablets at the Musée du Louvre! Cuneiform is the very first manifestation of human writing, produced by imprinting cuneiform letters in soft clay. Four hundred of the 13 000 tablets preserved at the Louvre are still enclosed in their clay envelopes – their content hidden to protect the often artistic envelopes. Until now! A team of experts from Deutsches Elektronen-Synchrotron DESY, University of Hamburg and CNRS designed and built a mobile tomographic X-ray scanner, and named it ENCI, which stands for Extracting Non-destructively Cuneiform Inscriptions. With the help of ENCI, the team was able reveal the secrets preserved within these fragile artifacts without causing any harm.

Read all about this exciting scientific endeavor in our new CONNECT blog post by Andreas Schropp.

Do you have a fascinating story in the realm of imaging to tell yourself? Share it with the community on CONNECT:

Image to promote Open-ST, an open-source experimental and computational method for the generation and analysis of 3D virtual tissue blocks
Daniel Leon Perinan, Marie Schott & Elena Splendiani

Open-ST – Reconstruction and Visualisation of multimodal 3D Virtual Tissue Blocks

Understanding the spatial organization of gene expression within tissues is essential to understand cellular function in health, development, and disease. The N. Rajewsky lab (MDC Berlin) recently introduced Open-ST, an open-source experimental and computational method for the generation and analysis of 3D virtual tissue blocks: multimodal objects combining tissue imaging, spatial gene expression, and analysis results (for example. cell type clusters, gene program). These enable an unprecedented visualization of tissues, for billions of single mRNA transcripts (>20,000 genes) across millions of cells, in any spatial direction. The Open-St package, now available in pip, leverages state-of-the-art tools for precise cell segmentation, multimodal alignment, and serial section registration. 

Read the preprint, explore the tool and tutorials & join the discussion channels 

Decorative image to promote Polarity-JaM, an open-source package for cell polarity, junction, and morphology quantification

Polarity-JaM: New Open-Source Package for the Analysis of Cell Polarity

Cell polarity involves asymmetries in cell shape and the distribution of organelles and signaling molecules, influenced by gradients and mechanical forces, and coordinated by cell-to-cell communication. Fluorescence microscopy, coupled with deep learning, enables detailed exploration of cell polarity in health and disease. Polarity-JaM, an open-source package for cell polarity, junction, and morphology quantification, facilitates reproducible analysis with multi-channel single-cell segmentation and interpretable feature extraction. Although Polarity-JaM focuses on endothelial cells, which are crucial in vascular health and disease, it is adaptable to other cell types. The software offers comprehensive visualization and statistical analysis, enhancing accurate and efficient image interpretation.

Read the paper, explore the online app & check out the documentation

Decorative image to promote Relaunched HI Homepage
Ben Kolde on Unsplash

Helmholtz Imaging Homepage Relaunched

The homepage of Helmholtz Imaging underwent a redesign! As part of our commitment to providing an enhanced user experience, we’ve introduced a dynamic new slider on the homepage, putting our mission in the spotlight. Now, you can easily explore our core values. 

In addition to the refreshed design, we’ve made accessing our support portfolio quicker and more intuitive. The support portfolio is now prominently featured on the homepage, ensuring that our website visitors can swiftly discover the comprehensive range of support we offer. Finding the support you need is just a click away.

Visit our revamped homepage to experience the new look and access our support portfolio

Group photo of Helmholtz Imaging team
Jörg Modrow

Meet Helmholtz Imaging

Say hello to Helmholtz Imaging team members at the following events:

News from our Sister Platforms

HIDA-Hackathon: Tackling heat leaks with data science

Group photo of HIDA Hackathon in Berlin in February 2024

Together with Helmholtz Imaging, HIDA hosted a computer vision hackathon in Berlin, where doctoral researchers used drone imagery to detect heat leaks in buildings. Participants used various methods, including deep learning, to automatically identify thermal bridges. Mentors from Helmholtz Centres supported the doctoral researchers and fostered the development of data science skills. 

Read more


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Visax on Unsplash

Women in Science Award 2024

Exciting opportunity for women in science: become one of four female early-career scientists – working at a German university, university of applied sciences, or non-university public research institution – to win the Women in Science Award worth 25,000 Euros! Applicants need to work in STEM disciplines (interpreted in a wide understanding, for example agricultural sciences, informatics, geosciences, medicine). Strongly encouraged are researchers with an inter- and transdisciplinary research profile.

Apply by 30 April 2024 for a chance to win the award

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Joshua Sortino on Unsplash

New publications

Understanding metric-related pitfalls in image analysis validation by Annika Reinke, Minu D. Tizabi, Paul Jäger, Lena Maier-Hein et al. 

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets by Andreas Müller, Deborah Schmidt et al.

Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification by Wolfang Giese, Jan Philipp Albrecht et al.

Discover all publications by Helmholtz Imaging

Job openings

Engineer “under-ice robotics and sea ice physics”

Geospatial Data Expert

Post-Doctoral Position In Single Cell Multiomics 

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