Helmholtz Imaging Newsletter Issue No. 24

Dear Imaging Enthusiast,

This issue brings together a broad collection of news from across the Helmholtz Imaging ecosystem: community initiatives where we need your voice, scientific highlights, new tools and funding programs, workshops, and strong international contributions in AI and imaging. Whether you’re looking to shape the next Helmholtz Imaging Conference, explore fresh training materials and new challenges, or catch up on recent events, there’s something here for everyone.

Here’s what’s inside this issue:

• Help Shape the Helmholtz Imaging Conference 2026: Take our short community survey (and maybe win one set of our Helmholtz Imaging espresso cups)
• PixelPatrol: A new tool to explore, validate, and debug your imaging datasets
• Training Highlight: Intro to Image Registration workshop, watch the recording and access all materials
• Best Scientific Image Contest: Instagram spotlight on winners & a preview of the 2026 call
• AI for Science Summit 2025: Strong Helmholtz contributions in Copenhagen
• Helmholtz Incubator Workshop: Key highlights & Helmholtz Software Award winners
• Community Recognition: nnU-Net listed among top GitHub repositories in medical imaging
• Workshop at DESY: Bridging AI and theory with the mathematics of transformers
• UNLOCK Projects Announced: Helmholtz funds first twelve benchmarking dataset projects
• MICCAI 2025: Excellent results for DKFZ, The Human Radiome Project & Helmholtz Imaging
• New AI/ML Challenge: Predict spectral properties of chemical compounds (and win a 1,000 € prize)
• Meet Us: Say hello at upcoming events
• Partner Updates: HMC Conference 2026, call for abstracts open
• Opportunities: Explore current funding calls, external events, recent publications, and job postings
• Season’s Greetings: Grateful for this year, cheers to 2026

As always, we welcome your contributions. Share your imaging-related news and events with us at katharina.kriegel@helmholtz-imaging.de. Let’s keep building our vibrant imaging community together.

Happy reading!

Your Helmholtz Imaging team

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A personal note from us:

Do you have an imaging challenge, no matter how big or small? We’re here to help you, free of charge. Contact us via our support hub. 

Also, if you haven’t yet, join our network of experts, modalities, instruments, and facilities! CONNECT with us.

Interested in receiving our newsletter directly in your mailbox? Subscribe here.

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Help Shape the Next Helmholtz Imaging Conference

We’re running a short community survey to make our next conference as useful, welcoming, and inspiring for you as possible. Tell us which formats, topics, and networking setups help you learn, connect, and get inspired. Your input will directly feed into the 2026 conference program design.

What we’re asking about (3–5 minutes):

• Interactive formats you value most (workshops, posters, lightning talks, panels, etc.)
• Thematic focus and interest in satellite workshops
• What makes networking and breaks effective for you
• Industry participation: how important is it?
• Barriers to attending and what we can improve

Espresso cup lottery: We’ll raffle one set of Helmholtz Imaging espresso cups among all participants. To enter the lottery, please include your name and email address at the end of the survey.

Take the survey (by February 28, 2026)

PixelPatrol: Explore, validate, and trust your image data

Curious whether your imaging dataset is ready for prime time? We invite you to explore PixelPatrol, an early-version quality control and data exploration tool for scientific image datasets, acting as an essential first step for you to understand your dataset before computationally intensive analysis.

Key Features:

• Dataset-wide visualization
• Early issue identification
• Experimental comparison
• Modular & extensible

PixelPatrol helps you proactively understand and debug your image datasets, supporting reliable, reproducible findings from the start.

Get started

Getting Aligned: Intro to Image Registration Workshop

On October 29 Ella Bahry from our Engineering and Support Unit at MDC led a virtual workshop on Intro to Image Registration. The session offered a structured overview of how to align multiple image datasets, a critical technique for data analysis in fields like microscopy, medical imaging, earth and material science. A total of 25 participants joined the training.

Workshop highlights:

• Core concepts: understanding image transformation types (rigid, affine, elastic) and the role of interpolation
• Techniques: exploring integrated methods (intensity-based), two-step feature-based pipelines (e.g., SIFT), and modern deep learning approaches (VoxelMorph)
• Practical tools: hands-on introduction to powerful open-source libraries like OpenCV and ITKElastix with a guideline for method selection.

Watch the recording

All training materials are available on our dedicated training webpage: https://helmholtz-imaging.de/training/

Our Best Scientific Image  Get your Images Ready

Discover the winning images in our Instagram campaign

We’re continuing our Instagram campaign featuring the winning images and top runners-up from this year’s Helmholtz Imaging Best Scientific Image Contest. Each week, we highlight one of these impressive entries that showcase the breadth, creativity, and scientific excellence across the Helmholtz Association. 

Follow us on Instagram @HelmholtzImaging to discover the stories behind the images and get inspired. 

Coming Soon: Call for the Best Scientific Image Contest 2026

Get your images ready! We’ll soon open the call for the 2026 edition of the Helmholtz Imaging Best Scientific Image Contest. 

If you’ve captured a striking scientific image, whether it’s from microscopy, modeling, medical imaging, environmental science, or beyond, now’s the time to prepare your submissions.

Stay tuned for the official announcement and make sure your best visuals are competition-ready

AI for Science Summit 2025: Helmholtz Expertise Well Represented

Want a glimpse of how Europe is shaping the future of AI in science? Our colleagues attended the AI for Science Summit in Copenhagen, and shared some key takeaways. The summit highlighted, as Eirini Kouskoumvekaki, Manager Data Science & AI – HFMI Synergy Unit at the Max Delbrück Center, put it, “how Europe’s road to AI innovation and sovereignty is driven by data, compute, talent and collaboration”.

Helmholtz researchers are well positioned in this evolving landscape:

• Helmholtz AI provides AI tools and expert guidance.
• The Helmholtz Model Zoo, developed by Helmholtz Imaging, DESY and HIFIS offers access to state-of-the-art AI models.
• The HFMI enables the development of domain-specific foundation models.

The summit made one thing clear: Europe’s AI for science community is ready to move forward, and Helmholtz is right at the forefront.

More impressions can be found in the LinkedIn posts by Eirini Kouskoumvekaki (HFMI) and Christoph Feest (Helmholtz AI)

Shaping Tomorrow’s Data Science

The second Helmholtz Information & Data Science Incubator Workshop of 2025 brought together data science experts from all Helmholtz Centers, colleagues from all five Helmholtz Information and Data Science platforms, and external experts. Hosted at the Max Delbrück Center, the workshop opened with welcome notes by MDC Directors Maike Sander and Kirsten Bodensiek, and continued with an interview featuring the new Helmholtz President, Martin Keller, who also delivered a keynote on day two on digital sovereignty. 

A highlight was the Helmholtz Software Award ceremony, celebrating outstanding tools that drive research forward: CP2K (Scientific Originality Prize), FastSurfer (Sustainability Prize), and MemBrain v2 (Newcomer Prize). Helmholtz Imaging is proud of having supported two of them. Their achievements highlight the importance of robust, sustainable software. 

More impressions can be found in the linked posts by Christoph Feest from Helmholtz AI (a short workshop recap), and HIDA (spotlight on the awardees).

nnU-Net Named a Community Favorite

We’re delighted to see nnU-Net, one of Helmholtz Imaging’s most influential solutions, listed as a top GitHub repository for medical imaging in a recent community post. Originally developed by Fabian Isensee and his team, nnU-Net has become the de facto standard for medical image segmentation. By automating the configuration of neural networks for different datasets, nnU-Net has significantly lowered the barrier for researchers and clinicians to apply AI-based image analysis.

More information about nnU-Net can be found on our CONNECT platform

Bridging AI and Theory: Workshop on the Mathematics of Transformers

Deep learning experts from across Europe met at DESY in Hamburg for a workshop dedicated to the mathematics of transformers. With five invited talks and lively discussions, the event brought together researchers from diverse disciplines to discuss driving questions and key insights that will impact our fundamental understanding of modern deep learning. The workshop sparked strong interest across disciplines and set the stage for future editions.

Read the full workshop report

Helmholtz Funds First UNLOCK Benchmarking Projects

The Helmholtz Association has selected the first twelve projects to be funded under its new UNLOCK call for benchmarking datasets, marking a major step toward strengthening reproducible and trustworthy AI across the community. By developing high-quality, multimodal, and cross-domain benchmarking datasets, the projects will set new standards for evaluating AI performance in scientific contexts. The projects will start in January 2026 and contribute to a series of workshops to share best practices and connect the emerging benchmarking community. The selected teams will collaborate with Helmholtz AI, Helmholtz Imaging, HIFIS, and HMC to ensure best practices in metadata, reproducibility, and open access.

Explore the twelve selected benchmarking projects

MICCAI 2025: Great Results for DKFZ, THRP & Helmholtz Imaging in Seoul

Want a glimpse of how Europe is shaping the future of AI in science? Our colleagues attended the AI for Science Summit in Copenhagen, and shared some key At MICCAI 2025 in Seoul, the teams from DKFZ’s Medical Image Computing (MIC) and Intelligent Medical Systems (IMSY), together with colleagues from The Human Radiome Project (THRP) and Helmholtz Imaging, delivered an outstanding performance: three accepted papers, one challenge workshop, and five challenge wins. 

Discover the challenge highlights

Call for Participation: AI/ML Challenge on Absorption and Fluorescence Prediction

AiChemist has launched a new community challenge focused on applying AI/ML and computational chemistry methods to predict spectral properties of chemical compounds. 

Participants can tackle tasks on Absorption (Transmittance, %T) and Fluorescence prediction. 

Each winning team will receive a 1,000 € prize and be invited to publish their results in SLAS Technology. The deadline for submissions is January 15.

The challenge is co-organised with EU-OPENSCREEN and SLAS.

More details on participation and rules 

Meet Helmholtz Imaging

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

• Meet us at the Helmholtz AI Yearly Planning meeting on February 2-3 in Munich.
• Save the Date: Join us at our next Helmholtz Imaging Conference 2026 in the week of November 9-13. Stay tuned for more information!

News from our Partner Platforms

Funding Opportunities

• HIDA Mobility Program: program to facilitate research stays at other Helmholtz Centers or international partner institutions for up to three months. Apply at any time. 
• Initiation of International Collaboration: grant program for applicants interested in es-tablishing collaborative scientific relationships with partners abroad. Apply at any time.

External events

• AI Impact Summit: February 16-20, 2026, New Dehli  
• Introduction to Image Analysis workshop: May 18-20, 2026, Cardiff, in collaboration with the Royal Microscopical Society, apply by January 16 
• IJCAI-ECAI 2026, the 35th International Joint Conference on Artificial Intelligence: August 15-21, 2026, Bremen, save the date 
• 16th XTOP Biennial Conference on High-Resolution X-Ray Diffraction and Imaging: September 21-25, 2026, Karlsruhe, save the date.

Do you know of any imaging-related events that could be of interest to our imaging community? We’d love to hear from you. Share the details with us at Katharina.Kriegel@helmholtz-imaging.de.

New publications

Characterizing sea ice melt pond fraction and geometry in relation to surface morphology by Buth, L.G., Krumpen, T., Neckel, N., Webster, M.A., Birnbaum, G., Fuchs, N., Heuser, P., Johannsen, O., Haas, C. 

Advancing standards in biomedical image analysis validation: A perspective on Metrics Reloaded by Reinke, A., Tizabi, M. D., & Maier‐Hein, L. 

Compact diamond x-ray lens cubes for nanofocusing By Wang, W., Döhrmann, R., Botta, S., Sharma, A., Madsen, A., Schroer, C. G., & Seiboth, F.

PhenoBench: A Comprehensive Benchmark for Cell Phenotyping by Winklmayr, C., Luescher, J., Koreuber, N., Franzen, J., Reith, F. H., Baumann, E., Schuerch, C. M., Kainmueller, D., & Rumberger, J. L. (accepted for presentation at MICCAI 2025)

Discover all publications by Helmholtz Imaging

Season’s Greetings

As we wrap up this final issue of the year, we would like to thank you for being part of our imaging community this year. Your contributions, collaborations, and curiosity continue to shape Helmholtz Imaging in meaningful ways. 

We wish you a restful holiday season and a joyful start to the new year. May 2026 bring inspiration, new opportunities and discoveries, and shared successes.

Job openings

Helmholtz Association

FZ Jülich
AI Systems and MLOps Engineer for Earth Observation 

PhD Position – Development of Methods and Workflows for Robust and Reproducible Mass Spectrometry Analysis and Multi-Omics Integration

Hereon
PhD – Multiscale Operando Super-Resolution Imaging of Water Imbibition 
Postdoctoral Researcher – Automated Correlative Image Analysis for BlueMaterials 

DESY / University of Hamburg
Research Associate for the Project “Cluster of Excellence ‚CUI: Advanced Imaging of Matter’ – Imaging attosecond electron dynamics in molecules”

More jobs at Helmholtz

External

Apple
Senior Calibration Scientist (Computational Imaging)  

University of Antwerp
Senior researcher whole-brain light-sheet microscopy

CCMAR Algarve
Accessible 3D Optical Imaging