Published on 17.05.2023

Helmholtz Imaging Newsletter Issue No. 8

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Dear Imaging Enthusiast,

Looking at our most recent newsletter we can – without any hesitation – say that spring has been quite busy and exciting, and that we have got a lot in store for you! So, without further ado, let’s dive right in: discover what’s new in the world of imaging science within the Helmholtz Association and beyond!

Helmholtz Imaging recently underwent a thorough review, and we are happy to report that we achieved a very good result in the evaluation.✳ On 14-16 June our Helmholtz Imaging Conference 2023 will take place in Hamburg. Submit your abstract now and share your topic for our Unconference on 14 June! ✳ During the conference we will announce the winners of the Best Scientific Image Contest 2023You can now vote for your favorite image in the category “Public Choice Award”! ✳We are also happy to share that the new call for Helmholtz Imaging Projects is open. ✳ In April, Martin Burger joined Helmholtz Imaging as Head of Research Unit at DESY. ✳ Don’t miss out on this opportunity: join the 2nd AI-HERO Hackathon on energy efficient AI on 19-21 June 2023 in Heidelberg. ✳ Talking about AI, our Support Unit at DKFZ integrated the Segment AI Anything Model into Napari, which makes annotating images so much easier. ✳ Save the Dates for our new Incubator Summer Academy on 18-29 September 2023! ✳ The Kidney and Kidney Tumor Segmentation Challenge is again looking for the best automatic semantic segmentation system. Participate for a chance to win $5,000! ✳ Our team member Tim Rädsch from the Support Unit at DKFZ won the Anton Fink Science Award for Artificial Intelligence with his study on labeling instructions in biomedical imaging. ✳ Meet our 100th Modalities Expert Jan Reimers from HEREON and Forschungszentrum Jülich! ✳ Check out HIFIS’ pilot implementation of Cloud Service Orchestration for our Helmholtz Imaging platform. ✳ The annual call for proposals from the Incubator platform Helmholtz Metadata Collaboration has just been published. ✳ Submit your abstract on mathematical applications for the KIT Center MathSEE! ✳ As always, we compiled the most recent publication and job listings for you. ✳ And last, but not least: We are now also on LinkedIn and Mastodon. We’re looking forward to connecting with you there. 

Enjoy the read!

Yours Helmholtz Imaging team


Group photo of Helmholtz Imaging team

Helmholtz Imaging was recently evaluated, and the entire team demonstrated that the platform is the core of a network that generates, provides, and brokers expertise in imaging science.

We are thrilled about the result: the first feedback from the reviewers was that Helmholtz Imaging fulfilled its mission, with extraordinary activity and enthusiasm of the whole team, and excellent performance. The panel emphasized that it sees a particular added value for the entire Helmholtz community and strongly supports the continuation and expansion of the platform.  This was a huge team effort, and we thank everyone involved for their commitment and contributions.  

The official report will be available in a few weeks. Stay tuned on this channel, our website and/or Twitter for updates!

Read more (more detailed information available soon) 

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Helmholtz Imaging Annual Conference: Call for Abstracts for Poster Presentations & Session Ideas for Unconference 

Call for Abstracts
You can still submit your abstract for the poster session at our conference. The deadline is 24 May 2023. 

Presentation slots are very limited. Nevertheless, please indicate if you are also interested in giving an oral presentation and in which section it would fit best: Reconstruction, Visualization, Image Analysis.

Call for Unconference Topics
As part of the joint conference day with Helmholtz.AI on 14 June, we are planning a community-driven unconference format on “Future Challenges” where different topics will be discussed in parallel sessions. 

There are two ways in which you can contribute: you can add a topic idea as an issue in this github repo (detailed instructions are in the readme) or you can vote on proposed sessions.

Make sure to register to join our conferenceMore details of the program will be announced continously on the Indico page, and will include inspiring keynotes and scientific talks spanning the entire imaging pipeline, a poster session and time to meet fellow colleagues and experts. 

We are looking forward to your ideas and contributions, and to seeing you in Hamburg soon!

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Best Scientific Image Contest 2023 Public Choice Award: Vote for Your Favorite Image!

We called for the Best Scientific Image 2023, and we are thrilled to announce that the results are in. The winners of our international Jury Award will be announced during our 3rd Annual Helmholtz Imaging Conference on 14-16 June 2023 in Hamburg. 

You can now vote for your favorite image from a variety of submissions for Best Scientific Image 2023 in the category “Public Choice Award”. Go to our awards platform and mark your favorite! Who will it be? Who will win the Best Scientific Image Contest Public Choice Award 2023? We accept votes until Monday, 31 May 2023.

Vote for your favorite Best Scientific Image 2023

Decorative image to promote the Helmholtz Imaging Projects Call 2023

New Call for Helmholtz Imaging Projects 2023: Apply by 30 July 2023

The 2023 call for Helmholtz Imaging Projects is now open! Submit your proposal by 30 July 2023 to receive funding for your collaborative, cross-disciplinary research project in the field of imaging and data science. Starting 1 June 2023 project proposals can be submitted via our project portal.

We will soon offer an information session where you can learn more about the call and the requirements to apply for funding! You will also have the opportunity to meet with potential project partners. Stay tuned here!

This event is open to all persons working at Helmholtz Centers interested in the Helmholtz Imaging Project Call 2023 and all potential collaboration, implementation and transfer partners.

Apply now for funding for your Helmholtz Imaging Project & join our information session on 23 May 

Martin Burger and Dagmar Kainmüller - new Heads of Research at DESY and MDC

Establishment of Research Unit at DESY: Helmholtz Imaging Now Complete

We are happy to report that our team is now complete: with Martin Burger and Dagmar Kainmüller joining as Heads of the Research Units at DESY and MDC, we now have a Research Unit established in each of our three host centers. The Helmholtz Imaging Research Units and Support Units as well as the Management Unit operate the platform, provide all administrative, operational, technical, and scientific services and coordinate networking and outreach for the entire community. 

Learn more about Dagmar’s and Martin’s research focus

2nd AI-HERO Hackathon in Heidelberg on 19-21 June 2023

AI-HERO Hackathon on energy efficient AI on 19-21 June 2023 in Heidelberg

Don’t miss out: join our 2nd AI-HERO hackathon on energy efficient AI on 19-21 June in Heidelberg! Registration is open and is on a first-come, first-served basis. 

This hackathon will feature two challenges: one use-case from the research field of health and another one from energy. Each task will be tackled by six teams of three participants. The main focus of the tasks is not a development of the model that achieves the best predictive performance, but rather finding and optimizing a model and its training to minimize energy consumption while still maintaining a target accuracy. Are you up for the challenge? 

Join the AI-HERO hackathon on 19-21 June in Heidelberg

This event is co-organized with KIT and our partner platforms Helmholtz AI and HMC.

Integration of Segment Anything Model in Napari

Meta AI has recently launched a cutting-edge segmentation system, the Segment Anything Model (SAM), which is set to revolutionize downstream applications. We are thrilled to announce that our Support Unit at DKFZ has integrated SAM into Napari for both 2D and 3D images and extended SAM to semantic and instance segmentation. Napari is a versatile Python-based scientific image viewer and annotation software. With the integration of SAM, annotating images has never been easier!

Learn more on MIC DKFZ’ GitHub page 

Incubator Summer Academy 2023 – Save the Dates: 18-29 September

Once again, the five platforms Helmholtz.AI, Helmholtz Imaging, HIFIS, HIDA and HMC are joining forces to assemble an exciting summer academy program. Save the Dates for the Incubator Summer Academy 2023: 18-29 September!

The Incubator Summer Academy is open to all PhD students and postdoctoral researchers in the Helmholtz Association. In addition, a small number of seats in our workshops are reserved for Master students, doctoral researchers and postdocs from other research institutions and universities.

More detailed information and the course program will be announced soon. 

Logo of KiTS 2023

Join the KiTS Challenge & win $5,000

For the 3rd time, the Kidney and Kidney Tumor Segmentation Challenge (KiTS) is inviting the greater research community to participate in a competition to develop the best automatic semantic segmentation system for kidney tumors. Join the 2023 challenge!

Download the data today & compete for the $5,000 prize!

This project is a collaboration between the University of Minnesota Robotics Institute (MnRI), Helmholtz Imaging at the German Cancer Research Center (DKFZ), and the Cleveland Clinic’s Urologic Cancer Program. 

Photo of Tim Rädsch

Tim Rädsch wins “Anton Fink Wissenschaftspreis“

The Technical University of Deggendorf announced the Anton Fink-Wissenschaftspreis für Künstliche Intelligenz (Anton Fink Science Award for Artificial Intelligence) for the second time in 2022. Our team member Tim Rädsch from the German Cancer Research Center convinced the jury the most. He received the prize money of 10,000 euros for his research. Tim presented the first systematic study on labeling instructions in biomedical imaging.

Learn more about Tim’s work

Jan Reimers, material scientist at HEREON and Forschungszentrum Jülich during beamtime at PETRA III at DESY.

We Are Growing: Material Scientist is 100th Modalities Expert

We recently welcomed our 100th expert on our modalities platform. Jan Reimers, material scientist at HEREON and Forschungszentrum Jülich, joined our Helmholtz Imaging Network. We met with Jan to learn more about his motivation to join Modalities.

Read the interview where Jan talks about his motivation to join and his research 

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Image by HIFIS

Pilot Use Case of HIFIS: Cloud Service Orchestration for Helmholtz Imaging

Our sister platform HIFIS set up the Helmholtz Cloud Portal, where users have access to IT services connecting all Helmholtz research fields and centers, and can combine them to suit their work flow. While our goal is to improve access for scientists on innovative imaging modalities, methodological richness and data treasures within the Helmholtz Association, HIFIS can support this mission through seamless interconnection of the cutting-edge IT infrastructures in Helmholtz as orchestrated services. In a pilot implementation of Cloud Service Orchestration for Helmholtz Imaging, HIFIS successfully showcased the interconnectivity of five different Helmholtz Centers. The pilot also demonstrates the modularity of such pipelines, allowing to exchange or scale up parts of the pipeline, whenever beneficial.

Learn more about this Pilot Use Case 

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Image by Possessed Photography on Unsplash

Helmholtz Metadata Collaboration Call for Proposals

The annual call for proposals from the Incubator platform Helmholtz Metadata Collaboration has just been published. You can submit your applications by 1 August 2023

The aim of the call is to initiate and enable activities that address practical challenges in the field of metadata generation and data enrichment. The call aims at funding promising collaborative projects with the potential to add new knowledge as well as solutions to the wider HMC framework at the end of the project’s lifetime and the potential to drive forward the respective metadata community.

More information about the call, information sessions & abstract submission

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KIT Center MathSEE (27-29 September 2023): Submit your abstract by 31 May

The KIT Center MathSEE is one of 9 interdisciplinary research centers at Karlsruhe Institute of Technology, engaging in applications of mathematical methods in the sciences, engineering and economics. The center is organizing its first in-person symposium at KIT in Karlsruhe on 27-29 September 2023. You can submit your abstract until 31 May for oral and poster presentations.

Visit MathSEE’s website for more information & abstract submission

Laptop on table; screen shows LinkedIn page of Helmholtz Imaging
Image by Samantha Borges on Unsplash (edited by Helmholtz Imaging)

We are now also on LinkedIn & Mastodon: Follow us!

We are happy to share with you that we are now also on LinkedIn and Mastodon, and invite you to follow us on these platforms.

Connect with us on LinkedIn & Mastodon

Image: Joshua Sortino on Unsplash

New Publication

Labelling instructions matter in biomedical image analysis by Tim Rädsch, Annika Reinke, Ali Emre Kavur, Lena Maier-Hein et al. 

Job openings

Helmholtz Imaging

DESY-Fellowships in Photon Science

Helmholtz Munich
Postdoc – Institute of AI for Health

Scientific Software Developer / Data Manager

More jobs