Solving imaging challenges together.

Decorative picture with puzzle pieces and hands

Helmholtz Imaging Collaborations are your opportunity to directly tap into the expertise of Helmholtz Imaging As part of a Collaboration, you will team up with one or multiple of our units and closely work together on solving imaging-related problems. A Collaboration is of collaborative nature and necessitates the active contribution of all parties involved. Collaborations can run for up to six months or longer, allowing us to take a deep dive into a specific problem and solve it for good!

Suitable topics for a collaboration are anything that is related to imaging and image analysis. Our Helmholtz Imaging Units offer a wide range of expertise covering the entire imaging pipeline, from the development of new imaging modalities all the way to AI-based image analysis. Whether you require support in (AI-based) image analysis, image reconstruction, annotation, data management, software solutions, addressing inverse problems, developing novel imaging modalities, 3D visualization and more - we are your partner. For more information about the expertise of our units, take a look at our team page. 

Interested in a Collaboration? Apply now!

The application process is simple and straightforward:
Send us your application: Applications are handled via the HelpDesk. Either send us an email or use our application form below.

Your application should include the following information:

  • Problem statement,
  • Desired outcome / how can HI help solve the problem,
  • List of participating researchers,
  • Contact information of main applicant,
  • Depending on the task additional information is considered beneficial (e.g. sample data, respective annotations, prior publications etc.),
  • (optional) If you have already been in contact with one of our units or this application has emerged from an interaction initiated by the HelpDesk feel free to name a desired Helmholtz Imaging unit to collaborate with

Review of your application: We will then review your application and, unless a desired partner unit is specified, match you with one of our units. If your application is accepted, you and the designated Helmholtz Imaging unit will then enter the evaluation phase.

Evaluation phase (duration 1-2 weeks): The goal of the exploration phase is to assess the feasibility of the project, agree on a desired (quantifiable) outcome and set a preliminary timeline.

Working Phase (up to 6 months): Following a successful evaluation phase, you and your Helmholtz Imaging collaborators work on the actual project. 

If the time is up and the predefined goals are not yet reached, both partners assess the current state of the project and evaluate whether a prolongation is desired and may lead to the desired outcome. If both parties agree, the Collaboration can be extended.

Just like the rest of our portfolio, Helmholtz Imaging Collaborations are free of charge. Helmholtz Imaging Collaborations do not offer opportunities for obtaining additional funding. Any contribution of Helmholtz Imaging is subject to our Publication Policy.

Collaborations Gallery

This gallery shows some of the Helmholtz Imaging Collaborations.

Green lung with red dots

Understanding lung diseases and optimizing their treatment

Understanding the distribution of nanoparticles after inhalation can lead to the discovery of novel, more effective drug delivering techniques. To this end we develop AI-based methods for semantic segmentation of the airways in non-dissected whole murine lungs, imaged with light sheet fluorescence microscopy. The analysis of airway properties in diseased lungs will furthermore shed light on the pathogenesis of common diseases such as COPD and may lead to novel therapeutic strategies.

Lin Yang, Otmar Schmid, Lung Health and Immunity & Comprehensive Pneumology Center, Helmholtz Munich
Gerome Vivar, Marie Piraud, Helmholtz AI, Helmholtz Munich

Involved Helmholtz Imaging Units
Applied Computer Vision Lab, DKFZ


Ultra Content Screening for Clinical Diagnostics and Deep Phenotyping

For the Helmholtz Imaging project UCS (Ultra Content Screening for Clinical Diagnostics and Deep Phenotyping) we developed software to allow the project partners to process their immunofluorescence labelled light microscopy data of nuclei and cells for single cell proteomics. The developed pipeline includes instance segmentation of nuclei and cells in the immunofluorescence assays, registration of the images and the respective quantitative analysis. Within 2021 the project has been provided with a first prototype implementation of the software. Testing and refinement are still ongoing depending on the data acquired.
UCS project with FZJ and KIT
Gabriel Crespo López-Urrutia, FZJ

Involved Helmholtz Imaging Units
Helmholtz Imaging Support Team at DESY


Decorative image

Paving the way for future mineral processing and recycling technologies through large-scale analysis of particulate samples

Understanding and quantifying the exact composition of mineral samples paves the way towards advanced methodologies that not only increase the effectiveness of ore processing but also enable future recycling technologies. To this end, samples consisting of ground particles embedded into an epoxy matrix are imaged with computed tomography (CT) at micrometer resolution. Due to the sheer amount of particles in each sample, automated image analysis is quintessential to unlocking the potential of his technique. As part of this collaboration we develop a precise and robust instance segmentation method that enables large scale analysis of samples.

Shuvam Gupta, Jose Ricardo da Assuncao Godinho, Helmholtz-Zentrum Dresden-Rossendorf / Helmholtz Institute Freiberg for Resource Technology (HZDR-HIF)

Involved Helmholtz Imaging Units
Applied Computer Vision Lab, DKFZ