Collaborations — Ongoing

Decorative Image for HI Collaboration Identifying structural features of zebrafishes, using Semantic Segmentation

Identifying structural features of zebrafishes, using Semantic Segmentation

Zebrafish have a certain genetic similarity to humans and vertebrates. Particularly, the use of embryos is attractive due to the small scale screening capacity. Furthermore, similar to genuine cellular in vitro approaches, zebrafish embryos are considered as alternatives to animal testing. Therefore, they play a fundamental role in the detection of environmental and human health […]

Decorative Image for HI Collaboration Automated Analysis of Evolutionary Experiments of Phytoplankton

Automated Analysis of Evolutionary Experiments of Phytoplankton

There is a strong interest in understanding community assembly and dynamics. Experimental approaches using phytoplankton have proven to be extremely insightful to unravel underlying biological processes. Imaging flow cytometry is an emerging method becoming more and more popular in different fields. It allows us to capture changes within a community or population in a more […]

Decorative Image for HI Collaboration for biopores and plant roots in soil cores using semantic segmentation of CT images

Understanding and analyzing biopores and plant roots in Soil Cores using Semantic Segmentation of CT Images

To understand how processes in ecosystems work and how they are connected the analysis of soil systems is essential. Since traditional computer vision methods for analysing soil cores reach their limits the next step is to integrate deep learning methods. Therefore a sufficient amount of labeled ground truth data is needed. Since labeling this large […]

Pick Yolo

Pick Yolo

In collaboration with the Center for Structural Systems biology, Helmholtz Imaging has developed and trained a convolutional neural network for the picking of instances of proteins in cryoelectrontomograms (CryoET). The so picked instances are subsequently used to reconstruct a 3D structure of the proteins using subtomogram averaging methods. The novel picking methods exploit the well […]


Plaque Assays

In collaboration with the Leibniz Institute of Virology and the Center for Structural Systems biology, Helmholtz Imaging is working on a processing pipeline for plaque assays. Plaque Assays are used to e.g. estimate the virus concentration in a given sample. For this high resolution images of cell cultures which have been infected with a virus […]


Segmentation of biodegradable bone implants

Together with the experts from Hereon the Helmholtz Imaging Support Team collaborates on segmenting synchrotron CT data. In 2021 the collaboration on semantic segmentation of biodegradable bone implants using a U-net resulted in two publications acknowledging the contribution of Helmholtz Imaging [1],[2]. Beyond that, we studied “Instance segmentation of paper fibers” imaged at the Hereon […]



In the context of the Unisef project funded by Helmholtz AI, we implemented the prototype of a webservice to allow training and application of deep learning networks for segmentation running on the HPC infrastructure of DESY. The main idea here is to make DL based segmentation accessible and usable by non-experts, as well as complementing […]


Active Learning-enabled Generation of (Patho-)Physiological Lung Architectures for Pulmonary Medicine (ALEGRA)

ALEGRA aims to discover new insights into the morphology, physiology, and functionality of mammalian lungs. Therefore, quantitative parameters will be extracted from light sheet fluorescence microscopy images featuring comprehensive annotations of unprecedented detail for structures of interest such as hollow airways, blood vessels, as well as alveoli. These annotations are made possible by a novel […]


Connecting membrane pores and production parameters via machine learning (COMPUTING)

Isoporous block-copolymer membranes play a fundamental role in the filtration of liquids and can, for example, be used to purify drinking water. Despite recent progress in understanding the membrane formation process, finding suitable production parameters for a given precursor material (such as polymers of a certain length) still occurs in a trial-and-error fashion, wasting materials, […]


Detecting Type-2 Diabetes in histopathological images for a better understanding of biological processes behind the disease

Type-2 diabetes is a chronic disease affecting about 500 million people worldwide. Despite extensive research over the last decades, exact biological processes leading to a deteriorating insulin production are not yet fully understood. By building models that are able to classify whether a patient has type-2 diabetes or not from whole slide images of the […]


Predicting Perovskite Thin-Film Photovoltaic Performance from Photoluminescence Videos

Photovoltaics are a key technology to decarbonize the generation of energy. While perovskite thin-films are a promising option to build powerful next generation photovoltaics demonstrating high power conversion efficiencies, their manufacturing process remains unstable. We build a model that directly predicts the solar cell performance based on a video capturing the perovskite layer formation prior […]


Optimizing electrode geometry and surface for hydrogen production

Electrolysis of water into oxygen and hydrogen is a cornerstone of modern energy storage, electric mobility and the transition towards a net-zero-emissions industry. Maximizing the efficiency of this technology is key to its economically viable wide scale adoption. One approach to both reduce the costs and improve the overall efficiency is to enhance the bubble […]


Extracting clinically relevant parameters from real-time MRI images of fontan hearts

Obtaining accurate segmentations of the heart in real-time MRI allows a more realistic view on clinically relevant parameters, such as the stroke volume. Cardiac real-time MRI can assess diastolic filling under breath maneuvers or other cardiac load situations which potentially enhances diagnostics other than CINE breath hold cardiac MRI. Real-time MRI allows rapid acquisitions during […]


Segmentation and identification of tooth instances in cone-beam CT scans

The three dimensional labeling and identification of teeth in cone-beam CT scans is a time-consuming and challenging process which is exacerbated by (partially) missing teeth, tooth misalignments as well as the presence of implants or other utilities like metal plates or wires. As part of this project we develop an AI-based instance segmentation algorithm to […]


Understanding and analyzing plant roots using semantic segmentation of MRI images

The optimization of plants has long focused on the above-ground parts. Recently, new efforts are being made to exploit the potential below ground. To this end, our partners at the FZJ have developed an imaging system which enables imaging the root system throughout the growth of the plants using MRI. Besides qualitative analysis, a precise […]