Aspergillus fumigatus infection in virtual alveolus
In this project, a virtual infection with A. fumigatus in human and murine alveolus is simulated. Aspergillus fumigatus, a lung pathogen, enters the lower respiratory tract via conidia, forms hyphae and poses life-threatening risks. Alveolar macrophages (AM) can recognise and eliminate this fungus, prompting an investigation into how AM numbers affect A. [...]
Automated Image Analysis of Liver Tissue Using JIPipe and ImageJ
Deaths due to liver disease have increased significantly. The liver is made up of key structures that functional components of the liver. Sinusoids are specialised porous blood vessels found mainly in the liver. They are a type of capillary that differs from typical capillaries because of their larger diameter and [...]
Bacterial Co-infection model
Bacterial Co-infection model Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are often found together in severe polymicrobial infections resistant to treatment. In this project a combination of wet-lab experiments and in silico modeling was used to explore the interactions, using both, representative laboratory strains and strains co-isolated from clinical samples. [...]
Characterizing the pore structure of cryo-polymers
Cryogels are porous, sponge-like materials comprising an interconnected network of macropores, which are of great importance for applications such as 3D scaffolds for tissue culture, filters, or membranes. The application of cryogels is dependent on the size of their interconnected pores. In this project, various cryogels were prepared and pores [...]
Detection of Bloodstream Infections
The prevention of sepsis requires the early detection of pathogens in bloodstream infections. It is known that neutrophils exhibit characteristic behaviors when infected with Candida species. In this study, blood samples from healthy donors were infected with Candida albicans and Candida glabrata, and neutrophils were imaged. This project applied advanced [...]
Droplet Analysis – Deep Learning based
Learning based This project addresses antibiotic resistance by developing a high-throughput platform for rapid antibiotic susceptibility testing. The platform integrates microfluidic droplet encapsulation of individual bacterial cells, (ii) 2D angle-resolved light scattering (ARS) for label-free imaging, and (iii) deep learning algorithms to analyze microbial growth dynamics. This project used advanced [...]
Gut-on-chip model, image-based analysis of Candida albicans
Microbial dysbiosis is closely associated with chronic inflammation and inflammatory bowel disease. Traditional in vitro models proposed to study the underlying mechanisms lack the required tissue complexity and therefore often fail to accurately reproduce the complex, multi-component structure of the intestinal wall. On the other hand, animal models are not [...]
IMFSegNet
The amount of fat in muscle tissue affects how well a muscle works. To distinguish fat from muscle tissue, ORO staining is utilized, as fat yields in a highly saturated red tone with the surrounding muscle tissue in a purple-blue to pale pink tone. Additionally, experts can distinguish fat areas, [...]
JIPipe
https://www.jipipe.org/ Developing image analysis pipelines without programming ImageJ is a powerful tool for image analysis that is easy to learn and can be extended with hundreds of plugins. Creating a batch processing pipeline on the other hand requires programming knowledge in langauges like ImageJ macros or Python, as well [...]
KITE – Epidemiological modelling of infection spread in child care facilities
During the global COVID-19 pandemic, numerous measures were taken to mitigate the spread of infection. Among these was the closure of childcare centers since non-pharmaceutical interventions like social distancing or mask-wearing are not applicable to preschool children. However, this has led to extensive negative effects, such as reducing educational, psychosocial, [...]
Modeling pathogen AMP evasion
In this project, an antimicrobial peptide (AMP) evasion mechanism is modeled and simulated. This mechanism, which we refer to as spatial distancing, consists of a pathogen cell secreting defense molecules that can bind to AMP and form complexes with the highest concentration close to the cell surface that diffuse away [...]
Mu Mo Sim
The Multi-Model Simulator (MuMoSim) project aims to advance modeling in infection research to the next level by introducing a novel quantitative and predictive simulation tool. The standout features of the framework are based on the self-consistent integration of various modeling approaches within a single framework. As a result, MuMoSim can [...]
Peroxisome motility analysis
Diffusion and mobility are essential for cellular functions, as they facilitate the meeting of molecules and organelles, thereby enabling them to interact and perform their respective roles within the cell. To observe these dynamics, it is necessary to have high spatial and temporal resolution, as well as accurate analysis of [...]
Virtual whole blood infection assay
Experiments – Whole blood infection assays In the wet lab whole blood experiments are performed where blood samples from healthy donors or immunocompromised individuals are infected with various pathogens such as the human-pathogenic fungi Candida albicans and Candida glabrata or the bacterial pathogen Staphylococcus aureus. With the aid of FACS analysis and survival assays temporal [...]