The bacterial pathogen Listeria monocytogenes (Lm) invades host cells, ruptures its internalization vacuole and reaches the cytosol for replication. A high-content siRNA microscopy screen allowed us to identify epithelial cell factors involved in Lm vacuolar rupture, among them the serine/threonine kinase Taok2. Kinase activity inhibition using a specific drug validated a role for Taok2 in...
Antibiotic resistance in bacteria is currently developing into one of the most challenging global health threads. Novel fast and reliable antibiotic resistance tests are the key to avoid unnecessary use of broad-spectrum antibiotics in calculated therapy and to administer tailored narrow-spectrum antibiotic therapy earlier.
Detecting the effect of an antibiotic with phenotypic susceptibility...
To survive and grow efficiently in harsh environments, bacterial cells make 3D colonies on surfaces, called biofilms. Biofilms are considered as the most abundant form of microbial life on Earth. To obtain an understanding of the development and heterogeneity inside biofilms, it is important to extract quantitative parameters for biofilms in space and time during growth. Single-cell...
In biomedical research, the migration behaviour of cells and interactions between various cell types are frequently studied subjects. An automated and quantitative analysis of time-lapse microscopy data is an essential component of these studies, especially when characteristic migration patterns need to be identified. Plenty of software tools have been developed to serve this need. However,...
Biological tissues are often dynamic and highly organized. Its Spatio-temporal patterns are relevant in many biological processes such as tissue homeostasis, viral infection, or tumor development. These processes can be studied by imaging techniques including light and fluorescence microscopy. Quantitative information about biological systems can be inferred from the biological imaging data,...
Candida albicans is a commensal fungus of the human microbiota that, under certain circumstances, can become pathogenic and cause life-threatening systemic infections. Several factors influence C. albicans virulence, but the specific triggers to this commensal-to-pathogenic shift are poorly understood. To study this in a more physiological approach, we are using a gut-on-chip model. This...
Bioimage analysis involves the development of novel algorithm pipelines that are easy to adapt to new data sets. A common way to create such tools is to develop scripts in languages like ImageJ macros [1], which requires programming experience and detailed knowledge of the available script functions. Alternatively, there are graphical programming languages like KNIME [2] and Icy protocols...
Computational modeling and simulation become increasingly important to analyze tissue morphogenesis. A number of corresponding software tools have been developed but require scientists to encode their models in an imperative programming language. Morpheus [1,2], on the other hand, is an extensible open-source software framework that is entirely based on declarative modeling. It uses the...
Fungal infections are emerging as a significant health risk for humans. The innate immune system is the first line of defense against pathogens and broadly protects against invading microorganisms. In this study we investigate the dynamics of the interaction of the fungus Candida glabrata and polymorphonuclear neutrophils (PMNs). We use confrontation assays with live cell imaging and...
Invasive pulmonary aspergillosis is a great threat to immunocompromised patients as treatment options are limited and only successful upon early diagnosis. Infectious agents are conidia of the mold Aspergillus fumigatus that enter the lung alveoli but, in immunocompetent humans, are cleared by innate immune cells such as macrophages. In immunocompromised patients, however, conidia can grow...
One of the prominent pathogens causing bacteremia is Staphylococcus aureus (S.aureus). The liver is a major player in the clearance of bloodstream-infections due to the high abundance of liver tissue macrophages. Macrophages possess a high phenotypic plasticity, including M0 (non-polarized), M1 (bactericidal) and M2 (tissue remodeling) phenotypes. In preliminary mono-culture experiments,...
Phagocytosis is a major immune response mechanism of professional phagocytes to combat invading pathogens. Therefore, the quantification and characterization of phagocytosis is essential for a better understanding of host-pathogen interactions. Typically, various phagocytosis measures, such as the phagocytosis ratio, the uptake ratio or the symmetrized phagocytic index are used for this...
The bacterial pathogen Listeria monocytogenes (Lm) invades host cells, ruptures its internalization vacuole and reaches the cytosol for replication. A high-content siRNA microscopy screen allowed us to identify epithelial cell factors involved in Lm vacuolar rupture, among them the serine/threonine kinase Taok2. Kinase activity inhibition using a specific drug validated a role for Taok2 in...
Antibiotic resistance in bacteria is currently developing into one of the most challenging global health threads. Novel fast and reliable antibiotic resistance tests are the key to avoid unnecessary use of broad-spectrum antibiotics in calculated therapy and to administer tailored narrow-spectrum antibiotic therapy earlier.
Detecting the effect of an antibiotic with phenotypic susceptibility...
To survive and grow efficiently in harsh environments, bacterial cells make 3D colonies on surfaces, called biofilms. Biofilms are considered as the most abundant form of microbial life on Earth. To obtain an understanding of the development and heterogeneity inside biofilms, it is important to extract quantitative parameters for biofilms in space and time during growth. Single-cell...
In biomedical research, the migration behaviour of cells and interactions between various cell types are frequently studied subjects. An automated and quantitative analysis of time-lapse microscopy data is an essential component of these studies, especially when characteristic migration patterns need to be identified. Plenty of software tools have been developed to serve this need. However,...
Biological tissues are often dynamic and highly organized. Its Spatio-temporal patterns are relevant in many biological processes such as tissue homeostasis, viral infection, or tumor development. These processes can be studied by imaging techniques including light and fluorescence microscopy. Quantitative information about biological systems can be inferred from the biological imaging data,...
Candida albicans is a commensal fungus of the human microbiota that, under certain circumstances, can become pathogenic and cause life-threatening systemic infections. Several factors influence C. albicans virulence, but the specific triggers to this commensal-to-pathogenic shift are poorly understood. To study this in a more physiological approach, we are using a gut-on-chip model. This...
Bioimage analysis involves the development of novel algorithm pipelines that are easy to adapt to new data sets. A common way to create such tools is to develop scripts in languages like ImageJ macros [1], which requires programming experience and detailed knowledge of the available script functions. Alternatively, there are graphical programming languages like KNIME [2] and Icy protocols...
Computational modeling and simulation become increasingly important to analyze tissue morphogenesis. A number of corresponding software tools have been developed but require scientists to encode their models in an imperative programming language. Morpheus [1,2], on the other hand, is an extensible open-source software framework that is entirely based on declarative modeling. It uses the...
Fungal infections are emerging as a significant health risk for humans. The innate immune system is the first line of defense against pathogens and broadly protects against invading microorganisms. In this study we investigate the dynamics of the interaction of the fungus Candida glabrata and polymorphonuclear neutrophils (PMNs). We use confrontation assays with live cell imaging and...
Invasive pulmonary aspergillosis is a great threat to immunocompromised patients as treatment options are limited and only successful upon early diagnosis. Infectious agents are conidia of the mold Aspergillus fumigatus that enter the lung alveoli but, in immunocompetent humans, are cleared by innate immune cells such as macrophages. In immunocompromised patients, however, conidia can grow...
One of the prominent pathogens causing bacteremia is Staphylococcus aureus (S.aureus). The liver is a major player in the clearance of bloodstream-infections due to the high abundance of liver tissue macrophages. Macrophages possess a high phenotypic plasticity, including M0 (non-polarized), M1 (bactericidal) and M2 (tissue remodeling) phenotypes. In preliminary mono-culture experiments,...
Phagocytosis is a major immune response mechanism of professional phagocytes to combat invading pathogens. Therefore, the quantification and characterization of phagocytosis is essential for a better understanding of host-pathogen interactions. Typically, various phagocytosis measures, such as the phagocytosis ratio, the uptake ratio or the symmetrized phagocytic index are used for this...
Image-based systems biology is emerging as a powerful new paradigm in cancer research. However, there is an exigent need for a new image-based systems biology framework to better understand the role of the vasculature in cancer progression, metastasis and therapeutic response. In spite of recent advances in vascular imaging, there is a dearth of methods that make blood vessels simultaneously...
Action recognition (AR) is a technique, widely used to analyze the behavior of humans from digital videos. AR detects specific motility patterns a displayed when performing certain actions (i.e. crossing a road, forming aggregates, or leaving a bag), with important applications in video-surveillance and autonomous driving. Similar to humans, the cells of the immune system display a broad range...
All our voluntary movements are actuated by striated muscle, where each muscle cell contains highly regular myofibrils comprising a periodic arrangement of sarcomere units built of actin filaments, myosin molecular motors and cross-linking proteins. How myofibrils self-assemble during myofibrillogenesis into such ‘cytoskeletal crystals’ remains poorly understood. To better understand this...
If the human immune system is weakened, fungal infections can lead to a life-threatening condition in humans. In order to determine the type of fungus, the pathologist has to cut out a piece of tissue from the organ to be examined. A common method of highlighting the fungi is to stain the entire sample slices. An alternative and relatively new method is MALDI-imaging (matrix-assisted laser...
Dynamical Bayesian networks (DBNs) are used to find causal relationships in time resolved data. They have, for example, been used to investigate spike dynamics in neuroscience [1, 2] and we will here demonstrate how DBNs can be used to analyse cell track data to find interactions between different events that we can observe. In this way we can investigate if the heterogeneity that is often...
The zoonotic obligate intracellular pathogen Coxiella burnetii causes infections in ruminants and humans. When untreated, the acute disease (Q fever) may lead to a chronic manifestation. During its biphasic life cycle, C. burnetii alternates between two morphoforms: the large cell variant (LCV) occurs exclusively inside the host cell; the spore-like small cell variant (SCV) is the major...
Light sheet fluorescence microscopy (LSFM) produces very large data sets that are difficult to analyze manually. An alternative to such a time-consuming and biased process is a fully automated analysis. Due to the large data volume, it is essential to improve the efficiency via parallelization and optimized memory-management. The programming language C++ is ideal for such high-performance...
Multispectral optoacoustic tomography (MSOT) is an emerging, non-invasive imaging modality that has gained wide application due to its ability to gather functional tissue information at high spatio-temporal resolution and imaging depth. However, quantitative analysis of MSOT image data is to date almost exclusively limited to the extraction of basic features, e.g. mean and maximum intensity,...
Here we demonstrate the use of 3Dscript to create high-quality 3D animations of multi-dimensional imaging data sets intuitively and reproducibly. In 3Dscript, animations are represented as text written in natural English language. Arbitrarily complex motion paths can be described by concatenating multiple elementary instructions in the form of “From frame 0 to frame 100 rotate by 180 degrees...
Fluorescence microscopy is one of the most useful techniques to investigate the location and the interactions between cells in vivo and in vitro. With that technique it’s possible to study cellular mechanisms in a non-invasive method by using the light emitted by matter when it is excited with electromagnetic waves. The main subsequent pros are the possibility to use in vivo approaches...
Studying embryo and tissue morphogenesis is challenging because of the large number of factors influencing each other and the complex and dynamic geometries in which this happens. Computational methods provide a way to disentangle the different processes by gaining control over specific parameters. In this work, we construct a three dimensional (3D) model of a developing zebrafish embryo...
Intercellular variability can be both a source of information and a confounding factor in understanding signal propagation in biological networks. It is crucial to properly sample the population, which demands high-throughput methods. In turn, these require not only automated microscopy, but also automated analysis. Therefore, we developed a set of algorithms to address that challenge. Using a...
Image-based systems biology is emerging as a powerful new paradigm in cancer research. However, there is an exigent need for a new image-based systems biology framework to better understand the role of the vasculature in cancer progression, metastasis and therapeutic response. In spite of recent advances in vascular imaging, there is a dearth of methods that make blood vessels simultaneously...
Action recognition (AR) is a technique, widely used to analyze the behavior of humans from digital videos. AR detects specific motility patterns a displayed when performing certain actions (i.e. crossing a road, forming aggregates, or leaving a bag), with important applications in video-surveillance and autonomous driving. Similar to humans, the cells of the immune system display a broad range...
All our voluntary movements are actuated by striated muscle, where each muscle cell contains highly regular myofibrils comprising a periodic arrangement of sarcomere units built of actin filaments, myosin molecular motors and cross-linking proteins. How myofibrils self-assemble during myofibrillogenesis into such ‘cytoskeletal crystals’ remains poorly understood. To better understand this...
If the human immune system is weakened, fungal infections can lead to a life-threatening condition in humans. In order to determine the type of fungus, the pathologist has to cut out a piece of tissue from the organ to be examined. A common method of highlighting the fungi is to stain the entire sample slices. An alternative and relatively new method is MALDI-imaging (matrix-assisted laser...
Dynamical Bayesian networks (DBNs) are used to find causal relationships in time resolved data. They have, for example, been used to investigate spike dynamics in neuroscience [1, 2] and we will here demonstrate how DBNs can be used to analyse cell track data to find interactions between different events that we can observe. In this way we can investigate if the heterogeneity that is often...
The zoonotic obligate intracellular pathogen Coxiella burnetii causes infections in ruminants and humans. When untreated, the acute disease (Q fever) may lead to a chronic manifestation. During its biphasic life cycle, C. burnetii alternates between two morphoforms: the large cell variant (LCV) occurs exclusively inside the host cell; the spore-like small cell variant (SCV) is the major...
Light sheet fluorescence microscopy (LSFM) produces very large data sets that are difficult to analyze manually. An alternative to such a time-consuming and biased process is a fully automated analysis. Due to the large data volume, it is essential to improve the efficiency via parallelization and optimized memory-management. The programming language C++ is ideal for such high-performance...
Multispectral optoacoustic tomography (MSOT) is an emerging, non-invasive imaging modality that has gained wide application due to its ability to gather functional tissue information at high spatio-temporal resolution and imaging depth. However, quantitative analysis of MSOT image data is to date almost exclusively limited to the extraction of basic features, e.g. mean and maximum intensity,...
Here we demonstrate the use of 3Dscript to create high-quality 3D animations of multi-dimensional imaging data sets intuitively and reproducibly. In 3Dscript, animations are represented as text written in natural English language. Arbitrarily complex motion paths can be described by concatenating multiple elementary instructions in the form of “From frame 0 to frame 100 rotate by 180 degrees...
Fluorescence microscopy is one of the most useful techniques to investigate the location and the interactions between cells in vivo and in vitro. With that technique it’s possible to study cellular mechanisms in a non-invasive method by using the light emitted by matter when it is excited with electromagnetic waves. The main subsequent pros are the possibility to use in vivo approaches...
Studying embryo and tissue morphogenesis is challenging because of the large number of factors influencing each other and the complex and dynamic geometries in which this happens. Computational methods provide a way to disentangle the different processes by gaining control over specific parameters. In this work, we construct a three dimensional (3D) model of a developing zebrafish embryo...
Intercellular variability can be both a source of information and a confounding factor in understanding signal propagation in biological networks. It is crucial to properly sample the population, which demands high-throughput methods. In turn, these require not only automated microscopy, but also automated analysis. Therefore, we developed a set of algorithms to address that challenge. Using a...
To survive and grow efficiently in harsh environments, bacterial cells make 3D colonies on surfaces, called biofilms. Biofilms are considered as the most abundant form of microbial life on Earth. To obtain an understanding of the development and heterogeneity inside biofilms, it is important to extract quantitative parameters for biofilms in space and time during growth. Single-cell...
To survive and grow efficiently in harsh environments, bacterial cells make 3D colonies on surfaces, called biofilms. Biofilms are considered as the most abundant form of microbial life on Earth. To obtain an understanding of the development and heterogeneity inside biofilms, it is important to extract quantitative parameters for biofilms in space and time during growth. Single-cell...
Single molecule localization microscopy (SMLM) has matured into one of the most powerful and widely used super-resolution imaging methods. In this talk, we'll highlight recent developments of our lab to push the limits of SMLM using computational approaches.
One long-standing challenge is to visualize cells at high resolution and with high throughput. SMLM delivers exquisite spatial...
Poster room (Zoom): tba
The necessity to analyze scientific images is as old as the ability to acquire such data. While this analysis did initially happen by observation only, modern microscopy techniques now enable us to image at unprecedented spatial and temporal resolutions, through the 'eyes' of many and very diverse imaging modalities.
The unfathomable amounts of data acquired in the...
Mitochondria form contacts to endosomes and endoplasmic reticulum, but little is known about the dynamics of such membrane contact sites (MCSs). Mitochondria receive cholesterol from late endosomes and lysosomes (LE/LYSs) and the plasma membrane (PM) for production of oxysterols and steroid hormones in a process depending on the endo-lysosomal sterol transfer protein Niemann Pick C2 (NPC2). In...
Mitochondria form contacts to endosomes and endoplasmic reticulum, but little is known about the dynamics of such membrane contact sites (MCSs). Mitochondria receive cholesterol from late endosomes and lysosomes (LE/LYSs) and the plasma membrane (PM) for production of oxysterols and steroid hormones in a process depending on the endo-lysosomal sterol transfer protein Niemann Pick C2 (NPC2). In...
In recent years, bio-medical research has made tremendous progress regarding imaging modalities and techniques for accurate patient diagnostics. On the other hand, these staggering amounts of imaging data from various modalities pose new challenges. Additionally, the underlying biological mechanisms that bring forth macroscopic image changes remain uncertain. Patient biopsies or autopsies can...
In recent years, bio-medical research has made tremendous progress regarding imaging modalities and techniques for accurate patient diagnostics. On the other hand, these staggering amounts of imaging data from various modalities pose new challenges. Additionally, the underlying biological mechanisms that bring forth macroscopic image changes remain uncertain. Patient biopsies or autopsies can...
