Related papers: Image-based Modelling of Organogenesis
Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
Living biological tissue is a complex system, constantly growing and changing in response to external and internal stimuli. These processes lead to remarkable and intricate changes in shape. Modeling and understanding both natural and…
We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems…
Medical image segmentation has advanced rapidly over the past two decades, largely driven by deep learning, which has enabled accurate and efficient delineation of cells, tissues, organs, and pathologies across diverse imaging modalities.…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
Human anatomy, morphology, and associated diseases can be studied using medical imaging data. However, access to medical imaging data is restricted by governance and privacy concerns, data ownership, and the cost of acquisition, thus…
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric…
Deep generative modeling has emerged as a powerful tool for synthesizing realistic medical images, driving advances in medical image analysis, disease diagnosis, and treatment planning. This chapter explores various deep generative models…
Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation,…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
The dynamics and processes of urban morphogenesis are a central issue regarding a long-term sustainability of urban systems. They however imply stakeholders and parameters at multiple temporal and spatial scales simultaneously, leading to…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…