Related papers: Automated three-dimensional single cell phenotypin…
We consider discrete dynamical systems and lattice models in statistical mechanics from the point of view of their symmetry groups. We describe a C program for symmetry analysis of discrete systems. Among other features, the program…
Two-dimensional (2D) mechanical models of confluent tissues have related the mechanical state of a monolayer of cells to the average perimeter length of the cell cross sections, predicting floppiness or rigidity of the material. For the…
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as morphological transitions, complex orientation dynamics or deformations. Characterising such complex behaviour under well controlled…
Foundation models such as Segment Anything Model 2 (SAM 2) exhibit strong generalization on natural images and videos but perform poorly on medical data due to differences in appearance statistics, imaging physics, and three-dimensional…
Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by…
Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…
In a probabilistic cellular automaton in which all local transitions have positive probability, the problem of keeping a bit of information indefinitely is nontrivial, even in an infinite automaton. Still, there is a solution in 2…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
Cellular automata are often used to model systems in physics, social sciences, biology that are inherently asynchronous. Over the past 20 years, studies have demonstrated that the behavior of cellular automata drastically changed under…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
This paper describes an Artificial Embryology method (called ``Epigenetic Tracking'') to generate predefined arbitrarily shaped 2-dimensional arrays of cells by means of evolutionary techniques. It is based on a model of development, whose…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of…
3-demensional (3D) culture model is a valuable in vitro tool to study liver biology, metabolism, organogenesis, tissue morphology, drug discovery and cell-based assays. Compelling evidence suggests that cells cultured in 3D model exhibit…
The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching…
As a fundamental part of computational healthcare, Computer Tomography (CT) and Magnetic Resonance Imaging (MRI) provide volumetric data, making the development of algorithms for 3D image analysis a necessity. Despite being computationally…
In this paper, we introduce a novel parametric method for segmentation of three-dimensional images. We consider a piecewise constant version of the Mumford-Shah and the Chan-Vese functionals and perform a region-based segmentation of 3D…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
The study of organoids, artificially grown cell aggregates with the functionality and small-scale anatomy of real organs, is one of the most active areas of research in biology and biophysics, yet the basic physical origins of their…