Related papers: Automated three-dimensional single cell phenotypin…

The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…

The initiation of directional cell motion requires symmetry breaking that can happen both with or without external stimuli. During cell crawling, forces generated by the cytoskeleton and their transmission through mechanosensitive adhesions…

The automated segmentation and tracking of macrophages during their migration are challenging tasks due to their dynamically changing shapes and motions. This paper proposes a new algorithm to achieve automatic cell tracking in time-lapse…

We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent…

Lipid droplets (LDs) are subcellular organelles with important roles in lipid storage and metabolism and involved in various diseases including cancer, obesity, and diabetes. Conventional methods, however, have limited ability to provide…

Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…

We present a dual-stage neural network architecture for analyzing fine shape details from microscopy recordings in 3D. The system, tested on red blood cells, uses training data from both healthy donors and patients with a congenital blood…

We present a novel approach to the detection and characterization of edges, ridges, and blobs in two-dimensional images which exploits the symmetry properties of directionally sensitive analyzing functions in multiscale systems that are…

Plant roots typically exhibit a highly complex and dense architecture, incorporating numerous slender lateral roots and branches, which significantly hinders the precise capture and modeling of the entire root system. Additionally, roots…

This paper describes the method of visualization of periodic constituents and instability areas in series of measurements, being based on the algorithm of smoothing out and concept of one-dimensional cellular automata. A method can be used…

We studied phase separation in a particle interacting system under a large drive along x. We here identify the basic growth mechanisms, and demonstrate time self-similarity, finite-size scaling, as well as other interesting features of both…

We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…

This contribution belongs to a combinatorial approach to hyperbolic geometry and it is aimed at possible applications to computer simulations. It is based on the splitting method which was introduced by the author and which is reminded in…

Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Synthetic devices mimicking these structures could sensitively monitor these cellular functions…

Accurate interpretation of street-level imagery is essential for large-scale urban mapping and the creation of Spatial Digital Twin (SDT) environments. This work presents a unified framework for joint 2D-3D segmentation and association that…

This article introduces new tools to study self-organisation in a family of simple cellular automata which contain some particle-like objects with good collision properties (coalescence) in their time evolution. We draw an initial…

Generators of space-time dynamics in bioimaging have become essential to build ground truth datasets for image processing algorithm evaluation such as biomolecule detectors and trackers, as well as to generate training datasets for deep…

Biological cell imaging has become one of the most crucial research interests due to its wide-ranging applications in biomedical and microbiology studies. However, three-dimensional (3D) imaging of biological cells remains critically…

The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…