相关论文: Automated three-dimensional single cell phenotypin…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
Tracking living cells in video sequence is difficult, because of cell morphology and high similarities between cells. Tracking-by-detection methods are widely used in multi-cell tracking. We perform multi-cell tracking based on the cell…
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to…
Inspired by recent findings that generative diffusion models learn semantically meaningful representations, we use them to discover the intrinsic hierarchical structure in biomedical 3D images using unsupervised segmentation. We show that…
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…
Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D…
3D cell tracking in a living organism has a crucial role in live cell image analysis. Cell tracking in C. elegans has two difficulties. First, cell migration in a consecutive frame is large since they move their head during scanning.…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
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…
Ascertaining the collective viability of cells in different cell culture conditions has typically relied on averaging colorimetric indicators and is often reported out in simple binary readouts. Recent research has combined viability…
The quantitative analysis of 3D confocal microscopy images of the shoot apical meristem helps understanding the growth process of some plants. Cell segmentation in these images is crucial for computational plant analysis and many automated…
Cells achieve size homeostasis by regulating their division timing based on their size, added size, and cell cycle time. Previous research under steady-state conditions demonstrated the robustness of these mechanisms. However, their dynamic…
Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates…
The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…
The interface dynamics of a 3D cell immersed in a 3D extracellular matrix is investigated. We suggest a 3D generalization of a known 2D minimal phase field model suggested in [1] for the description of keratocyte motility. Our model…
Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving,…
Cell division is a process that involves many biochemical steps and complex biophysical mechanisms. To simplify the understanding of what triggers cell division, three basic models that subsume more microscopic cellular processes associated…