Related papers: 3D mesh processing using GAMer 2 to enable reactio…
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for…
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…
Traditional methods for biological shape inference, such as deep learning (DL) and active contour models, face important limitations in 3D. DL approaches require large annotated datasets, which are often impractical to obtain, while active…
Computer representations of three-dimensional (3D) geometries are crucial for simulating systems and processes in engineering and science. In medicine, and more specifically, biomechanics and orthopaedics, obtaining and using 3D geometries…
While high-resolution microscopic techniques are crucial for studying cellular structures in cell biology, obtaining such images from thick 3D engineered tissues remains challenging. In this review, we explore advancements in fluorescence…
3D cell segmentation methods are often hindered by \emph{oversegmentation}, where a single cell is incorrectly split into multiple fragments. This degrades the final segmentation quality and is notoriously difficult to resolve, as…
In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
Finite element meshes for 3D models simulating realistic malignant melanoma (MM) growth, incorporating accurate dielectric properties of the skin, have been developed. Numerical simulations illustrate how 3D finite element meshes can be…
Computational meshes, as a way to partition space, form the basis of much of PDE simulation technology, for instance for the finite element and finite volume discretization methods. In complex simulations, we are often driven to modify an…
The traditional workflow in continuum mechanics simulations is that a geometry description -- for example obtained using Constructive Solid Geometry or Computer Aided Design tools -- forms the input for a mesh generator. The mesh is then…
We consider the task of generating realistic 3D shapes, which is useful for a variety of applications such as automatic scene generation and physical simulation. Compared to other 3D representations like voxels and point clouds, meshes are…
Modern 3D Computer-Aided-Design (CAD) systems use mainly two types of geometric models. Classically, objects are defined by a Boundary Representation (B-Rep), where only the objects' surfaces with their corresponding edges and nodes are…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
Many engineering systems require accurate simulations of complex physical systems. Yet, analytical solutions are only available for simple problems, necessitating numerical approximations such as the Finite Element Method (FEM). The cost…
Recent 3D-based manipulation methods either directly predict the grasp pose using 3D neural networks, or solve the grasp pose using similar objects retrieved from shape databases. However, the former faces generalizability challenges when…
We consider problems related to initial meshing and adaptive mesh refinement for the electromagnetic simulation of various structures. The quality of the initial mesh and the performance of the adaptive refinement are of great importance…
3D meshes are a fundamental representation widely used in computer science and engineering. In robotics, they are particularly valuable because they capture objects in a form that aligns directly with how robots interact with the physical…
Despite the rapidly evolving field of computational electromagnetics, few open-source tools have managed to tackle the problem of automatic mesh generation for properly discretizing the problem of interest into a finite set of elements…