Related papers: 3D mesh processing using GAMer 2 to enable reactio…
We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries,…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
Converting a three-dimensional medical image into a 3D mesh that satisfies both the quality and fidelity constraints of predictive simulations and image-guided surgical procedures remains a critical problem. Presented is an image-to-mesh…
The devices designed for the Internet-of-Things encompass a large variety of distinct processor architectures, forming a highly heterogeneous zoo. In order to tackle this, we employ a simulator to estimate the performance of the…
We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
Mesh processing pipelines are mature, but adapting them to newer non-mesh surface representations -- which enable fast rendering with compact file size -- requires costly meshing or transmitting bulky meshes, negating their core benefits…
Implicit neural representations have emerged as a powerful approach for encoding complex geometries as continuous functions. These implicit models are widely used in computer vision and 3D content creation, but their integration into…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
Accurate modeling of moving boundaries and interfaces is a difficulty present in many situations of computational mechanics. We use the eXtreme Mesh deformation approach (X-Mesh) to simulate the interaction between two immiscible flows…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
Sketching is used as a ubiquitous tool of expression by novices and experts alike. In this thesis I explore two methods that help a system provide a geometric machine-understanding of sketches, and in-turn help a user accomplish a…
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 cost and accuracy of simulating complex physical systems using the Finite Element Method (FEM) scales with the resolution of the underlying mesh. Adaptive meshes improve computational efficiency by refining resolution in critical…
CNN-based volumetric methods that label individual voxels now dominate the field of biomedical segmentation. However, 3D surface representations are often required for proper analysis. They can be obtained by post-processing the labeled…
We propose an end-to-end deep learning architecture that produces a 3D shape in triangular mesh from a single color image. Limited by the nature of deep neural network, previous methods usually represent a 3D shape in volume or point cloud,…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
During the last ten years, increasing efforts were made to improve and simplify the process from Computer Aided Design (CAD) modeling to a numerical simulation. It has been shown that the transition from one model to another, i.e. the…
Partial differential equations can be solved on general polygonal and polyhedral meshes, through Polytopal Element Methods (PEMs). Unfortunately, the relation between geometry and analysis is still unknown and subject to ongoing research in…