Tetrahedral meshing in the wild

Hu, Yixin; Zhou, Qun; Gao, Xifeng; Jacobson, Alec; Zorin, Denis; Panozzo, Daniele

doi:10.1145/3197517.3201353

Cited by 195 publications

(168 citation statements)

References 84 publications

(78 reference statements)

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“…For simulations that track concentrations in the volume, the conditioned surface mesh is tetrahedralized ( Fig 1E). We note that although there exist advanced tetrahedral mesh generation tools, such as TetWild [40], and others [41][42][43][44][45][46], which can generate Finite Element Analysis (FEA) compatible volume meshes from these poor quality initial surfaces, these tools are general purpose and currently not adapted to the length scales of single cells and subcellular structures. Mesh defects such as disconnects in the Endoplasmic Reticulum (ER) arising from the limited resolving powers of EM or errors in segmentation (e.g., Fig 2C and 2D) require more careful and often manual curation.…”

Section: Plos Computational Biologymentioning

confidence: 99%

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

et al. 2020

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Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the finite element method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.

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Section: Plos Computational Biologymentioning

confidence: 99%

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

et al. 2020

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“…These classes are the focus of recent research works (e.g. [78] and [28] respectively). Many of the mechanisms employed by Hex-aLab are, in principle, extendible to them, including the filtering tools, the visualization modes, the internal data structures.…”

Section: Current Limitations and Future Workmentioning

confidence: 99%

HexaLab.net: An online viewer for hexahedral meshes

Bracci

Tarini

Pietroni

et al. 2019

Computer-Aided Design

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We introduce HexaLab: a WebGL application for real time visualization, exploration and assessment of hexahedral meshes. HexaLab can be used by simply opening www.hexalab.net. Our visualization tool targets both users and scholars. Practitioners who employ hexmeshes for Finite Element Analysis, can readily check mesh quality and assess its usability for simulation. Researchers involved in mesh generation may use HexaLab to perform a detailed analysis of the mesh structure, isolating weak points and testing new solutions to improve on the state of the art and generate high quality images. To this end, we support a wide variety of visualization and volume inspection tools. Our system offers also immediate access to a repository containing all the publicly available meshes produced with the most recent techniques for hexmesh generation. We believe HexaLab, providing a common tool for visualizing, assessing and distributing results, will push forward the recent strive for replicability in our scientific community. Figure 1: A screen-shot of HexaLab running inside Chrome under macOS. Model courtesy of [1]. Intended usagesVisualization: the main function of HexaLab is to serve as an advanced 3D visualizer for hex-meshes, for the purpose of providing a visual insight on the inspected models, and thus, indirectly, on the algorithms that produced them. The visualization of a hex-mesh is complicated by the resolution of the model and, even more so, by the presence of non-trivial 3D internal structures. HexaLab faces this task by offering a set of interactively controlled tools (cutting planes, etc), a shape-revealing realistic lighting (drastically improving the readability of images), novel modalities specifically designed to better communicate the shape of the cells, as well as colormaps and spatial glyphs, to reveal the quality, the topological characteristics, and so on. Assessment: for the same purpose, HexaLab can be used

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“…2. We note that although there exist advanced tetrahedral mesh generation tools, such as TetWild [11], which can generate Finite Element Analysis (FEA) compatible volume meshes automatically from these poor quality initial surfaces, many mesh defects are the result of the limited resolving powers of EM (e.g., Fig. 2A1, A2) and require more careful curation.…”

Section: Meshing Challengesmentioning

confidence: 99%

GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

Lee

Laughlin

Beaumelle

et al. 2019

Preprint

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Recent advances in electron microscopy have, for the first time, enabled imaging of single cells in 3D at a nanometer length scale resolution. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations will require a system for going from electron micrographs to 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method (FEM). In this paper, we develop an end-to-end pipeline for this task by adapting and extending computer graphics mesh processing and smoothing algorithms. Our workflow makes use of our recently rewritten mesh processing software, GAMer 2, which implements several mesh conditioning algorithms and serves as a platform to connect different pipeline steps. We apply this pipeline to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and demonstrate that the resultant meshes are suitable for finite element simulations. Our pipeline, which consists of free and open-source community driven tools, is a step towards routine physical simulations of biological processes in realistic geometries. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery. Author summary3D imaging of cellular components and associated reconstruction methods have made great strides in the past decade, opening windows into the complex intraceullar organization. These advances also mean that computational tools need to be developed to work with these images not just for purposes of visualization but also for biophysical simulations. Here, we describe a pipeline that takes images from electron microscopy as input and produces smooth surface and volume meshes as output. These meshes are suitable for building high-quality finite element simulations of cellular processes modeled by ordinary and partial differential equations, bringing us closer to realizing the goal of generating high-resolution simulations of such phenomena in realistic geometries. We demonstrate the utility of this pipeline by meshing 3D reconstructions of dendritic spines, calculating 1 the curvatures of the different component membranes, and conducting finite-element simulations of reaction-diffusion equations using the generated meshes. The software tools employed in our pipeline are community driven, open source, and free. We believe that technologies such as those presented will enable a new frontier in biophysical simulations in realistic geometries.

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Tetrahedral meshing in the wild

Cited by 195 publications

References 84 publications

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

HexaLab.net: An online viewer for hexahedral meshes

GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

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