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

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.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

VOLMAP: a Large Scale Benchmark for Volume Mappings to Simple Base Domains

Correspondences between geometric domains (mappings) are ubiquitous in computer graphics and engineering, both for a variety of downstream applications and as core building blocks for higher level algorithms. In particular, mapping a shape to a convex or star-shaped domain with simple geometry is a fundamental module in existing pipelines for mesh generation, solid texturing, generation of shape correspondences, advanced manufacturing etc. For the case of surfaces, computing such a mapping with guarantees of injectivity is a solved problem. Conversely, robust algorithms for the generation of injective volume mappings to simple polytopes are yet to be found, making this a fundamental open problem in volume mesh processing. VOLMAP is a large scale benchmark aimed to support ongoing research in volume mapping algorithms. The dataset contains 4.7K tetrahedral meshes, whose boundary vertices are mapped to a variety of simple domains, either convex or star-shaped. This data constitutes the input for candidate algorithms, which are then required to position interior vertices in the domain to obtain a volume map. Overall, this yields more than 22K alternative test cases. VOLMAP also comprises tools to process this data, analyze the resulting maps, and extend the dataset with new meshes, boundary maps and base domains. This article provides a brief overview of the field, discussing its importance and the lack of effective techniques. We then introduce both the dataset and its major features. An example of comparative analysis between two existing methods is also present

Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw

Developing computational models of the human jaw acquired from cone-beam computed tomography (CBCT) scans is time-consuming and labor-intensive. Besides, a quantitative comparison is not attainable in the literature due to the involved manual tasks and the lack of surface/volumetric meshes. We share an open-access repository of 17 patient-specific finite-element (FE) models of human jaws acquired from CBCT scans and the utilized pipeline for generating them. The proposed pipeline minimizes model generation time and potential errors caused by human interventions. It gets dense surface meshes and provides reduced conformal surface/volumetric meshes suitable for FE analysis. We have quantified the geometrical variations of developed models and assessed models' accuracy from different aspects; (1) the maximum deviations from the input meshes, (2) the mesh quality, and (3) the simulation results. Our results indicate that the developed computational models are precise and have quality meshes suitable for various FE scenarios. Therefore, we believe this dataset will pave the way for future population studies

At-Most-Hexa Meshes

AbstractVolumetric polyhedral meshes are required in many applications, especially for solving partial differential equations on finite element simulations. Still, their construction bears several additional challenges compared to boundary‐based representations. Tetrahedral meshes and (pure) hex‐meshes are two popular formats in scenarios like CAD applications, offering opposite advantages and disadvantages. Hex‐meshes are more intricate to construct due to the global structure of the meshing, but feature much better regularity, alignment, are more expressive, and offer the same simulation accuracy with fewer elements. Hex‐dominant meshes, where most but not all cell elements have a hexahedral structure, constitute an attractive compromise, potentially unlocking benefits from both structures, but their generality makes their employment in downstream applications difficult. In this work, we introduce a strict subset of general hex‐dominant meshes, which we term 'at‐most‐hexa meshes', in which most cells are still hexahedral, but no cell has more than six boundary faces, and no face has more than four sides. We exemplify the ease of construction of at‐most‐hexa meshes by proposing a frugal and straightforward method to generate high‐quality meshes of this kind, starting directly from hulls or point clouds, for example, from a 3D scan. In contrast to existing methods for (pure) hexahedral meshing, ours does not require an intermediate parameterization of other costly pre‐computations and can start directly from surfaces or samples. We leverage a Lloyd relaxation process to exploit the synergistic effects of aligning an orientation field in a modified 3D Voronoi diagram using the norm for cubical cells. The extracted geometry incorporates regularity as well as feature alignment, following sharp edges and curved boundary surfaces. We introduce specialized operations on the three‐dimensional graph structure to enforce consistency during the relaxation. The resulting algorithm allows for an efficient evaluation with parallel algorithms on GPU hardware and completes even large reconstructions within minutes

EIT Reconstruction Algorithms: Pitfalls, Challenges and Recent Developments

We review developments, issues and challenges in Electrical Impedance Tomography (EIT), for the 4th Workshop on Biomedical Applications of EIT, Manchester 2003. We focus on the necessity for three dimensional data collection and reconstruction, efficient solution of the forward problem and present and future reconstruction algorithms. We also suggest common pitfalls or ``inverse crimes'' to avoid.Comment: A review paper for the 4th Workshop on Biomedical Applications of EIT, Manchester, UK, 200

Parallel software tool for decomposing and meshing of 3d structures

An algorithm for automatic parallel generation of three-dimensional unstructured computational meshes based on geometrical domain decomposition is proposed in this paper. Software package build upon proposed algorithm is described. Several practical examples of mesh generation on multiprocessor computational systems are given. It is shown that developed parallel algorithm enables us to reduce mesh generation time significantly (dozens of times). Moreover, it easily produces meshes with number of elements of order 5 · 107, construction of those on a single CPU is problematic. Questions of time consumption, efficiency of computations and quality of generated meshes are also considered