19,126 research outputs found
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
Procedural function-based modelling of volumetric microstructures
We propose a new approach to modelling heterogeneous objects containing internal volumetric structures with size of details orders of magnitude smaller than the overall size of the object. The proposed function-based procedural representation provides compact, precise, and arbitrarily parameterised models of coherent microstructures, which can undergo blending, deformations, and other geometric operations, and can be directly rendered and fabricated without generating any auxiliary representations (such as polygonal meshes and voxel arrays). In particular, modelling of regular lattices and cellular microstructures as well as irregular porous media is discussed and illustrated. We also present a method to estimate parameters of the given model by fitting it to microstructure data obtained with magnetic resonance imaging and other measurements of natural and artificial objects. Examples of rendering and digital fabrication of microstructure models are presented
Image Sampling with Quasicrystals
We investigate the use of quasicrystals in image sampling. Quasicrystals
produce space-filling, non-periodic point sets that are uniformly discrete and
relatively dense, thereby ensuring the sample sites are evenly spread out
throughout the sampled image. Their self-similar structure can be attractive
for creating sampling patterns endowed with a decorative symmetry. We present a
brief general overview of the algebraic theory of cut-and-project quasicrystals
based on the geometry of the golden ratio. To assess the practical utility of
quasicrystal sampling, we evaluate the visual effects of a variety of
non-adaptive image sampling strategies on photorealistic image reconstruction
and non-photorealistic image rendering used in multiresolution image
representations. For computer visualization of point sets used in image
sampling, we introduce a mosaic rendering technique.Comment: For a full resolution version of this paper, along with supplementary
materials, please visit at
http://www.Eyemaginary.com/Portfolio/Publications.htm
Single-picture reconstruction and rendering of trees for plausible vegetation synthesis
State-of-the-art approaches for tree reconstruction either put limiting constraints on the input side (requiring multiple photographs, a scanned point cloud or intensive user input) or provide a representation only suitable for front views of the tree. In this paper we present a complete pipeline for synthesizing and rendering detailed trees from a single photograph with minimal user effort. Since the overall shape and appearance of each tree is recovered from a single photograph of the tree crown, artists can benefit from georeferenced images to populate landscapes with native tree species. A key element of our approach is a compact representation of dense tree crowns through a radial distance map. Our first contribution is an automatic algorithm for generating such representations from a single exemplar image of a tree. We create a rough estimate of the crown shape by solving a thin-plate energy minimization problem, and then add detail through a simplified shape-from-shading approach. The use of seamless texture synthesis results in an image-based representation that can be rendered from arbitrary view directions at different levels of detail. Distant trees benefit from an output-sensitive algorithm inspired on relief mapping. For close-up trees we use a billboard cloud where leaflets are distributed inside the crown shape through a space colonization algorithm. In both cases our representation ensures efficient preservation of the crown shape. Major benefits of our approach include: it recovers the overall shape from a single tree image, involves no tree modeling knowledge and minimal authoring effort, and the associated image-based representation is easy to compress and thus suitable for network streaming.Peer ReviewedPostprint (author's final draft
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