33,394 research outputs found

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

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

    Geometry Modeling for Unstructured Mesh Adaptation

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    The quantification and control of discretization error is critical to obtaining reliable simulation results. Adaptive mesh techniques have the potential to automate discretization error control, but have made limited impact on production analysis workflow. Recent progress has matured a number of independent implementations of flow solvers, error estimation methods, and anisotropic mesh adaptation mechanics. However, the poor integration of initial mesh generation and adaptive mesh mechanics to typical sources of geometry has hindered adoption of adaptive mesh techniques, where these geometries are often created in Mechanical Computer- Aided Design (MCAD) systems. The difficulty of this coupling is compounded by two factors: the inherent complexity of the model (e.g., large range of scales, bodies in proximity, details not required for analysis) and unintended geometry construction artifacts (e.g., translation, uneven parameterization, degeneracy, self-intersection, sliver faces, gaps, large tolerances be- tween topological elements, local high curvature to enforce continuity). Manual preparation of geometry is commonly employed to enable fixed-grid and adaptive-grid workflows by reducing the severity and negative impacts of these construction artifacts, but manual process interaction inhibits workflow automation. Techniques to permit the use of complex geometry models and reduce the impact of geometry construction artifacts on unstructured grid workflows are models from the AIAA Sonic Boom and High Lift Prediction are shown to demonstrate the utility of the current approach

    Face image super-resolution using 2D CCA

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    In this paper a face super-resolution method using two-dimensional canonical correlation analysis (2D CCA) is presented. A detail compensation step is followed to add high-frequency components to the reconstructed high-resolution face. Unlike most of the previous researches on face super-resolution algorithms that first transform the images into vectors, in our approach the relationship between the high-resolution and the low-resolution face image are maintained in their original 2D representation. In addition, rather than approximating the entire face, different parts of a face image are super-resolved separately to better preserve the local structure. The proposed method is compared with various state-of-the-art super-resolution algorithms using multiple evaluation criteria including face recognition performance. Results on publicly available datasets show that the proposed method super-resolves high quality face images which are very close to the ground-truth and performance gain is not dataset dependent. The method is very efficient in both the training and testing phases compared to the other approaches. © 2013 Elsevier B.V

    UG^2: a Video Benchmark for Assessing the Impact of Image Restoration and Enhancement on Automatic Visual Recognition

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    Advances in image restoration and enhancement techniques have led to discussion about how such algorithmscan be applied as a pre-processing step to improve automatic visual recognition. In principle, techniques like deblurring and super-resolution should yield improvements by de-emphasizing noise and increasing signal in an input image. But the historically divergent goals of the computational photography and visual recognition communities have created a significant need for more work in this direction. To facilitate new research, we introduce a new benchmark dataset called UG^2, which contains three difficult real-world scenarios: uncontrolled videos taken by UAVs and manned gliders, as well as controlled videos taken on the ground. Over 160,000 annotated frames forhundreds of ImageNet classes are available, which are used for baseline experiments that assess the impact of known and unknown image artifacts and other conditions on common deep learning-based object classification approaches. Further, current image restoration and enhancement techniques are evaluated by determining whether or not theyimprove baseline classification performance. Results showthat there is plenty of room for algorithmic innovation, making this dataset a useful tool going forward.Comment: Supplemental material: https://goo.gl/vVM1xe, Dataset: https://goo.gl/AjA6En, CVPR 2018 Prize Challenge: ug2challenge.or

    Tangible user interfaces : past, present and future directions

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    In the last two decades, Tangible User Interfaces (TUIs) have emerged as a new interface type that interlinks the digital and physical worlds. Drawing upon users' knowledge and skills of interaction with the real non-digital world, TUIs show a potential to enhance the way in which people interact with and leverage digital information. However, TUI research is still in its infancy and extensive research is required in or- der to fully understand the implications of tangible user interfaces, to develop technologies that further bridge the digital and the physical, and to guide TUI design with empirical knowledge. This paper examines the existing body of work on Tangible User In- terfaces. We start by sketching the history of tangible user interfaces, examining the intellectual origins of this field. We then present TUIs in a broader context, survey application domains, and review frame- works and taxonomies. We also discuss conceptual foundations of TUIs including perspectives from cognitive sciences, phycology, and philoso- phy. Methods and technologies for designing, building, and evaluating TUIs are also addressed. Finally, we discuss the strengths and limita- tions of TUIs and chart directions for future research

    A framework for working with digitized cultural heritage artefacts

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    In this paper, we present our work in designing, implementing, and evaluating a set of 3D interactive spatial measurement tools in the context of Cultural Heritage Toolbox (CH Toolbox), a framework for computer-aided cultural heritage research. Our application utilizes a bi-manual, spaceball and mouse driven user interface to help the user manage visualized 3D models digitized from real artifacts. We have developed a virtual radius estimator, useful for analyzing incomplete pieces of radial artifacts, and a virtual tape measure, useful in measurement of geodesic distances between two points on the surface of an artifact. We tested the tools on the special case of pottery analysis
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