Fast reliable interrogation of procedurally defined implicit surfaces using extended revised affine arithmetic.

Techniques based on interval and previous termaffine arithmetic next term and their modifications are shown to provide previous term reliable next term function range evaluation for the purposes of previous termsurface interrogation.next term In this paper we present a technique for the previous termreliable interrogation of implicit surfacesnext term using a modification of previous termaffine arithmeticnext term called previous term revised affine arithmetic.next term We extend the range of functions presented in previous termrevised affine arithmeticnext term by introducing previous termaffinenext term operations for arbitrary functions such as set-theoretic operations with R-functions, blending and conditional operators. The obtained previous termaffinenext term forms of arbitrary functions provide previous termfasternext term and tighter function range evaluation. Several case studies for operations using previous termaffinenext term forms are presented. The proposed techniques for previous termsurface interrogationnext term are tested using ray-previous termsurfacenext term intersection for ray-tracing and spatial cell enumeration for polygonisation. These applications with our extensions provide previous termfast and reliablenext term rendering of a wide range of arbitrary previous termprocedurally defined implicit surfacesnext term (including polynomial previous termsurfaces,next term constructive solids, pseudo-random objects, previous termprocedurally definednext term microstructures, and others). We compare the function range evaluation technique based on previous termextended revised affine arithmeticnext term with other previous termreliablenext term techniques based on interval and previous termaffine arithmeticnext term to show that our technique provides the previous termfastestnext term and tightest function range evaluation for previous termfast and reliable interrogation of procedurally defined implicit surfaces.next term Research Highlights The main contributions of this paper are as follows. ► The widening of the scope of previous termreliablenext term ray-tracing and spatial enumeration algorithms for previous termsurfacesnext term ranging from algebraic previous termsurfaces (definednext term by polynomials) to general previous termimplicit surfaces (definednext term by function evaluation procedures involving both previous termaffinenext term and non-previous termaffinenext term operations based on previous termrevised affine arithmetic)next term. ► The introduction of a technique for representing procedural models using special previous termaffinenext term forms (illustrated by case studies of previous termaffinenext term forms for set-theoretic operations in the form of R-functions, blending operations and conditional operations). ► The detailed derivation of special previous termaffinenext term forms for arbitrary operators

Hybrid model for vascular tree structures

This paper proposes a new representation scheme of the cerebral blood vessels. This model provides information on the semantics of the vascular structure: the topological relationships between vessels and the labeling of vascular accidents such as aneurysms and stenoses. In addition, the model keeps information of the inner surface geometry as well as of the vascular map volume properties, i.e. the tissue density, the blood flow velocity and the vessel wall elasticity. The model can be constructed automatically in a pre-process from a set of segmented MRA images. Its memory requirements are optimized on the basis of the sparseness of the vascular structure. It allows fast queries and efficient traversals and navigations. The visualizations of the vessel surface can be performed at different levels of detail. The direct rendering of the volume is fast because the model provides a natural way to skip over empty data. The paper analyzes the memory requirements of the model along with the costs of the most important operations on it.Postprint (published version

An embedding technique for the solution of reaction-fiffusion equations on algebraic surfaces with isolated singularities

In this paper we construct a parametrization-free embedding technique for numerically evolving reaction-diffusion PDEs defined on algebraic curves that possess an isolated singularity. In our approach, we first desingularize the curve by appealing to techniques from algebraic geometry.\ud We create a family of smooth curves in higher dimensional space that correspond to the original curve by projection. Following this, we pose the analogous reaction-diffusion PDE on each member of this family and show that the solutions (their projection onto the original domain) approximate the solution of the original problem. Finally, we compute these approximants numerically by applying the Closest Point Method which is an embedding technique for solving PDEs on smooth surfaces of arbitrary dimension or codimension, and is thus suitable for our situation. In addition, we discuss the potential to generalize the techniques presented for higher-dimensional surfaces with multiple singularities

Modelling cell motility and chemotaxis with evolving surface finite elements

We present a mathematical and a computational framework for the modelling of cell motility. The cell membrane is represented by an evolving surface, with the movement of the cell determined by the interaction of various forces that act normal to the surface. We consider external forces such as those that may arise owing to inhomogeneities in the medium and a pressure that constrains the enclosed volume, as well as internal forces that arise from the reaction of the cells' surface to stretching and bending. We also consider a protrusive force associated with a reaction-diffusion system (RDS) posed on the cell membrane, with cell polarization modelled by this surface RDS. The computational method is based on an evolving surface finite-element method. The general method can account for the large deformations that arise in cell motility and allows the simulation of cell migration in three dimensions. We illustrate applications of the proposed modelling framework and numerical method by reporting on numerical simulations of a model for eukaryotic chemotaxis and a model for the persistent movement of keratocytes in two and three space dimensions. Movies of the simulated cells can be obtained from http://homepages.warwick.ac.uk/maskae/CV_Warwick/Chemotaxis.html

Principal component and Voronoi skeleton alternatives for curve reconstruction from noisy point sets

Surface reconstruction from noisy point samples must take into consideration the stochastic nature of the sample -- In other words, geometric algorithms reconstructing the surface or curve should not insist in following in a literal way each sampled point -- Instead, they must interpret the sample as a “point cloud” and try to build the surface as passing through the best possible (in the statistical sense) geometric locus that represents the sample -- This work presents two new methods to find a Piecewise Linear approximation from a Nyquist-compliant stochastic sampling of a quasi-planar C1 curve C(u) : R → R3, whose velocity vector never vanishes -- One of the methods articulates in an entirely new way Principal Component Analysis (statistical) and Voronoi-Delaunay (deterministic) approaches -- It uses these two methods to calculate the best possible tape-shaped polygon covering the planarised point set, and then approximates the manifold by the medial axis of such a polygon -- The other method applies Principal Component Analysis to find a direct Piecewise Linear approximation of C(u) -- A complexity comparison of these two methods is presented along with a qualitative comparison with previously developed ones -- It turns out that the method solely based on Principal Component Analysis is simpler and more robust for non self-intersecting curves -- For self-intersecting curves the Voronoi-Delaunay based Medial Axis approach is more robust, at the price of higher computational complexity -- An application is presented in Integration of meshes originated in range images of an art piece -- Such an application reaches the point of complete reconstruction of a unified mes

Highly Parallel Geometric Characterization and Visualization of Volumetric Data Sets

Volumetric 3D data sets are being generated in many different application areas. Some examples are CAT scans and MRI data, 3D models of protein molecules represented by implicit surfaces, multi-dimensional numeric simulations of plasma turbulence, and stacks of confocal microscopy images of cells. The size of these data sets has been increasing, requiring the speed of analysis and visualization techniques to also increase to keep up. Recent advances in processor technology have stopped increasing clock speed and instead begun increasing parallelism, resulting in multi-core CPUS and many-core GPUs. To take advantage of these new parallel architectures, algorithms must be explicitly written to exploit parallelism. In this thesis we describe several algorithms and techniques for volumetric data set analysis and visualization that are amenable to these modern parallel architectures. We first discuss modeling volumetric data with Gaussian Radial Basis Functions (RBFs). RBF representation of a data set has several advantages, including lossy compression, analytic differentiability, and analytic application of Gaussian blur. We also describe a parallel volume rendering algorithm that can create images of the data directly from the RBF representation. Next we discuss a parallel, stochastic algorithm for measuring the surface area of volumetric representations of molecules. The algorithm is suitable for implementation on a GPU and is also progressive, allowing it to return a rough answer almost immediately and refine the answer over time to the desired level of accuracy. After this we discuss the concept of Confluent Visualization, which allows the visualization of the interaction between a pair of volumetric data sets. The interaction is visualized through volume rendering, which is well suited to implementation on parallel architectures. Finally we discuss a parallel, stochastic algorithm for classifying stem cells as having been grown on a surface that induces differentiation or on a surface that does not induce differentiation. The algorithm takes as input 3D volumetric models of the cells generated from confocal microscopy. This algorithm builds on our algorithm for surface area measurement and, like that algorithm, this algorithm is also suitable for implementation on a GPU and is progressive

CAD-Based Porous Scaffold Design of Intervertebral Discs in Tissue Engineering

With the development and maturity of three-dimensional (3D) printing technology over the past decade, 3D printing has been widely investigated and applied in the field of tissue engineering to repair damaged tissues or organs, such as muscles, skin, and bones, Although a number of automated fabrication methods have been developed to create superior bio-scaffolds with specific surface properties and porosity, the major challenges still focus on how to fabricate 3D natural biodegradable scaffolds that have tailor properties such as intricate architecture, porosity, and interconnectivity in order to provide the needed structural integrity, strength, transport, and ideal microenvironment for cell- and tissue-growth. In this dissertation, a robust pipeline of fabricating bio-functional porous scaffolds of intervertebral discs based on different innovative porous design methodologies is illustrated. Firstly, a triply periodic minimal surface (TPMS) based parameterization method, which has overcome the integrity problem of traditional TPMS method, is presented in Chapter 3. Then, an implicit surface modeling (ISM) approach using tetrahedral implicit surface (TIS) is demonstrated and compared with the TPMS method in Chapter 4. In Chapter 5, we present an advanced porous design method with higher flexibility using anisotropic radial basis function (ARBF) and volumetric meshes. Based on all these advanced porous design methods, the 3D model of a bio-functional porous intervertebral disc scaffold can be easily designed and its physical model can also be manufactured through 3D printing. However, due to the unique shape of each intervertebral disc and the intricate topological relationship between the intervertebral discs and the spine, the accurate localization and segmentation of dysfunctional discs are regarded as another obstacle to fabricating porous 3D disc models. To that end, we discuss in Chapter 6 a segmentation technique of intervertebral discs from CT-scanned medical images by using deep convolutional neural networks. Additionally, some examples of applying different porous designs on the segmented intervertebral disc models are demonstrated in Chapter 6

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

Robust interactive simulation of deformable solids with detailed geometry using corotational FEM

This thesis focuses on the interactive simulation of highly detailed deformable solids modelled with the Corotational Finite Element Method. Starting from continuum mechanics we derive the discrete equations of motion and present a simulation scheme with support for user-in-the-loop interaction, geometric constraints and contact treatment. The interplay between accuracy and computational cost is discussed in depth, and practical approximations are analyzed with an emphasis on robustness and efficiency, as required by interactive simulation. The first part of the thesis focuses on deformable material discretization using the Finite Element Method with simplex elements and a corotational linear constitutive model, and presents our contributions to the solution of widely reported robustness problems in case of large stretch deformations and finite element degeneration. First,we introduce a stress differential approximation for quasi-implicit corotational linear FEM that improves its results for large deformations and closely matches the fullyimplicit solution with minor computational overhead. Next, we address the problem ofrobustness and realism in simulations involving element degeneration, and show that existing methods have previously unreported flaws that seriously threaten robustness and physical plausibility in interactive applications. We propose a new continuous-time approach, degeneration-aware polar decomposition, that avoids such flaws and yields robust degeneration recovery. In the second part we focus on geometry representation and contact determination for deformable solids with highly detailed surfaces. Given a high resolution closed surface mesh we automatically build a coarse embedding tetrahedralization and a partitioned representation of the collision geometry in a preprocess. During simulation, our proposed contact determination algorithm finds all intersecting pairs of deformed triangles using a memory-efficient barycentric bounding volume hierarchy, connects them into potentially disjoint intersection curves and performs a topological flood process on the exact intersection surfaces to discover a minimal set of contact points. A novel contact normal definition is used to find contact point correspondences suitable for contact treatment.Aquesta tesi tracta sobre la simulació interactiva de sòlids deformables amb superfícies detallades, modelats amb el Mètode dels Elements Finits (FEM) Corotacionals. A partir de la mecànica del continuu derivem les equacions del moviment discretes i presentem un esquema de simulació amb suport per a interacció d'usuari, restriccions geomètriques i tractament de contactes. Aprofundim en la interrelació entre precisió i cost de computació, i analitzem aproximacions pràctiques fent èmfasi en la robustesa i l'eficiència necessàries per a la simulació interactiva. La primera part de la tesi es centra en la discretització del material deformable mitjançant el Mètode dels Elements Finits amb elements de tipus s'implex i un model constituent basat en elasticitat linial corotacional, i presenta les nostres contribucions a la solució de problemes de robustesa àmpliament coneguts que apareixen en cas de sobreelongament i degeneració dels elements finits. Primer introduïm una aproximació dels diferencials d'estress per a FEM linial corotacional amb integració quasi-implícita que en millora els resultats per a deformacions grans i s'apropa a la solució implícita amb un baix cost computacional. A continuació tractem el problema de la robustesa i el realisme en simulacions que inclouen degeneració d'elements finits, i mostrem que els mètodes existents presenten inconvenients que posen en perill la robustesa plausibilitat de la simulació en aplicacions interactives. Proposem un enfocament nou basat en temps continuu, la descomposició polar amb coneixement de degeneració, que evita els inconvenients esmentats i permet corregir la degeneració de forma robusta. A la segona part de la tesi ens centrem en la representació de geometria i la determinació de contactes per a sòlids deformables amb superfícies detallades. A partir d'una malla de superfície tancada construím una tetraedralització englobant de forma automàtica en un preprocés, i particionem la geometria de colisió. Proposem un algorisme de detecció de contactes que troba tots els parells de triangles deformats que intersecten mitjançant una jerarquia de volums englobants en coordenades baricèntriques, els connecta en corbes d'intersecció potencialment disjuntes i realitza un procés d'inundació topològica sobre les superfícies d'intersecció exactes per tal de descobrir un conjunt mínim de punts de contacte. Usem una definició nova de la normal de contacte per tal de calcular correspondències entre punts de contacte útils per al seu tractament.Postprint (published version