A brief review of surface meshing in medical images for biomedical computing and visualization

A visual representation of the interior of a body is important for clinical analysis and medical intervention. The technique, process and art of creating this visual representation are called medical imaging. The images produced from medical imaging need to be analyses by using Finite Element Method (FEM) especially for intraoperative registration and biomechanical modeling of the tissues. This medical model ranges from the smallest vascular to bones and the complex brain. In order to use FEM, the images need to go through surface meshing generator. Although numerous mesh generation methods have been described to date, there is a few which can deal with medical data input. In this paper, a briefing review of surface meshing that can deal in medical images is presented especially in biomedical computing and visualization. Some automatic mesh generators software used in medical imaging is also discussed such as ScanIP, MIMICS, TETGEN, NetGen, BioMesh3D,CUBITMesh and Gmsh

Computational steering of a multi-objective evolutionary algorithm for engineering design

The execution process of an evolutionary algorithm typically involves some trial and error. This is due to the difficulty in setting the initial parameters of the algorithm—especially when little is known about the problem domain. This problem is magnified when applied to many-objective optimisation, as care is needed to ensure that the final population of candidate solutions is representative of the trade-off surface. We propose a computational steering system that allows the engineer to interact with the optimisation routine during execution. This interaction can be as simple as monitoring the values of some parameters during the execution process, or could involve altering those parameters to influence the quality of the solutions produced by the optimisation process. The implementation of this steering system should provide the ability to tailor the client to the hardware available, for example providing a lightweight steering and visualisation client for use on a PDA

Integrating component-based scientific computing software

Book ChapterIn recent years, component technology has been a successful methodology for large-scale commercial software development. Component technology combines a set of frequently used functions in a component and makes the implementation transparent to users. Software application developers typically connect a group of components from a component repository, connecting them to create a single application

ITK y VTK : Ingeniería inversa y análisis de arquitectura Pipeline

Proyecto de Trabajo de Grado en donde se utilizó una versión modificada de la metodología RUP para realizar un proceso de investigación a partir de un proceso de ingeniería inversa en donde se identificó la arquitectura de pipelines de las librerías de procesamiento de imágenes ITK y VTK. Así mismo, se realizó un prototipo de una interfaz para la edición de pipelines que aporte al desarrollo de flujo de datos para la creación de nuevos algoritmos de procesamiento.Degree work project where a modified version of the RUP methodology was used to do an investigation where a reverse engineer process was used to identify the pipeline architecture of the image processing libraries ITK and VTK. At the same time, a prototype of a user interface for the edition of pipelines was done to contribute in the development of data flows for the creation of new processing algorithms.Ingeniero (a) de SistemasPregrad

Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples

Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results—a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology

THE SEVEN CASES UNSTRUCTURED TRIANGULATION TECHNIQUE FOR RADIATIVE HEAT TRANSFER APPROXIMATION IN AN ETHYLENE FURNACE CRACKER

Radiative heat distribution inside an ethylene cracker furnace is often modelled using the finite volume and finite element methods. In both cases, meshes in the form of rectangles and triangles are needed to serve as the approximating points in the domain. In this paper, a new method called the Seven Cases Unstructured Triangulation Technique (7CUTT) is proposed for meshing the domain inside the cracker furnace, integrated with the deployment of sensors on the wall to obtain the boundary value. 7CUTT is an enhanced version of the Standard Advancing Front Technique (SAFT) which two normal cases in SAFT are extended to the total of seven cases for consideration during the element creation procedure for initial mesh generation. The focus of this method is to construct the initial triangular meshes with the requirement of (1) having the location of sensors deployed along the wall as boundary nodes as well as forming boundary elements, (2) generating nodes at a certain boundary with linearly different lengths of boundary edges as interior gradation controls and (3) constructing the triangular element directly in every iteration without having to re-order the Front or delete the existing elements. There are three contributions from this paper, the first one is the introduction of seven extended cases for consideration for the element creation procedure, the second is the layer concept to generate edges with linearly different lengths and the third is the post-processing mesh procedure to improve the quality of the mesh that is suitable for 7CUTT. The final mesh is obtained once the post-processing procedure of improving the mesh quality is applied to the initial mesh. 7CUTT provides the framework for the heat to be approximated using the discrete ordinate method, which is a variant of the finite volume method. Simulation results produced using FLUENT support the findings for effectively approximating the flue gas temperature distribution, the circumferential radiative heat flux incident at the reactor coils as well as the circumferential reactor coil temperature in the furnace at the end of the study

I-Light Symposium 2005 Proceedings

I-Light was made possible by a special appropriation by the State of Indiana. The research described at the I-Light Symposium has been supported by numerous grants from several sources. Any opinions, findings and conclusions, or recommendations expressed in the 2005 I-Light Symposium Proceedings are those of the researchers and authors and do not necessarily reflect the views of the granting agencies.Indiana University Office of the Vice President for Research and Information Technology, Purdue University Office of the Vice President for Information Technology and CI

Virtual Worlds and Conservational Channel Evolution and Pollutant Transport Systems (Concepts)

Many models exist that predict channel morphology. Channel morphology is defined as the change in geometric parameters of a river. Channel morphology is affected by many factors. Some of these factors are caused either by man or by nature. To combat the adverse effects that man and nature may cause to a water system, scientists and engineers develop stream rehabilitation plans. Stream rehabilitation as defined by Shields et al., states that restoration is the return from a degraded ecosystem back to a close approximation of its remaining natural potential [Shields et al., 2003]. Engineers construct plans that will restore streams back to their natural state by using techniques such as field investigation, analytical models, or numerical models. Each of these techniques is applied to projects based on specified criteria, objectives, and the expertise of the individuals devising the plan. The utilization of analytical and numerical models can be difficult, for many reasons, one of which is the intuitiveness of the modeling process. Many numerical models exist in the field of hydraulic engineering, fluvial geomorphology, landscape architecture, and stream ecology that evaluate and formulate stream rehabilitation plans. This dissertation will explore, in the field of Hydroscience , the creation of models that are not only accurate but also span the different disciplines. The goal of this dissertation is to transform a discrete numerical model (CONCEPTS) into a realistic 3D environment using open source game engines, while at the same time, conveying at least the equivalent information that was presented in the 1D numerical model

Doctor of Philosophy

dissertationInverse Electrocardiography (ECG) aims to noninvasively estimate the electrophysiological activity of the heart from the voltages measured at the body surface, with promising clinical applications in diagnosis and therapy. The main challenge of this emerging technique lies in its mathematical foundation: an inverse source problem governed by partial differential equations (PDEs) which is severely ill-conditioned. Essential to the success of inverse ECG are computational methods that reliably achieve accurate inverse solutions while harnessing the ever-growing complexity and realism of the bioelectric simulation. This dissertation focuses on the formulation, optimization, and solution of the inverse ECG problem based on finite element methods, consisting of two research thrusts. The first thrust explores the optimal finite element discretization specifically oriented towards the inverse ECG problem. In contrast, most existing discretization strategies are designed for forward problems and may become inappropriate for the corresponding inverse problems. Based on a Fourier analysis of how discretization relates to ill-conditioning, this work proposes refinement strategies that optimize approximation accuracy o f the inverse ECG problem while mitigating its ill-conditioning. To fulfill these strategies, two refinement techniques are developed: one uses hybrid-shaped finite elements whereas the other adapts high-order finite elements. The second research thrust involves a new methodology for inverse ECG solutions called PDE-constrained optimization, an optimization framework that flexibly allows convex objectives and various physically-based constraints. This work features three contributions: (1) fulfilling optimization in the continuous space, (2) formulating rigorous finite element solutions, and (3) fulfilling subsequent numerical optimization by a primal-dual interiorpoint method tailored to the given optimization problem's specific algebraic structure. The efficacy o f this new method is shown by its application to localization o f cardiac ischemic disease, in which the method, under realistic settings, achieves promising solutions to a previously intractable inverse ECG problem involving the bidomain heart model. In summary, this dissertation advances the computational research of inverse ECG, making it evolve toward an image-based, patient-specific modality for biomedical research