Software for Stereotactic Navigation System in Epileptosurgery

Tato práce je zaměřena na návrh a implementaci poloautomatického nástroje pro plánování implantace hloubkových elektrod v oboru epileptochirurgie. Navržené řešení je implementováno jako rozšíření do platformy 3D Slicer. Volumetrická data znázorňující omezující podmínky a seznam cílů navigace jsou použity jako vstupy pro automatické zpracování. Systém navrhuje seznam kandidátů na řešení, která mohou být interaktivně ohodnoceny. Toto je první iterace implementace, která obsahuje základní funkcionalitu zahrnující dávkové zpracování vstupních dat, automatické ohodnocení navigační trajektorie a uživatelské rozhraní pro interaktivní ohodnocení navrhovaných řešení.The thesis is focused on the design and implementation of semi-automatic navigation planner for implantation of deep brain electrodes in epileptosurgery. The solution is implemented as an extension into 3D Slicer platform. It uses volumetric data model of restricted areas and list of navigation targets as inputs to automatic processing. The system suggests the list of solution candidates which can be interactively evaluated. This is the first iteration of the implementation which incorporates basic functionality including batch processing of the input data, automatic evaluation of navigation paths and user interface for interactive evaluation

Accurate geometry reconstruction of vascular structures using implicit splines

3-D visualization of blood vessel from standard medical datasets (e.g. CT or MRI) play an important role in many clinical situations, including the diagnosis of vessel stenosis, virtual angioscopy, vascular surgery planning and computer aided vascular surgery. However, unlike other human organs, the vasculature system is a very complex network of vessel, which makes it a very challenging task to perform its 3-D visualization. Conventional techniques of medical volume data visualization are in general not well-suited for the above-mentioned tasks. This problem can be solved by reconstructing vascular geometry. Although various methods have been proposed for reconstructing vascular structures, most of these approaches are model-based, and are usually too ideal to correctly represent the actual variation presented by the cross-sections of a vascular structure. In addition, the underlying shape is usually expressed as polygonal meshes or in parametric forms, which is very inconvenient for implementing ramification of branching. As a result, the reconstructed geometries are not suitable for computer aided diagnosis and computer guided minimally invasive vascular surgery. In this research, we develop a set of techniques associated with the geometry reconstruction of vasculatures, including segmentation, modelling, reconstruction, exploration and rendering of vascular structures. The reconstructed geometry can not only help to greatly enhance the visual quality of 3-D vascular structures, but also provide an actual geometric representation of vasculatures, which can provide various benefits. The key findings of this research are as follows: 1. A localized hybrid level-set method of segmentation has been developed to extract the vascular structures from 3-D medical datasets. 2. A skeleton-based implicit modelling technique has been proposed and applied to the reconstruction of vasculatures, which can achieve an accurate geometric reconstruction of the vascular structures as implicit surfaces in an analytical form. 3. An accelerating technique using modern GPU (Graphics Processing Unit) is devised and applied to rendering the implicitly represented vasculatures. 4. The implicitly modelled vasculature is investigated for the application of virtual angioscopy

Study of the interaction with a virtual 3D environment displayed on a smartphone

Les environnements virtuels à 3D (EV 3D) sont de plus en plus utilisés dans différentes applications telles que la CAO, les jeux ou la téléopération. L'évolution des performances matérielles des Smartphones a conduit à l'introduction des applications 3D sur les appareils mobiles. En outre, les Smartphones offrent de nouvelles capacités bien au-delà de la communication vocale traditionnelle qui sont consentis par l'intégrité d'une grande variété de capteurs et par la connectivité via Internet. En conséquence, plusieurs intéressantes applications 3D peuvent être conçues en permettant aux capacités de l'appareil d'interagir dans un EV 3D. Sachant que les Smartphones ont de petits et aplatis écrans et que EV 3D est large, dense et contenant un grand nombre de cibles de tailles différentes, les appareils mobiles présentent certaines contraintes d'interaction dans l'EV 3D comme : la densité de l'environnement, la profondeur de cibles et l'occlusion. La tâche de sélection fait face à ces trois problèmes pour sélectionner une cible. De plus, la tâche de sélection peut être décomposée en trois sous-tâches : la Navigation, le Pointage et la Validation. En conséquence, les chercheurs dans un environnement virtuel 3D ont développé de nouvelles techniques et métaphores pour l'interaction en 3D afin d'améliorer l'utilisation des applications 3D sur les appareils mobiles, de maintenir la tâche de sélection et de faire face aux problèmes ou facteurs affectant la performance de sélection. En tenant compte de ces considérations, cette thèse expose un état de l'art des techniques de sélection existantes dans un EV 3D et des techniques de sélection sur Smartphone. Il expose les techniques de sélection dans un EV 3D structurées autour des trois sous-tâches de sélection: navigation, pointage et validation. En outre, il décrit les techniques de désambiguïsation permettant de sélectionner une cible parmi un ensemble d'objets présélectionnés. Ultérieurement, il expose certaines techniques d'interaction décrites dans la littérature et conçues pour être implémenter sur un Smartphone. Ces techniques sont divisées en deux groupes : techniques effectuant des tâches de sélection bidimensionnelle sur un Smartphone et techniques exécutant des tâches de sélection tridimensionnelle sur un Smartphone. Enfin, nous exposons les techniques qui utilisaient le Smartphone comme un périphérique de saisie. Ensuite, nous discuterons la problématique de sélection dans un EV 3D affichée sur un Smartphone. Il expose les trois problèmes identifiés de sélection : la densité de l'environnement, la profondeur des cibles et l'occlusion. Ensuite, il établit l'amélioration offerte par chaque technique existante pour la résolution des problèmes de sélection. Il analyse les atouts proposés par les différentes techniques, la manière dont ils éliminent les problèmes, leurs avantages et leurs inconvénients. En outre, il illustre la classification des techniques de sélection pour un EV 3D en fonction des trois problèmes discutés (densité, profondeur et occlusion) affectant les performances de sélection dans un environnement dense à 3D. Hormis pour les jeux vidéo, l'utilisation d'environnement virtuel 3D sur Smartphone n'est pas encore démocratisée. Ceci est dû au manque de techniques d'interaction proposées pour interagir avec un dense EV 3D composé de nombreux objets proches les uns des autres et affichés sur un petit écran aplati et les problèmes de sélection pour afficher l' EV 3D sur un petit écran plutôt sur un grand écran. En conséquence, cette thèse se concentre sur la proposition et la description du fruit de cette étude : la technique d'interaction DichotoZoom. Elle compare et évalue la technique proposée à la technique de circulation suggérée par la littérature. L'analyse comparative montre l'efficacité de la technique DichotoZoom par rapport à sa contrepartie. Ensuite, DichotoZoom a été évalué selon les différentes modalités d'interaction disponibles sur les Smartphones. Cette évaluation montre la performance de la technique de sélection proposée basée sur les quatre modalités d'interaction suivantes : utilisation de boutons physiques ou sous forme de composants graphiques, utilisation d'interactions gestuelles via l'écran tactile ou le déplacement de l'appareil lui-même. Enfin, cette thèse énumère nos contributions dans le domaine des techniques d'interaction 3D utilisées dans un environnement virtuel 3D dense affiché sur de petits écrans et propose des travaux futurs.3D Virtual Environments (3D VE) are more and more used in different applications such as CAD, games, or teleoperation. Due to the improvement of smartphones hardware performance, 3D applications were also introduced to mobile devices. In addition, smartphones provide new computing capabilities far beyond the traditional voice communication. They are permitted by the variety of built-in sensors and the internet connectivity. In consequence, interesting 3D applications can be designed by enabling the device capabilities to interact in a 3D VE. Due to the fact that smartphones have small and flat screens and that a 3D VE is wide and dense with a large number of targets of various sizes, mobile devices present some constraints in interacting on the 3D VE like: the environment density, the depth of targets and the occlusion. The selection task faces these three problems to select a target. In addition, the selection task can be decomposed into three subtasks: Navigation, Pointing and Validation. In consequence, researchers in 3D virtual environment have developed new techniques and metaphors for 3D interaction to improve 3D application usability on mobile devices, to support the selection task and to face the problems or factors affecting selection performance. In light of these considerations, this thesis exposes a state of the art of the existing selection techniques in 3D VE and the selection techniques on smartphones. It exposes the selection techniques in 3D VE structured around the selection subtasks: navigation, pointing and validation. Moreover, it describes disambiguation techniques providing the selection of a target from a set of pre-selected objects. Afterward, it exposes some interaction techniques described in literature and designed for implementation on Smartphone. These techniques are divided into two groups: techniques performing two-dimensional selection tasks on smartphones, and techniques performing three-dimensional selection tasks on smartphones. Finally, we expose techniques that used the smartphone as an input device. Then, we will discuss the problematic of selecting in 3D VE displayed on a Smartphone. It exposes the three identified selection problems: the environment density, the depth of targets and the occlusion. Afterward, it establishes the enhancement offered by each existing technique in solving the selection problems. It analysis the assets proposed by different techniques, the way they eliminates the problems, their advantages and their inconvenient. Furthermore, it illustrates the classification of the selection techniques for 3D VE according to the three discussed problems (density, depth and occlusion) affecting the selection performance in a dense 3D VE. Except for video games, the use of 3D virtual environment (3D VE) on Smartphone has not yet been popularized. This is due to the lack of interaction techniques to interact with a dense 3D VE composed of many objects close to each other and displayed on a small and flat screen and the selection problems to display the 3D VE on a small screen rather on a large screen. Accordingly, this thesis focuses on defining and describing the fruit of this study: DichotoZoom interaction technique. It compares and evaluates the proposed technique to the Circulation technique, suggested by the literature. The comparative analysis shows the effectiveness of DichotoZoom technique compared to its counterpart. Then, DichotoZoom was evaluated in different modalities of interaction available on Smartphones. It reports on the performance of the proposed selection technique based on the following four interaction modalities: using physical buttons, using graphical buttons, using gestural interactions via touchscreen or moving the device itself. Finally, this thesis lists our contributions to the field of 3D interaction techniques used in a dense 3D virtual environment displayed on small screens and proposes some future works

A Multi-Resolution Interactive Previewer for Volumetric Data on Arbitary Meshes

In this paper we describe a rendering method suitable for interactive previewing of large-scale arbitary-mesh volume data sets. A data set to be visualized is represented by a ''point cloud,'' i. e., a set of points and associated data values without known connectivity between the points. The method uses a multi-resolution approach to achieve interactive rendering rates of several frames per second for arbitrarily large data sets. Lower-resolution approximations of an original data set are created by iteratively applying a point- decimation operation to higher-resolution levels. The goal of this method is to provide the user with an interactive navigation and exploration tool to determine good viewpoints and transfer functions to pass on to a high-quality volume renderer that uses a standard algorithm

An interface to virtual environments for people who are blind using Wii technology - mental models and navigation

Accessible games, both for serious and for entertainment purposes, would allow inclusion and participation for those with disabilities. Research into the development of accessible games, and accessible virtual environments, is discussed. Research into accessible Virtual Environments has demonstrated great potential for allowing people who are blind to explore new spaces, reducing their reliance on guides, and aiding development of more efficient spatial maps and strategies. Importantly, Lahav and Mioduser (2005, 2008) have demonstrated that, when exploring virtual spaces, people who are blind use more and different strategies than when exploring real physical spaces, and develop relatively accurate spatial representations of them. The present paper describes the design, development and evaluation of a system in which a virtual environment may be explored by people who are blind using Nintendo Wii devices, with auditory and haptic feedback. The nature of the various types of feedback is considered, with the aim of creating an intuitive and usable system. Using Wii technology has many advantages, not least of which are that it is mainstream, readily available and cheap. The potential of the system for exploration and navigation is demonstrated. Results strongly support the possibilities of the system for facilitating and supporting the construction of cognitive maps and spatial strategies. Intelligent support is discussed. Systems such as the present one will facilitate the development of accessible games, and thus enable Universal Design and accessible interactive technology to become more accepted and widespread

Ubiquitous volume rendering in the web platform

176 p.The main thesis hypothesis is that ubiquitous volume rendering can be achieved using WebGL. The thesis enumerates the challenges that should be met to achieve that goal. The results allow web content developers the integration of interactive volume rendering within standard HTML5 web pages. Content developers only need to declare the X3D nodes that provide the rendering characteristics they desire. In contrast to the systems that provide specific GPU programs, the presented architecture creates automatically the GPU code required by the WebGL graphics pipeline. This code is generated directly from the X3D nodes declared in the virtual scene. Therefore, content developers do not need to know about the GPU.The thesis extends previous research on web compatible volume data structures for WebGL, ray-casting hybrid surface and volumetric rendering, progressive volume rendering and some specific problems related to the visualization of medical datasets. Finally, the thesis contributes to the X3D standard with some proposals to extend and improve the volume rendering component. The proposals are in an advance stage towards their acceptance by the Web3D Consortium

Applications of CSP solving in computer games (camera control)

While camera control systems of commercial 3D games have improved greatly in recent years, they are not as fully developed as are other game components such as graphics and physics engines. Bourne and Sattar (2006) have proposed a reactive constraint based third person perspective camera control system. We have extended the capability of their system to handle occlusion while following the main character, and have used camera cuts to find appropriate camera positions for a few difficult situations. We have developed a reactive constraint based third person perspective chase camera control system to follow a character in a 3D environment. The camera follows the character from (near) optimal positions defined by a camera profile. The desired values of the height and distance constraints of the camera profile are changed appropriately whenever the character enters a semi-enclosed or an enclosed area, and the desired value of the orientation constraint of the camera profile is changed incrementally whenever theoptimal camera view is obstructed. Camera cuts are used whenever the main character backs up to a wall or any other obstructions, or comes out of a semi-enclosed or an enclosed area. Two auxiliary cameras to observe the main camera positions from top and side views have been added. The chase camera control system achieved real-time performance while following the main character in a typical 3D environment, and maintained an optimal view based on a user specified/selected camera profile

Recent trends, technical concepts and components of computer-assisted orthopedic surgery systems: A comprehensive review

Computer-assisted orthopedic surgery (CAOS) systems have become one of the most important and challenging types of system in clinical orthopedics, as they enable precise treatment of musculoskeletal diseases, employing modern clinical navigation systems and surgical tools. This paper brings a comprehensive review of recent trends and possibilities of CAOS systems. There are three types of the surgical planning systems, including: systems based on the volumetric images (computer tomography (CT), magnetic resonance imaging (MRI) or ultrasound images), further systems utilize either 2D or 3D fluoroscopic images, and the last one utilizes the kinetic information about the joints and morphological information about the target bones. This complex review is focused on three fundamental aspects of CAOS systems: their essential components, types of CAOS systems, and mechanical tools used in CAOS systems. In this review, we also outline the possibilities for using ultrasound computer-assisted orthopedic surgery (UCAOS) systems as an alternative to conventionally used CAOS systems.Web of Science1923art. no. 519

Ubiquitous volume rendering in the web platform

176 p.The main thesis hypothesis is that ubiquitous volume rendering can be achieved using WebGL. The thesis enumerates the challenges that should be met to achieve that goal. The results allow web content developers the integration of interactive volume rendering within standard HTML5 web pages. Content developers only need to declare the X3D nodes that provide the rendering characteristics they desire. In contrast to the systems that provide specific GPU programs, the presented architecture creates automatically the GPU code required by the WebGL graphics pipeline. This code is generated directly from the X3D nodes declared in the virtual scene. Therefore, content developers do not need to know about the GPU.The thesis extends previous research on web compatible volume data structures for WebGL, ray-casting hybrid surface and volumetric rendering, progressive volume rendering and some specific problems related to the visualization of medical datasets. Finally, the thesis contributes to the X3D standard with some proposals to extend and improve the volume rendering component. The proposals are in an advance stage towards their acceptance by the Web3D Consortium