Non-photorealistic rendering of virtual implant models for computer-assisted fluoroscopy-based surgical procedures

Surgical navigation systems visualize the positions and orientations of surgical instruments and implants as graphical overlays onto a medical image of the operated anatomy on a computer monitor. The orthopaedic surgical navigation systems could be categorized according to the image modalities that are used for the visualization of surgical action. In the so-called CT-based systems or 'surgeon-defined anatomy' based systems, where a 3D volume or surface representation of the operated anatomy could be constructed from the preoperatively acquired tomographic data or through intraoperatively digitized anatomy landmarks, a photorealistic rendering of the surgical action has been identified to greatly improve usability of these navigation systems. However, this may not hold true when the virtual representation of surgical instruments and implants is superimposed onto 2D projection images in a fluoroscopy-based navigation system due to the so-called image occlusion problem. Image occlusion occurs when the field of view of the fluoroscopic image is occupied by the virtual representation of surgical implants or instruments. In these situations, the surgeon may miss part of the image details, even if transparency and/or wire-frame rendering is used. In this paper, we propose to use non-photorealistic rendering to overcome this difficulty. Laboratory testing results on foamed plastic bones during various computer-assisted fluoroscopybased surgical procedures including total hip arthroplasty and long bone fracture reduction and osteosynthesis are shown.

Hip2Norm: an object-oriented cross-platform program for 3D analysis of hip joint morphology using 2D pelvic radiographs

We developed an object-oriented cross-platform program to perform three-dimensional (3D) analysis of hip joint morphology using two-dimensional (2D) anteroposterior (AP) pelvic radiographs. Landmarks extracted from 2D AP pelvic radiographs and optionally an additional lateral pelvic X-ray were combined with a cone beam projection model to reconstruct 3D hip joints. Since individual pelvic orientation can vary considerably, a method for standardizing pelvic orientation was implemented to determine the absolute tilt/rotation. The evaluation of anatomically morphologic differences was achieved by reconstructing the projected acetabular rim and the measured hip parameters as if obtained in a standardized neutral orientation. The program had been successfully used to interactively objectify acetabular version in hips with femoro-acetabular impingement or developmental dysplasia. Hip(2)Norm is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway) for graphical user interface (GUI) and is transportable to any platform.

Design and implementation of a 3D computer game controller using inertial MEMS sensors

Though 3D computer graphics has seen tremendous advancement in the past two decades, most available mechanisms for computer interaction in 3D are high cost and targeted for industry and virtual reality applications. Recent advances in Micro-Electro-Mechanical-System (MEMS) devices have brought forth a variety of new low-cost, low-power, miniature sensors with high accuracy, which are well suited for hand-held devices. In this work a novel design for a 3D computer game controller using inertial sensors is proposed, and a prototype device based on this design is implemented. The design incorporates MEMS accelerometers and gyroscopes from Analog Devices to measure the three components of the acceleration and angular velocity. From these sensor readings, the position and orientation of the hand-held compartment can be calculated using numerical methods. The implemented prototype is utilizes a USB 2.0 compliant interface for power and communication with the host system. A Microchip dsPIC microcontroller is used in the design. This microcontroller integrates the analog to digital converters, the program memory flash, as well as the core processor, on a single integrated circuit. A PC running Microsoft Windows operating system is used as the host machine. Prototype firmware for the microcontroller is developed and tested to establish the communication between the design and the host, and perform the data acquisition and initial filtering of the sensor data. A PC front-end application with a graphical interface is developed to communicate with the device, and allow real-time visualization of the acquired data.

Integrated solar energy and absorption cooling model for HVAC (heating, ventilating, and air conditioning) applications in buildings

The demands in production and associate costs at power generation through non renewable resources are increasing at an alarming rate. Solar energy is one of the renewable resource that has the potential to minimize this increase. Utilization of solar energy have been concentrated mainly on heating application. The use of solar energy in cooling systems in building would benefit greatly achieving the goal of non-renewable energy minimization. The approaches of solar energy heating system research done by initiation such as University of Wisconsin at Madison and building heat flow model research conducted by Oklahoma State University can be used to develop and optimize solar cooling building system. The research uses two approaches to develop a Graphical User Interface (GUI) software for an integrated solar absorption cooling building model, which is capable of simulating and optimizing the absorption cooling system using solar energy as the main energy source to drive the cycle. The software was then put through a number of litmus test to verify its integrity. The litmus test was conducted on various building cooling system data sets of similar applications around the world. The output obtained from the software developed were identical with established experimental results from the data sets used. Software developed by other research are catered for advanced users. The software developed by this research is not only reliable in its code integrity but also through its integrated approach which is catered for new entry users. Hence, this dissertation aims to correctly model a complete building with the absorption cooling system in appropriate climate as a cost effective alternative to conventional vapor compression system.

Quantification of relativistic perturbation forces on spacecraft trajectories

The intent of the work presented in this thesis is to show that relativistic perturbations should be considered in the same manner as well known perturbations currently taken into account in planet-satellite systems. It is also the aim of this research to show that relativistic perturbations are comparable to standard perturbations in speciffc force magnitude and effects. This work would have been regarded as little more then a curiosity to most engineers until recent advancements in space propulsion methods { e.g. the creation of a artiffcial neutron stars, light sails, and continuous propulsion techniques. These cutting-edge technologies have the potential to thrust the human race into interstellar, and hopefully intergalactic, travel in the not so distant future. The relativistic perturbations were simulated on two orbit cases: (1) a general orbit and (2) a Molniya type orbit. The simulations were completed using Matlab's ODE45 integration scheme. The methods used to organize, execute, and analyze these simulations are explained in detail. The results of the simulations are presented in graphical and statistical form. The simulation data reveals that the speciffc forces that arise from the relativistic perturbations do manifest as variations in the classical orbital elements. It is also apparent from the simulated data that the speciffc forces do exhibit similar magnitudes and effects that materialize from commonly considered perturbations that are used in trajectory design, optimization, and maintenance. Due to the similarities in behavior of relativistic versus non-relativistic perturbations, a case is made for the development of a fully relativistic formulation for the trajectory design and trajectory optimization problems. This new framework would afford the possibility of illuminating new more optimal solutions to the aforementioned problems that do not arise in current formulations. This type of reformulation has already showed promise when the previously unknown Space Superhighways arose as a optimal solution when classical astrodynamics was reformulated using geometric mechanics.

IDENTIFICATION OF GENES CONTROLLING BIOLOGICAL PROCESSES AND PATHWAYS THROUGH STATISTICAL ANALYSIS AND NETWORK RECONSTRUCTION

The developmental processes and functions of an organism are controlled by the genes and the proteins that are derived from these genes. The identification of key genes and the reconstruction of gene networks can provide a model to help us understand the regulatory mechanisms for the initiation and progression of biological processes or functional abnormalities (e.g. diseases) in living organisms. In this dissertation, I have developed statistical methods to identify the genes and transcription factors (TFs) involved in biological processes, constructed their regulatory networks, and also evaluated some existing association methods to find robust methods for coexpression analyses. Two kinds of data sets were used for this work: genotype data and gene expression microarray data. On the basis of these data sets, this dissertation has two major parts, together forming six chapters. The first part deals with developing association methods for rare variants using genotype data (chapter 4 and 5). The second part deals with developing and/or evaluating statistical methods to identify genes and TFs involved in biological processes, and construction of their regulatory networks using gene expression data (chapter 2, 3, and 6). For the first part, I have developed two methods to find the groupwise association of rare variants with given diseases or traits. The first method is based on kernel machine learning and can be applied to both quantitative as well as qualitative traits. Simulation results showed that the proposed method has improved power over the existing weighted sum method (WS) in most settings. The second method uses multiple phenotypes to select a few top significant genes. It then finds the association of each gene with each phenotype while controlling the population stratification by adjusting the data for ancestry using principal components. This method was applied to GAW 17 data and was able to find several disease risk genes. For the second part, I have worked on three problems. First problem involved evaluation of eight gene association methods. A very comprehensive comparison of these methods with further analysis clearly demonstrates the distinct and common performance of these eight gene association methods. For the second problem, an algorithm named the bottom-up graphical Gaussian model was developed to identify the TFs that regulate pathway genes and reconstruct their hierarchical regulatory networks. This algorithm has produced very significant results and it is the first report to produce such hierarchical networks for these pathways. The third problem dealt with developing another algorithm called the top-down graphical Gaussian model that identifies the network governed by a specific TF. The network produced by the algorithm is proven to be of very high accuracy.

A PETROPHYSICAL EVALUATION OF THE TRENTON-BLACK RIVER FORMATION OF THE MICHIGAN BASIN

This work is conducted to study the geological and petrophysical features of the Trenton- Black River limestone formation. Log curves, crossplots and mineral identification methods using well-log data are used to determine the components and analyze changes in lithology. Thirty-five wells from the Michigan Basin are used to define the mineralogy of Trenton-Black River limestone. Using the different responses of a few log curves, especially gamma-ray, resistivity and neutron porosity, the formation tops for the Utica shale, the Trenton limestone, the Black River limestone and the Prairie du Chien sandstone are identified to confirm earlier authors’ work and provide a basis for my further work. From these, an isopach map showing the thickness of Trenton-Black River formation is created, indicating that its maximum thickness lies in the eastern basin and decreases gradually to the west. In order to obtain more detailed lithological information about the limestone formations at the thirty-five wells, (a) neutron-density and neutron-sonic crossplots, (b) mineral identification methods, including the M-N plot, MID plot, ϱmaa vs. Umaa MID plot, and the PEF plot, and (c) a modified mineral identification technique are applied to these wells. From this, compositions of the Trenton-Black River formation can be divided into three different rock types: pure limestone, partially dolomitized limestone, and shaly limestone. Maps showing the fraction of dolomite and shale indicate their geographic distribution, with dolomite present more in the western and southwestern basin, and shale more common in the north-central basin. Mineral identification is an independent check on the distribution found from other authors, who found similar distributions based on core descriptions. The Thomas Stieber method of analysis is best suited to sand-shale sequences, interpreting hree different distributions of shale within sand, including dispersed, laminated and structural. Since this method is commonly applied in clastic rocks, my work using the Thomas Stieber method is new, as an attempt to apply this technique, developed for clastics, to carbonate rocks. Based on the original assumption and equations with a corresponding change to the Trenton-Black River formation, feasibility of using the Thomas Stieber method in carbonates is tested. A graphical display of gamma-ray versus density porosity, using the properties of clean carbonate and pure shale, suggests the presence of laminated shale in fourteen wells in this study. Combined with Wilson’s study (2001), it is safe to conclude that when shale occurs in the Trenton-Black River formation, it tends to be laminated shale.

On Graphically Checking Goodness-of-fit of Binary Logistic Regression Models

OBJECTIVES: This paper is concerned with checking goodness-of-fit of binary logistic regression models. For the practitioners of data analysis, the broad classes of procedures for checking goodness-of-fit available in the literature are described. The challenges of model checking in the context of binary logistic regression are reviewed. As a viable solution, a simple graphical procedure for checking goodness-of-fit is proposed. METHODS: The graphical procedure proposed relies on pieces of information available from any logistic analysis; the focus is on combining and presenting these in an informative way. RESULTS: The information gained using this approach is presented with three examples. In the discussion, the proposed method is put into context and compared with other graphical procedures for checking goodness-of-fit of binary logistic models available in the literature. CONCLUSION: A simple graphical method can significantly improve the understanding of any logistic regression analysis and help to prevent faulty conclusions.

High-Level Modeling of Multimodal Interaction Techniques Using NiMMiT

The past few years, multimodal interaction has been gaining importance in virtual environments. Although multimodality renders interacting with an environment more natural and intuitive, the development cycle of such an application is often long and expensive. In our overall field of research, we investigate how modelbased design can facilitate the development process by designing environments through the use of highlevel diagrams. In this scope, we present ‘NiMMiT’, a graphical notation for expressing and evaluating multimodal user interaction; we elaborate on the NiMMiT primitives and demonstrate its use by means of a comprehensive example.

Recent Developments in NEURON

We describe four recent additions to NEURON's suite of graphical tools that make it easier for users to create and manage models: an enhancement to the Channel Builder that facilitates the specification and efficient simulation of stochastic channel models

tkCybernetics

tkCybernetics is a simulation software that can be used to create and evaluate simple cybernetic circuits as a combination of lowpass and highpass filters and several nonlinear elements. tkCybernetics has been developed for and successfully applied to introductory courses on biological cybernetics at Bielefeld University. Therefore, it is recommended for students who start learning about cybernetics. Students can quickly grasp the concepts used in the graphical user interface and are able to create their own circuits after a short introduction to the program. Its usefulness for advanced students and researchers is limited to quickly testing circuits. This article provides detailed tutorial information on how to install and work with tkCybernetics for self-learning and for higher education.

Exploring Urban Environments Using Virtual and Augmented Reality

In this paper, we propose the use of specific system architecture, based on mobile device, for navigation in urban environments. The aim of this work is to assess how virtual and augmented reality interface paradigms can provide enhanced location based services using real-time techniques in the context of these two different technologies. The virtual reality interface is based on faithful graphical representation of the localities of interest, coupled with sensory information on the location and orientation of the user, while the augmented reality interface uses computer vision techniques to capture patterns from the real environment and overlay additional way-finding information, aligned with real imagery, in real-time. The knowledge obtained from the evaluation of the virtual reality navigational experience has been used to inform the design of the augmented reality interface. Initial results of the user testing of the experimental augmented reality system for navigation are presented.

Marker-Based Embodied Interaction for Handheld Augmented Reality Games

This article deals with embodied user interfaces for handheld augmented reality games, which consist of both physical and virtual components. We have developed a number of spatial interaction techniques that optically capture the device's movement and orientation relative to a visual marker. Such physical interactions in 3-D space enable manipulative control of mobile games. In addition to acting as a physical controller that recognizes multiple game-dependent gestures, the mobile device augments the camera view with graphical overlays. We describe three game prototypes that use ubiquitous product packaging and other passive media as backgrounds for handheld augmentation. The prototypes can be realized on widely available off-the-shelf hardware and require only minimal setup and infrastructure support.

Teaching Cognitive Modeling Using PDP++

PDP++ is a freely available, open source software package designed to support the development, simulation, and analysis of research-grade connectionist models of cognitive processes. It supports most popular parallel distributed processing paradigms and artificial neural network architectures, and it also provides an implementation of the LEABRA computational cognitive neuroscience framework. Models are typically constructed and examined using the PDP++ graphical user interface, but the system may also be extended through the incorporation of user-written C++ code. This article briefly reviews the features of PDP++, focusing on its utility for teaching cognitive modeling concepts and skills to university undergraduate and graduate students. An informal evaluation of the software as a pedagogical tool is provided, based on the author’s classroom experiences at three research universities and several conference-hosted tutorials.

The TViews Table Role-Playing Game

The TViews Table Role-Playing Game (TTRPG) is a digital tabletop role-playing game that runs on the TViews table, bridging the separate worlds of traditional role-playing games with the growing area of massively multiplayer online role-playing games. The TViews table is an interactive tabletop media platform that can track the location of multiple tagged objects in real-time as they are moved around its surface, providing a simultaneous and coincident graphical display. In this paper we present the implementation of the first version of TTRPG, with a content set based on the traditional Dungeons & Dragons rule-set. We also discuss the results of a user study that used TTRPG to explore the possible social context of digital tabletop role-playing games.