Advanced Visualization and Intuitive User Interface Systems for Biomedical Applications

Modern scientific research produces data at rates that far outpace our ability to comprehend and analyze it. Such sources include medical imaging data and computer simulations, where technological advancements and spatiotemporal resolution generate increasing amounts of data from each scan or simulation. A bottleneck has developed whereby medical professionals and researchers are unable to fully use the advanced information available to them. By integrating computer science, computer graphics, artistic ability and medical expertise, scientific visualization of medical data has become a new field of study. The objective of this thesis is to develop two visualization systems that use advanced visualization, natural user interface technologies and the large amount of biomedical data available to produce results that are of clinical utility and overcome the data bottleneck that has developed. Computational Fluid Dynamics (CFD) is a tool used to study the quantities associated with the movement of blood by computer simulation. We developed methods of processing spatiotemporal CFD data and displaying it in stereoscopic 3D with the ability to spatially navigate through the data. We used this method with two sets of display hardware: a full-scale visualization environment and a small-scale desktop system. The advanced display and data navigation abilities provide the user with the means to better understand the relationship between the vessel\u27s form and function. Low-cost 3D, depth-sensing cameras capture and process user body motion to recognize motions and gestures. Such devices allow users to use hand motions as an intuitive interface to computer applications. We developed algorithms to process and prepare the biomedical and scientific data for use with a custom control application. The application interprets user gestures as commands to a visualization tool and allows the user to control the visualization of multi-dimensional data. The intuitive interface allows the user to control the visualization of data without manual contact with an interaction device. In developing these methods and software tools we have leveraged recent trends in advanced visualization and intuitive interfaces in order to efficiently visualize biomedical data in such a way that provides meaningful information that can be used to further appreciate it

Augmented reality device for first response scenarios

A prototype of a wearable computer system is proposed and implemented using commercial off-shelf components. The system is designed to allow the user to access location-specific information about an environment, and to provide capability for user tracking. Areas of applicability include primarily first response scenarios, with possible applications in maintenance or construction of buildings and other structures. Necessary preparation of the target environment prior to system\u27s deployment is limited to noninvasive labeling using optical fiducial markers. The system relies on computational vision methods for registration of labels and user position. With the system the user has access to on-demand information relevant to a particular real-world location. Team collaboration is assisted by user tracking and real-time visualizations of team member positions within the environment. The user interface and display methods are inspired by Augmented Reality1 (AR) techniques, incorporating a video-see-through Head Mounted Display (HMD) and fingerbending sensor glove.*. 1Augmented reality (AR) is a field of computer research which deals with the combination of real world and computer generated data. At present, most AR research is concerned with the use of live video imagery which is digitally processed and augmented by the addition of computer generated graphics. Advanced research includes the use of motion tracking data, fiducial marker recognition using machine vision, and the construction of controlled environments containing any number of sensors and actuators. (Source: Wikipedia) *This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Adobe Acrobat; Microsoft Office; Windows MediaPlayer or RealPlayer

3D Modelling from Real Data

The genesis of a 3D model has basically two definitely different paths. Firstly we can consider the CAD generated models, where the shape is defined according to a user drawing action, operating with different mathematical “bricks” like B-Splines, NURBS or subdivision surfaces (mathematical CAD modelling), or directly drawing small polygonal planar facets in space, approximating with them complex free form shapes (polygonal CAD modelling). This approach can be used for both ideal elements (a project, a fantasy shape in the mind of a designer, a 3D cartoon, etc.) or for real objects. In the latter case the object has to be first surveyed in order to generate a drawing coherent with the real stuff. If the surveying process is not only a rough acquisition of simple distances with a substantial amount of manual drawing, a scene can be modelled in 3D by capturing with a digital instrument many points of its geometrical features and connecting them by polygons to produce a 3D result similar to a polygonal CAD model, with the difference that the shape generated is in this case an accurate 3D acquisition of a real object (reality-based polygonal modelling). Considering only device operating on the ground, 3D capturing techniques for the generation of reality-based 3D models may span from passive sensors and image data (Remondino and El-Hakim, 2006), optical active sensors and range data (Blais, 2004; Shan & Toth, 2008; Vosselman and Maas, 2010), classical surveying (e.g. total stations or Global Navigation Satellite System - GNSS), 2D maps (Yin et al., 2009) or an integration of the aforementioned methods (Stumpfel et al., 2003; Guidi et al., 2003; Beraldin, 2004; Stamos et al., 2008; Guidi et al., 2009a; Remondino et al., 2009; Callieri et al., 2011). The choice depends on the required resolution and accuracy, object dimensions, location constraints, instrument’s portability and usability, surface characteristics, working team experience, project’s budget, final goal, etc. Although aware of the potentialities of the image-based approach and its recent developments in automated and dense image matching for non-expert the easy usability and reliability of optical active sensors in acquiring 3D data is generally a good motivation to decline image-based approaches. Moreover the great advantage of active sensors is the fact that they deliver immediately dense and detailed 3D point clouds, whose coordinate are metrically defined. On the other hand image data require some processing and a mathematical formulation to transform the two-dimensional image measurements into metric three-dimensional coordinates. Image-based modelling techniques (mainly photogrammetry and computer vision) are generally preferred in cases of monuments or architectures with regular geometric shapes, low budget projects, good experience of the working team, time or location constraints for the data acquisition and processing. This chapter is intended as an updated review of reality-based 3D modelling in terrestrial applications, with the different categories of 3D sensing devices and the related data processing pipelines

Image processing techniques for mixed reality and biometry

2013 - 2014This thesis work is focused on two applicative fields of image processing research, which, for different reasons, have become particularly active in the last decade: Mixed Reality and Biometry. Though the image processing techniques involved in these two research areas are often different, they share the key objective of recognizing salient features typically captured through imaging devices. Enabling technologies for augmented/mixed reality have been improved and refined throughout the last years and more recently they seems to have finally passed the demo stage to becoming ready for practical industrial and commercial applications. To this regard, a crucial role will likely be played by the new generation of smartphones and tablets, equipped with an arsenal of sensors connections and enough processing power for becoming the most portable and affordable AR platform ever. Within this context, techniques like gesture recognition by means of simple, light and robust capturing hardware and advanced computer vision techniques may play an important role in providing a natural and robust way to control software applications and to enhance onthe- field operational capabilities. The research described in this thesis is targeted toward advanced visualization and interaction strategies aimed to improve the operative range and robustness of mixed reality applications, particularly for demanding industrial environments... [edited by Author]XIII n.s

Virtual and Augmented Reality Techniques for Minimally Invasive Cardiac Interventions: Concept, Design, Evaluation and Pre-clinical Implementation

While less invasive techniques have been employed for some procedures, most intracardiac interventions are still performed under cardiopulmonary bypass, on the drained, arrested heart. The progress toward off-pump intracardiac interventions has been hampered by the lack of adequate visualization inside the beating heart. This thesis describes the development, assessment, and pre-clinical implementation of a mixed reality environment that integrates pre-operative imaging and modeling with surgical tracking technologies and real-time ultrasound imaging. The intra-operative echo images are augmented with pre-operative representations of the cardiac anatomy and virtual models of the delivery instruments tracked in real time using magnetic tracking technologies. As a result, the otherwise context-less images can now be interpreted within the anatomical context provided by the anatomical models. The virtual models assist the user with the tool-to-target navigation, while real-time ultrasound ensures accurate positioning of the tool on target, providing the surgeon with sufficient information to ``see\u27\u27 and manipulate instruments in absence of direct vision. Several pre-clinical acute evaluation studies have been conducted in vivo on swine models to assess the feasibility of the proposed environment in a clinical context. Following direct access inside the beating heart using the UCI, the proposed mixed reality environment was used to provide the necessary visualization and navigation to position a prosthetic mitral valve on the the native annulus, or to place a repair patch on a created septal defect in vivo in porcine models. Following further development and seamless integration into the clinical workflow, we hope that the proposed mixed reality guidance environment may become a significant milestone toward enabling minimally invasive therapy on the beating heart

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

3D BrachyView System

Prostate cancer is quickly becoming the most common form of cancer across the globe, and is commonly treated with low dose rate brachytherapy due to its curative measures and highly conformal dose delivery. It is important to ensure there is a means of real time monitoring of the dose and seed placements when radioactive seeds are implanted in the prostate gland during a low dose rate brachytherapy treatment. The BrachyView system presents as a unique system that provides the capability of 3D seed reconstruction within an intraoperative setting. In this thesis the BrachyView system is tested for its suitability, accuracy and the system is further developed so that its application in real-time intraoperative dosime-try can become a reality. The system was tested with a clinically relevant number of seeds, 98, where previously the system had only been tested with a maximum number of 30 seeds. The BrachyView system was able to reconstruct 91.8% of implanted seeds from the 98 seed dataset with an average overall discrepancy of 3.65 mm without the application of the baseline subtraction algorithm, however with its application to the data the detection efficiency was improved to 100% and an overall positional accuracy of 11.5%, correlating to a reduced overall discrepancy of 3.23 mm, was noted. It was found that with seed numbers of 30 or lower that the addition of a background subtrac-tion algorithm was not necessary, whereas for datasets containing a clinically relevant number of seeds the application of a background subtraction algorithm was paramount to reducing the noise, scatter and means for identification of newly implanted seeds that may be masked by those seed previously implanted

Real-time Illumination and Visual Coherence for Photorealistic Augmented/Mixed Reality

A realistically inserted virtual object in the real-time physical environment is a desirable feature in augmented reality (AR) applications and mixed reality (MR) in general. This problem is considered a vital research area in computer graphics, a field that is experiencing ongoing discovery. The algorithms and methods used to obtain dynamic and real-time illumination measurement, estimating, and rendering of augmented reality scenes are utilized in many applications to achieve a realistic perception by humans. We cannot deny the powerful impact of the continuous development of computer vision and machine learning techniques accompanied by the original computer graphics and image processing methods to provide a significant range of novel AR/MR techniques. These techniques include methods for light source acquisition through image-based lighting or sampling, registering and estimating the lighting conditions, and composition of global illumination. In this review, we discussed the pipeline stages with the details elaborated about the methods and techniques that contributed to the development of providing a photo-realistic rendering, visual coherence, and interactive real-time illumination results in AR/MR

Imagination makes things perfect

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