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

Visual Perception and Cognition in Image-Guided Intervention

Surgical image visualization and interaction systems can dramatically affect the efficacy and efficiency of surgical training, planning, and interventions. This is even more profound in the case of minimally-invasive surgery where restricted access to the operative field in conjunction with limited field of view necessitate a visualization medium to provide patient-specific information at any given moment. Unfortunately, little research has been devoted to studying human factors associated with medical image displays and the need for a robust, intuitive visualization and interaction interfaces has remained largely unfulfilled to this day. Failure to engineer efficient medical solutions and design intuitive visualization interfaces is argued to be one of the major barriers to the meaningful transfer of innovative technology to the operating room. This thesis was, therefore, motivated by the need to study various cognitive and perceptual aspects of human factors in surgical image visualization systems, to increase the efficiency and effectiveness of medical interfaces, and ultimately to improve patient outcomes. To this end, we chose four different minimally-invasive interventions in the realm of surgical training, planning, training for planning, and navigation: The first chapter involves the use of stereoendoscopes to reduce morbidity in endoscopic third ventriculostomy. The results of this study suggest that, compared with conventional endoscopes, the detection of the basilar artery on the surface of the third ventricle can be facilitated with the use of stereoendoscopes, increasing the safety of targeting in third ventriculostomy procedures. In the second chapter, a contour enhancement technique is described to improve preoperative planning of arteriovenous malformation interventions. The proposed method, particularly when combined with stereopsis, is shown to increase the speed and accuracy of understanding the spatial relationship between vascular structures. In the third chapter, an augmented-reality system is proposed to facilitate the training of planning brain tumour resection. The results of our user study indicate that the proposed system improves subjects\u27 performance, particularly novices\u27, in formulating the optimal point of entry and surgical path independent of the sensorimotor tasks performed. In the last chapter, the role of fully-immersive simulation environments on the surgeons\u27 non-technical skills to perform vertebroplasty procedure is investigated. Our results suggest that while training surgeons may increase their technical skills, the introduction of crisis scenarios significantly disturbs the performance, emphasizing the need of realistic simulation environments as part of training curriculum

Stereoscopic Sketchpad: 3D Digital Ink

--Context-- This project looked at the development of a stereoscopic 3D environment in which a user is able to draw freely in all three dimensions. The main focus was on the storage and manipulation of the ‘digital ink’ with which the user draws. For a drawing and sketching package to be effective it must not only have an easy to use user interface, it must be able to handle all input data quickly and efficiently so that the user is able to focus fully on their drawing. --Background-- When it comes to sketching in three dimensions the majority of applications currently available rely on vector based drawing methods. This is primarily because the applications are designed to take a users two dimensional input and transform this into a three dimensional model. Having the sketch represented as vectors makes it simpler for the program to act upon its geometry and thus convert it to a model. There are a number of methods to achieve this aim including Gesture Based Modelling, Reconstruction and Blobby Inflation. Other vector based applications focus on the creation of curves allowing the user to draw within or on existing 3D models. They also allow the user to create wire frame type models. These stroke based applications bring the user closer to traditional sketching rather than the more structured modelling methods detailed. While at present the field is inundated with vector based applications mainly focused upon sketch-based modelling there are significantly less voxel based applications. The majority of these applications focus on the deformation and sculpting of voxmaps, almost the opposite of drawing and sketching, and the creation of three dimensional voxmaps from standard two dimensional pixmaps. How to actually sketch freely within a scene represented by a voxmap has rarely been explored. This comes as a surprise when so many of the standard 2D drawing programs in use today are pixel based. --Method-- As part of this project a simple three dimensional drawing program was designed and implemented using C and C++. This tool is known as Sketch3D and was created using a Model View Controller (MVC) architecture. Due to the modular nature of Sketch3Ds system architecture it is possible to plug a range of different data structures into the program to represent the ink in a variety of ways. A series of data structures have been implemented and were tested for efficiency. These structures were a simple list, a 3D array, and an octree. They have been tested for: the time it takes to insert or remove points from the structure; how easy it is to manipulate points once they are stored; and also how the number of points stored effects the draw and rendering times. One of the key issues brought up by this project was devising a means by which a user is able to draw in three dimensions while using only two dimensional input devices. The method settled upon and implemented involves using the mouse or a digital pen to sketch as one would in a standard 2D drawing package but also linking the up and down keyboard keys to the current depth. This allows the user to move in and out of the scene as they draw. A couple of user interface tools were also developed to assist the user. A 3D cursor was implemented and also a toggle, which when on, highlights all of the points intersecting the depth plane on which the cursor currently resides. These tools allow the user to see exactly where they are drawing in relation to previously drawn lines. --Results-- The tests conducted on the data structures clearly revealed that the octree was the most effective data structure. While not the most efficient in every area, it manages to avoid the major pitfalls of the other structures. The list was extremely quick to render and draw to the screen but suffered severely when it comes to finding and manipulating points already stored. In contrast the three dimensional array was able to erase or manipulate points effectively while the draw time rendered the structure effectively useless, taking huge amounts of time to draw each frame. The focus of this research was on how a 3D sketching package would go about storing and accessing the digital ink. This is just a basis for further research in this area and many issues touched upon in this paper will require a more in depth analysis. The primary area of this future research would be the creation of an effective user interface and the introduction of regular sketching package features such as the saving and loading of images

Development and evaluation of a novel method for in-situ medical image display

Three-dimensional (3D) medical imaging, including computed tomography (CT) and magnetic resonance (MR), and other modalities, has become a standard of care for diagnosis of disease and guidance of interventional procedures. As the technology to acquire larger, more magnificent, and more informative medical images advances, so too must the technology to display, interact with, and interpret these data.This dissertation concerns the development and evaluation of a novel method for interaction with 3D medical images called "grab-a-slice," which is a movable, tracked stereo display. It is the latest in a series of displays developed in our laboratory that we describe as in-situ, meaning that the displayed image is embedded in a physical 3D coordinate system. As the display is moved through space, a continuously updated tomographic slice of a 3D medical image is shown on the screen, corresponding to the position and orientation of the display. The act of manipulating the display through a "virtual patient" preserves the perception of 3D anatomic relationships in a way that is not possible with conventional, fixed displays. The further addition of stereo display capabilities permits augmentation of the tomographic image data with out-of-plane structures using 3D graphical methods.In this dissertation we describe the research and clinical motivations for such a device. We describe the technical development of grab-a-slice as well as psychophysical experiments to evaluate the hypothesized perceptual and cognitive benefits. We speculate on the advantages and limitations of the grab-a-slice display and propose future directions for its use in psychophysical research, clinical settings, and image analysis

Scalable multi-view stereo camera array for real world real-time image capture and three-dimensional displays

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2004.Includes bibliographical references (leaves 71-75).The number of three-dimensional displays available is escalating and yet the capturing devices for multiple view content are focused on either single camera precision rigs that are limited to stationary objects or the use of synthetically created animations. In this work we will use the existence of inexpensive digital CMOS cameras to explore a multi- image capture paradigm and the gathering of real world real-time data of active and static scenes. The capturing system can be developed and employed for a wide range of applications such as portrait-based images for multi-view facial recognition systems, hypostereo surgical training systems, and stereo surveillance by unmanned aerial vehicles. The system will be adaptable to capturing the correct stereo views based on the environmental scene and the desired three-dimensional display. Several issues explored by the system will include image calibration, geometric correction, the possibility of object tracking, and transfer of the array technology into other image capturing systems. These features provide the user more freedom to interact with their specific 3-D content while allowing the computer to take on the difficult role of stereoscopic cinematographer.Samuel L. Hill.S.M

Augmented reality (AR) for surgical robotic and autonomous systems: State of the art, challenges, and solutions

Despite the substantial progress achieved in the development and integration of augmented reality (AR) in surgical robotic and autonomous systems (RAS), the center of focus in most devices remains on improving end-effector dexterity and precision, as well as improved access to minimally invasive surgeries. This paper aims to provide a systematic review of different types of state-of-the-art surgical robotic platforms while identifying areas for technological improvement. We associate specific control features, such as haptic feedback, sensory stimuli, and human-robot collaboration, with AR technology to perform complex surgical interventions for increased user perception of the augmented world. Current researchers in the field have, for long, faced innumerable issues with low accuracy in tool placement around complex trajectories, pose estimation, and difficulty in depth perception during two-dimensional medical imaging. A number of robots described in this review, such as Novarad and SpineAssist, are analyzed in terms of their hardware features, computer vision systems (such as deep learning algorithms), and the clinical relevance of the literature. We attempt to outline the shortcomings in current optimization algorithms for surgical robots (such as YOLO and LTSM) whilst providing mitigating solutions to internal tool-to-organ collision detection and image reconstruction. The accuracy of results in robot end-effector collisions and reduced occlusion remain promising within the scope of our research, validating the propositions made for the surgical clearance of ever-expanding AR technology in the future

Augmented Reality and Its Application

Augmented Reality (AR) is a discipline that includes the interactive experience of a real-world environment, in which real-world objects and elements are enhanced using computer perceptual information. It has many potential applications in education, medicine, and engineering, among other fields. This book explores these potential uses, presenting case studies and investigations of AR for vocational training, emergency response, interior design, architecture, and much more

Stereoscopic bimanual interaction for 3D visualization

Virtual Environments (VE) are being widely used in various research fields for several decades such as 3D visualization, education, training and games. VEs have the potential to enhance the visualization and act as a general medium for human-computer interaction (HCI). However, limited research has evaluated virtual reality (VR) display technologies, monocular and binocular depth cues, for human depth perception of volumetric (non-polygonal) datasets. In addition, a lack of standardization of three-dimensional (3D) user interfaces (UI) makes it challenging to interact with many VE systems. To address these issues, this dissertation focuses on evaluation of effects of stereoscopic and head-coupled displays on depth judgment of volumetric dataset. It also focuses on evaluation of a two-handed view manipulation techniques which support simultaneous 7 degree-of-freedom (DOF) navigation (x,y,z + yaw,pitch,roll + scale) in a multi-scale virtual environment (MSVE). Furthermore, this dissertation evaluates auto-adjustment of stereo view parameters techniques for stereoscopic fusion problems in a MSVE. Next, this dissertation presents a bimanual, hybrid user interface which combines traditional tracking devices with computer-vision based "natural" 3D inputs for multi-dimensional visualization in a semi-immersive desktop VR system. In conclusion, this dissertation provides a guideline for research design for evaluating UI and interaction techniques

Pulse Oxigraphy: And other new in-depth perspectives through the near infrared window

The aim of this thesis was to investigate the feasability of contactless imaging pulse oximetry (proposed term: pulse oxigraphy). The patent disclosed in chapter 2 claims that such pulse oxigraphy can be achieved with camera-derived photoplethysmographic pulse waves at three wavelengths, preferably being 660, 810 and 940nm. From the absorption curves of hemoglobin and oxyhemoglobin it can be easily derived that two of these wavelengths (660 and 940nm) contain oxygenation-related information, and they have proven to be useful for conventional pulse oximetry (in transmission- mode as well as in reflectance-mode). The additional third wavelength (810nm) lies at a so-called isobestic point where the absorption curves of hemoglobin and oxyhemoglobin intersect. Thus, images and/or plethysmographic pulse waves recorded at 810nm do not contain oxygenation-related information, which is useful for reference purposes when dealing with shadows, reflections, movement artifacts and variations in geometry. With regard to pulse oxigraphy the following results were obtained: In chapter 3 we proved that it is possible to derive photoplethysmographic pulse waves containing the heart rythm of a living person at all three required wavelengths from camera recordings collected at a distance of 72 cm. To investigate and validate the capabilities for pulse oxigraphy with this set up, direct measurements on volunteers were sub optimal, because of: Signal-to-noise issues, sequentially recorded heartbeats for oxygen saturation calculations, and lack of a method to induce prolonged stable and adjustable oxygen saturation levels