MedVir: 3D visual interface applied to gene profile analysis

The use of data mining techniques for the gene profile discovery of diseases, such as cancer, is becoming usual in many researches. These techniques do not usually analyze the relationships between genes in depth, depending on the different variety of manifestations of the disease (related to patients). This kind of analysis takes a considerable amount of time and is not always the focus of the research. However, it is crucial in order to generate personalized treatments to fight the disease. Thus, this research focuses on finding a mechanism for gene profile analysis to be used by the medical and biologist experts. Results: In this research, the MedVir framework is proposed. It is an intuitive mechanism based on the visualization of medical data such as gene profiles, patients, clinical data, etc. MedVir, which is based on an Evolutionary Optimization technique, is a Dimensionality Reduction (DR) approach that presents the data in a three dimensional space. Furthermore, thanks to Virtual Reality technology, MedVir allows the expert to interact with the data in order to tailor it to the experience and knowledge of the expert.

Dysfunctional 3D model based on structural and neuropsychological information

Acquired brain injury (ABI) 1-2 refers to any brain damage occurring after birth. It usually causes certain damage to portions of the brain. ABI may result in a significant impairment of an individuals physical, cognitive and/or psychosocial functioning. The main causes are traumatic brain injury (TBI), cerebrovascular accident (CVA) and brain tumors. The main consequence of ABI is a dramatic change in the individuals daily life. This change involves a disruption of the family, a loss of future income capacity and an increase of lifetime cost. One of the main challenges in neurorehabilitation is to obtain a dysfunctional profile of each patient in order to personalize the treatment. This paper proposes a system to generate a patient s dysfunctional profile by integrating theoretical, structural and neuropsychological information on a 3D brain imaging-based model. The main goal of this dysfunctional profile is to help therapists design the most suitable treatment for each patient. At the same time, the results obtained are a source of clinical evidence to improve the accuracy and quality of our rehabilitation system. Figure 1 shows the diagram of the system. This system is composed of four main modules: image-based extraction of parameters, theoretical modeling, classification and co-registration and visualization module.

Analysis of quality of experience in 3D video systems

Esta tesis presenta un estudio exhaustivo sobre la evaluación de la calidad de experiencia (QoE, del inglés Quality of Experience) percibida por los usuarios de sistemas de vídeo 3D, analizando el impacto de los efectos introducidos por todos los elementos de la cadena de procesamiento de vídeo 3D. Por lo tanto, se presentan varias pruebas de evaluación subjetiva específicamente diseñadas para evaluar los sistemas considerados, teniendo en cuenta todos los factores perceptuales relacionados con la experiencia visual tridimensional, tales como la percepción de profundidad y la molestia visual. Concretamente, se describe un test subjetivo basado en la evaluación de degradaciones típicas que pueden aparecer en el proceso de creación de contenidos de vídeo 3D, por ejemplo debidas a calibraciones incorrectas de las cámaras o a algoritmos de procesamiento de la señal de vídeo (p. ej., conversión de 2D a 3D). Además, se presenta el proceso de generación de una base de datos de vídeos estereoscópicos de alta calidad, disponible gratuitamente para la comunidad investigadora y que ha sido utilizada ampliamente en diferentes trabajos relacionados con vídeo 3D. Asimismo, se presenta otro estudio subjetivo, realizado entre varios laboratorios, con el que se analiza el impacto de degradaciones causadas por la codificación de vídeo, así como diversos formatos de representación de vídeo 3D. Igualmente, se describen tres pruebas subjetivas centradas en el estudio de posibles efectos causados por la transmisión de vídeo 3D a través de redes de televisión sobre IP (IPTV, del inglés Internet Protocol Television) y de sistemas de streaming adaptativo de vídeo. Para estos casos, se ha propuesto una innovadora metodología de evaluación subjetiva de calidad vídeo, denominada Content-Immersive Evaluation of Transmission Impairments (CIETI), diseñada específicamente para evaluar eventos de transmisión simulando condiciones realistas de visualización de vídeo en ámbitos domésticos, con el fin de obtener conclusiones más representativas sobre la experiencia visual de los usuarios finales. Finalmente, se exponen dos experimentos subjetivos comparando varias tecnologías actuales de televisores 3D disponibles en el mercado de consumo y evaluando factores perceptuales de sistemas Super Multiview Video (SMV), previstos a ser la tecnología futura de televisores 3D de consumo, gracias a una prometedora visualización de contenido 3D sin necesidad de gafas específicas. El trabajo presentado en esta tesis ha permitido entender los factores perceptuales y técnicos relacionados con el procesamiento y visualización de contenidos de vídeo 3D, que pueden ser de utilidad en el desarrollo de nuevas tecnologías y técnicas de evaluación de la QoE, tanto metodologías subjetivas como métricas objetivas. ABSTRACT This thesis presents a comprehensive study of the evaluation of the Quality of Experience (QoE) perceived by the users of 3D video systems, analyzing the impact of effects introduced by all the elements of the 3D video processing chain. Therefore, various subjective assessment tests are presented, particularly designed to evaluate the systems under consideration, and taking into account all the perceptual factors related to the 3D visual experience, such as depth perception and visual discomfort. In particular, a subjective test is presented, based on evaluating typical degradations that may appear during the content creation, for instance due to incorrect camera calibration or video processing algorithms (e.g., 2D to 3D conversion). Moreover, the process of generation of a high-quality dataset of 3D stereoscopic videos is described, which is freely available for the research community, and has been already widely used in different works related with 3D video. In addition, another inter-laboratory subjective study is presented analyzing the impact of coding impairments and representation formats of stereoscopic video. Also, three subjective tests are presented studying the effects of transmission events that take place in Internet Protocol Television (IPTV) networks and adaptive streaming scenarios for 3D video. For these cases, a novel subjective evaluation methodology, called Content-Immersive Evaluation of Transmission Impairments (CIETI), was proposed, which was especially designed to evaluate transmission events simulating realistic home-viewing conditions, to obtain more representative conclusions about the visual experience of the end users. Finally, two subjective experiments are exposed comparing various current 3D displays available in the consumer market, and evaluating perceptual factors of Super Multiview Video (SMV) systems, expected to be the future technology for consumer 3D displays thanks to a promising visualization of 3D content without specific glasses. The work presented in this thesis has allowed to understand perceptual and technical factors related to the processing and visualization of 3D video content, which may be useful in the development of new technologies and approaches for QoE evaluation, both subjective methodologies and objective metrics.

Mejoras y extensiones en el Front-End de un modelo de predicción de acciones de un estudiante en un laboratorio virtual 3D

Este documento presenta las mejoras y las extensiones introducidas en la herramienta de visualización del modelo predictivo del comportamiento del estudiante o Student Behavior Predictor Viewer (SBPV), implementada en un trabajo anterior. El modelo predictivo del comportamiento del estudiante es parte de un sistema inteligente de tutoría, y se construye a partir de los registros de actividad de los estudiantes en un laboratorio virtual 3D, como el Laboratorio Virtual de Biotecnología Agroforestal, implementado en un trabajo anterior, y cuyos registros de actividad de los estudiantes se han utilizado para validar este trabajo fin de grado. El SBPV es una herramienta para visualizar una representación gráfica 2D del grafo extendido asociado con cualquiera de los clusters del modelo predictivo del estudiante. Además de la visualización del grafo extendido, el SBPV controla la navegación a través del grafo por medio del navegador web. Más concretamente, el SBPV permite al usuario moverse a través del grafo, ampliar o reducir el zoom del gráfico o buscar un determinado estado. Además, el SBPV también permite al usuario modificar el diseño predeterminado del grafo en la pantalla al cambiar la posición de los estados con el ratón. Como parte de este trabajo fin de grado, se han corregido errores existentes en la versión anterior y se han introducido una serie de mejoras en el rendimiento y la usabilidad. En este sentido, se han implementado nuevas funcionalidades, tales como la visualización del modelo de comportamiento de cada estudiante individualmente o la posibilidad de elegir el método de clustering para crear el modelo predictivo del estudiante; así como ha sido necesario rediseñar la interfaz de usuario cambiando el tipo de estructuras gráficas con que se muestran los elementos del modelo y mejorando la visualización del grafo al interaccionar el usuario con él. Todas estas mejoras se explican detenidamente en el presente documento.---ABSTRACT---This document presents the improvements and extensions made to the visualization tool Student Behavior Predictor Viewer (SBPV), implemented in a previous job. The student behavior predictive model is part of an intelligent tutoring system, and is built from the records of students activity in a 3D virtual laboratory, like the “Virtual Laboratory of Agroforestry Biotechnology” implemented in a previous work, and whose records of students activity have been used to validate this final degree work. The SBPV is a tool for visualizing a 2D graphical representation of the extended graph associated with any of the clusters of the student predictive model. Apart from visualizing the extended graph, the SBPV supports the navigation across the graph by means of desktop devices. More precisely, the SBPV allows user to move through the graph, to zoom in/out the graphic or to locate a given state. In addition, the SBPV also allows user to modify the default layout of the graph on the screen by changing the position of the states by means of the mouse. As part of this work, some bugs of the previous version have been fixed and some enhancements have been implemented to improve the performance and the usability. In this sense, we have implemented new features, such as the display of the model behavior of only one student or the possibility of selecting the clustering method to create the student predictive model; as well as it was necessary to redesign the user interface changing the type of graphic structures that show model elements and improving the rendering of the graph when the user interacts with it. All these improvements are explained in detail in the next sections.

Geometric 3D point cloud compression

The use of 3D data in mobile robotics applications provides valuable information about the robot’s environment but usually the huge amount of 3D information is unmanageable by the robot storage and computing capabilities. A data compression is necessary to store and manage this information but preserving as much information as possible. In this paper, we propose a 3D lossy compression system based on plane extraction which represent the points of each scene plane as a Delaunay triangulation and a set of points/area information. The compression system can be customized to achieve different data compression or accuracy ratios. It also supports a color segmentation stage to preserve original scene color information and provides a realistic scene reconstruction. The design of the method provides a fast scene reconstruction useful for further visualization or processing tasks.

A multimodal tablet-based interface for designing and reviewing 3D engineering models

The ability to view and interact with 3D models has been happening for a long time. However, vision-based 3D modeling has only seen limited success in applications, as it faces many technical challenges. Hand-held mobile devices have changed the way we interact with virtual reality environments. Their high mobility and technical features, such as inertial sensors, cameras and fast processors, are especially attractive for advancing the state of the art in virtual reality systems. Also, their ubiquity and fast Internet connection open a path to distributed and collaborative development. However, such path has not been fully explored in many domains. VR systems for real world engineering contexts are still difficult to use, especially when geographically dispersed engineering teams need to collaboratively visualize and review 3D CAD models. Another challenge is the ability to rendering these environments at the required interactive rates and with high fidelity. In this document it is presented a virtual reality system mobile for visualization, navigation and reviewing large scale 3D CAD models, held under the CEDAR (Collaborative Engineering Design and Review) project. It’s focused on interaction using different navigation modes. The system uses the mobile device's inertial sensors and camera to allow users to navigate through large scale models. IT professionals, architects, civil engineers and oil industry experts were involved in a qualitative assessment of the CEDAR system, in the form of direct user interaction with the prototypes and audio-recorded interviews about the prototypes. The lessons learned are valuable and are presented on this document. Subsequently it was prepared a quantitative study on the different navigation modes to analyze the best mode to use it in a given situation.

Methods of visualization and analysis of cardiac depolarization in the three dimensional space

The master thesis presents methods for intellectual analysis and visualization 3D EKG in order to increase the efficiency of ECG analysis by extracting additional data. Visualization is presented as part of the signal analysis tasks considered imaging techniques and their mathematical description. Have been developed algorithms for calculating and visualizing the signal attributes are described using mathematical methods and tools for mining signal. The model of patterns searching for comparison purposes of accuracy of methods was constructed, problems of a clustering and classification of data are solved, the program of visualization of data is also developed. This approach gives the largest accuracy in a task of the intellectual analysis that is confirmed in this work. Considered visualization and analysis techniques are also applicable to the multi-dimensional signals of a different kind.

Direct mesh: A multiresolution approach to terrain visualization

Terrain can be approximated by a triangular mesh consisting millions of 3D points. Multiresolution triangular mesh (MTM) structures are designed to support applications that use terrain data at variable levels of detail (LOD). Typically, an MTM adopts a tree structure where a parent node represents a lower-resolution approximation of its descendants. Given a region of interest (ROI) and a LOD, the process of retrieving the required terrain data from the database is to traverse the MTM tree from the root to reach all the nodes satisfying the ROI and LOD conditions. This process, while being commonly used for multiresolution terrain visualization, is inefficient as either a large number of sequential I/O operations or fetching a large amount of extraneous data is incurred. Various spatial indexes have been proposed in the past to address this problem, however level-by-level tree traversal remains a common practice in order to obtain topological information among the retrieved terrain data. A new MTM data structure called direct mesh is proposed. We demonstrate that with direct mesh the amount of data retrieval can be substantially reduced. Comparing with existing MTM indexing methods, a significant performance improvement has been observed for real-life terrain data.

Visual data mining: integrating machine learning with information visualization

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. Most existing systems concentrate either on mining algorithms or on visualization techniques. Though visual methods developed in information visualization have been helpful, for improved understanding of a complex large high-dimensional dataset, there is a need for an effective projection of such a dataset onto a lower-dimension (2D or 3D) manifold. This paper introduces a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualization domain. The framework follows Shneiderman’s mantra to provide an effective user interface. The advantage of such an interface is that the user is directly involved in the data mining process. We integrate principled projection methods, such as Generative Topographic Mapping (GTM) and Hierarchical GTM (HGTM), with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, billboarding, and user interaction facilities, to provide an integrated visual data mining framework. Results on a real life high-dimensional dataset from the chemoinformatics domain are also reported and discussed. Projection results of GTM are analytically compared with the projection results from other traditional projection methods, and it is also shown that the HGTM algorithm provides additional value for large datasets. The computational complexity of these algorithms is discussed to demonstrate their suitability for the visual data mining framework.

3D Environment for Virtual Collections

This paper describes a framework for building virtual collections of several digital objects and presenting them in an interactive 3D environment, rendered in a web browser. Using that environment, the website visitor can examine a given collection from a first-person perspective by walking around and inspecting each object in detail by viewing it from any angle. The rendering and visualization of the models is done solely by the web browser with the use of HTML5 and the Three.js JavaScript library, without any additional requirements.

3D TerraFly: Quality of service management for online interactive 3D geographic information system

3D geographic information system (GIS) is data and computation intensive in nature. Internet users are usually equipped with low-end personal computers and network connections of limited bandwidth. Data reduction and performance optimization techniques are of critical importance in quality of service (QoS) management for online 3D GIS. In this research, QoS management issues regarding distributed 3D GIS presentation were studied to develop 3D TerraFly, an interactive 3D GIS that supports high quality online terrain visualization and navigation. ^ To tackle the QoS management challenges, multi-resolution rendering model, adaptive level of detail (LOD) control and mesh simplification algorithms were proposed to effectively reduce the terrain model complexity. The rendering model is adaptively decomposed into sub-regions of up-to-three detail levels according to viewing distance and other dynamic quality measurements. The mesh simplification algorithm was designed as a hybrid algorithm that combines edge straightening and quad-tree compression to reduce the mesh complexity by removing geometrically redundant vertices. The main advantage of this mesh simplification algorithm is that grid mesh can be directly processed in parallel without triangulation overhead. Algorithms facilitating remote accessing and distributed processing of volumetric GIS data, such as data replication, directory service, request scheduling, predictive data retrieving and caching were also proposed. ^ A prototype of the proposed 3D TerraFly implemented in this research demonstrates the effectiveness of our proposed QoS management framework in handling interactive online 3D GIS. The system implementation details and future directions of this research are also addressed in this thesis. ^

Multi-Scale Visualization and Interpretation of Geological Relationships

Visualization and interpretation of geological observations into a cohesive geological model are essential to Earth sciences and related fields. Various emerging technologies offer approaches to multi-scale visualization of heterogeneous data, providing new opportunities that facilitate model development and interpretation processes. These include increased accessibility to 3D scanning technology, global connectivity, and Web-based interactive platforms. The geological sciences and geological engineering disciplines are adopting these technologies as volumes of data and physical samples greatly increase. However, a standardized and universally agreed upon workflow and approach have yet to properly be developed. In this thesis, the 3D scanning workflow is presented as a foundation for a virtual geological database. This database provides augmented levels of tangibility to students and researchers who have little to no access to locations that are remote or inaccessible. A Web-GIS platform was utilized jointly with customized widgets developed throughout the course of this research to aid in visualizing hand-sized/meso-scale geological samples within a geologic and geospatial context. This context is provided as a macro-scale GIS interface, where geophysical and geodetic images and data are visualized. Specifically, an interactive interface is developed that allows for simultaneous visualization to improve the understanding of geological trends and relationships. These developed tools will allow for rapid data access and global sharing, and will facilitate comprehension of geological models using multi-scale heterogeneous observations.

Navigating 3d Scatter Plots in Immersive Virtual Reality

Thesis (Master's)--University of Washington, 2016-01

Sistema integrado de generación de mapas de profundidad para videoconferencia 3D en tiempo real

This paper presents the implementation of a high quality real-time 3D video system intended for 3D videoconferencing -- Basically, the system is able to extract depth information from a pair of images coming from a short-baseline camera setup -- The system is based on the use of a variant of the adaptive support-weight algorithm to be applied on GPU-based architectures -- The reason to do it is to get real-time results without compromising accuracy and also to reduce costs by using commodity hardware -- The complete system runs over the GStreamer multimedia software platform to make it even more flexible -- Moreover, an autoestereoscopic display has been used as the end-up terminal for 3D content visualization

Direct Visualization Of The Action Of Triton X-100 On Giant Vesicles Of Erythrocyte Membrane Lipids.

The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their compositions. In fact, the impact of detergents in membrane organization is still controversial. Here, we use phase contrast and fluorescence microscopy to observe giant unilamellar vesicles (GUVs) made of erythrocyte membrane lipids (erythro-GUVs) when exposed to the detergent Triton X-100 (TX-100). We clearly show that TX-100 has a restructuring action on biomembranes. Contact with TX-100 readily induces domain formation on the previously homogeneous membrane of erythro-GUVs at physiological and room temperatures. The shape and dynamics of the formed domains point to liquid-ordered/liquid-disordered (Lo/Ld) phase separation, typically found in raft-like ternary lipid mixtures. The Ld domains are then separated from the original vesicle and completely solubilized by TX-100. The insoluble vesicle left, in the Lo phase, represents around 2/3 of the original vesicle surface at room temperature and decreases to almost 1/2 at physiological temperature. This chain of events could be entirely reproduced with biomimetic GUVs of a simple ternary lipid mixture, 2:1:2 POPC/SM/chol (phosphatidylcholine/sphyngomyelin/cholesterol), showing that this behavior will arise because of fundamental physicochemical properties of simple lipid mixtures. This work provides direct visualization of TX-100-induced domain formation followed by selective (Ld phase) solubilization in a model system with a complex biological lipid composition.