Uncertainty visualization in 3D scalar data

One problem in most three-dimensional (3D) scalar data visualization techniques is that they often overlook to depict uncertainty that comes with the 3D scalar data and thus fail to faithfully present the 3D scalar data and have risks which may mislead users’ interpretations, conclusions or even decisions. Therefore this thesis focuses on the study of uncertainty visualization in 3D scalar data and we seek to create better uncertainty visualization techniques, as well as to find out the advantages/disadvantages of those state-of-the-art uncertainty visualization techniques. To do this, we address three specific hypotheses: (1) the proposed Texture uncertainty visualization technique enables users to better identify scalar/error data, and provides reduced visual overload and more appropriate brightness than four state-of-the-art uncertainty visualization techniques, as demonstrated using a perceptual effectiveness user study. (2) The proposed Linked Views and Interactive Specification (LVIS) uncertainty visualization technique enables users to better search max/min scalar and error data than four state-of-the-art uncertainty visualization techniques, as demonstrated using a perceptual effectiveness user study. (3) The proposed Probabilistic Query uncertainty visualization technique, in comparison to traditional Direct Volume Rendering (DVR) methods, enables radiologists/physicians to better identify possible alternative renderings relevant to a diagnosis and the classification probabilities associated to the materials appeared on these renderings; this leads to improved decision support for diagnosis, as demonstrated in the domain of medical imaging. For each hypothesis, we test it by following/implementing a unified framework that consists of three main steps: the first main step is uncertainty data modeling, which clearly defines and generates certainty types of uncertainty associated to given 3D scalar data. The second main step is uncertainty visualization, which transforms the 3D scalar data and their associated uncertainty generated from the first main step into two-dimensional (2D) images for insight, interpretation or communication. The third main step is evaluation, which transforms the 2D images generated from the second main step into quantitative scores according to specific user tasks, and statistically analyzes the scores. As a result, the quality of each uncertainty visualization technique is determined.

3D vanadium oxide inverse opal growth by electrodeposition

Three-dimensional vanadium pentoxide (V2O5) material architectures in the form of inverse opals (IOs) were fabricated using a simple electrodeposition process into artificial opal templates on stainless steel foil using an aqueous solution of VOSO4.χH2O with added ethanol. The direct deposition of V2O5 IOs was compared with V2O5 planar electrodeposition and confirms a similar progressive nucleation and growth mechanism. An in-depth examination of the chemical and morphological nature of the IO material was performed using X-ray crystallography, X-ray photoelectron spectroscopy, Raman scattering and scanning/transmission electron microscopy. Electrodeposition is demonstrated to be a function of the interstitial void fraction of the artificial opal and ionic diffusivity that leads to high quality, phase pure V2O5 inverse opals is not adversely affected by diffusion pathway tortuosity. Methods to alleviate electrodeposited overlayer formation on the artificial opal templates for the fabrication of the porous 3D structures are also demonstrated. Such a 3D material is ideally suited as a cathode for lithium ion batteries, electrochromic devices, sensors and for applications requiring high surface area electrochemically active metal oxides.

A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.

Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. An element located within a DNase I-hypersensitive site (DHS) 10 kb into the first intron was previously shown to augment CFTR promoter activity in a tissue-specific manner. Here, we reveal the mechanism by which this element influences CFTR transcription. We employed a high-resolution method of mapping DHS using tiled microarrays to accurately locate the intron 1 DHS. Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. Moreover, using chromosome conformation capture (3C) analysis, we show that this element interacts with the CFTR promoter in CFTR-expressing cells. These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression.

Optical-CT 3D Dosimetry Using Fresnel Lenses with Minimal Refractive-Index Matching Fluid.

Telecentric optical computed tomography (optical-CT) is a state-of-the-art method for visualizing and quantifying 3-dimensional dose distributions in radiochromic dosimeters. In this work a prototype telecentric system (DFOS-Duke Fresnel Optical-CT Scanner) is evaluated which incorporates two substantial design changes: the use of Fresnel lenses (reducing lens costs from $10-30K t0 $1-3K) and the use of a 'solid tank' (which reduces noise, and the volume of refractively matched fluid from 1 ltr to 10 cc). The efficacy of DFOS was evaluated by direct comparison against commissioned scanners in our lab. Measured dose distributions from all systems were compared against the predicted dose distributions from a commissioned treatment planning system (TPS). Three treatment plans were investigated including a simple four-field box treatment, a multiple small field delivery, and a complex IMRT treatment. Dosimeters were imaged within 2 h post irradiation, using consistent scanning techniques (360 projections acquired at 1 degree intervals, reconstruction at 2mm). DFOS efficacy was evaluated through inspection of dose line-profiles, and 2D and 3D dose and gamma maps. DFOS/TPS gamma pass rates with 3%/3mm dose difference/distance-to-agreement criteria ranged from 89.3% to 92.2%, compared to from 95.6% to 99.0% obtained with the commissioned system. The 3D gamma pass rate between the commissioned system and DFOS was 98.2%. The typical noise rates in DFOS reconstructions were up to 3%, compared to under 2% for the commissioned system. In conclusion, while the introduction of a solid tank proved advantageous with regards to cost and convenience, further work is required to improve the image quality and dose reconstruction accuracy of the new DFOS optical-CT system.

Modelling and prototyping the conceptual design of 3D CMM micro-probe

This paper details the prototyping of a novel three axial micro probe based on utilisation of piezoelectric sensors and actuators for true three dimensional metrology and measurements at micro- and nanometre scale. Computational mechanics is used first to model and simulate the performance of the conceptual design of the micro-probe. Piezoelectric analysis is conducted to understand performance of three different materials - silicon, glassy carbon, and nickel - and the effect of load parameters (amplitude, frequency, phase angle) on the magnitude of vibrations. Simulations are also used to compare several design options for layout of the lead zirconium titanate (PZT) sensors and to identify the most feasible from fabrication point of view design. The material options for the realisation of the device have been also tested. Direct laser machining was selected as the primary means of production. It is found that a Yb MOPA based fiber laser was capable of providing the necessary precision on glassy carbon (GC), although machining trials on Si and Ni were less successful due to residual thermal effects.To provide the active and sensing elements on the flexures of the probe, PZT thick films are developed and deposited at low temperatures (Lt720 degC) allowing a high quality functional ceramic to be directly integrated with selected materials. Characterisation of the materials has shown that the film has a homogenous and small pore microstructure.

A comparison of nonstaggered compact FDTD schemes for the 3D wave equation

This paper aims at providing a better insight into the 3D approximations of the wave equation using compact finite-difference time-domain (FDTD) schemes in the context of room acoustic simulations. A general family of 3D compact explicit and implicit schemes based on a nonstaggered rectilinear grid is analyzed in terms of stability, numerical error, and accuracy. Various special cases are compared and the most accurate explicit and implicit schemes are identified. Further considerations presented in the paper include the direct relationship with other numerical approaches found in the literature on room acoustic modeling such as the 3D digital waveguide mesh and Yee's staggered grid technique.

3D die shape optimisation for net-shape forging of aerofoil blades

This paper reports on work in developing a finite element (FE) based die shape optimisation for net-shape forging of 3D aerofoil blades for aeroengine applications. Quantitative representations of aerofoil forging tolerances were established to provide a correlation between conventional dimensional and shape specifications in forging production and those quantified in FE simulation. A new direct compensation method was proposed, employing variable weighting factors to minimise the total forging tolerances in forging optimisation computations. A surface approximation using a B-spline surface was also developed to ensure improved die surface quality for die shape representation and design. For a Ni-alloy blade test case, substantial reduction in dimensional and shape tolerances was achieved using the developed die shape optimisation system.

Direct assembly of three-dimensional mesh plasmonic rolls

A direct-assembly method to construct three-dimensional (3D) plasmonic nanostructures yields porous plasmonic rolls through the strain-induced self-rolling up of two-dimensional metallic nanopore films. This route is scalable to different hole sizes and film thicknesses, and applicable to a variety of materials, providing general routes towards a diverse family of 3D metamaterials with nano-engineerable optical properties. These plasmonic rolls can be dynamically driven by light irradiation, rolling or unrolling with increasing or decreasing light intensity. Such dynamically controllable 3D plasmonic nanostructures offer opportunities both for sensing and feedback in active nano-actuators. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4711923]

Mechanisms of DNA Damage Response to Targeted Irradiation in Organotypic 3D Skin Cultures

DNA damage (caused by direct cellular exposure and bystander signaling) and the complex pathways involved in its repair are critical events underpinning cellular and tissue response following radiation exposures. There are limited data addressing the dynamics of DNA damage induction and repair in the skin particularly in areas not directly exposed. Here we investigate the mechanisms regulating DNA damage, repair, intracellular signalling and their impact on premature differentiation and development of inflammatory-like response in the irradiated and surrounding areas of a 3D organotypic skin model. Following localized low-LET irradiation (225 kVp X-rays), low levels of 53BP1 foci were observed in the 3D model (3.8±0.28 foci/Gy/cell) with foci persisting and increasing in size up to 48 h post irradiation. In contrast, in cell monolayers 14.2±0.6 foci/Gy/cell and biphasic repair kinetics with repair completed before 24 h was observed. These differences are linked to differences in cellular status with variable level of p21 driving apoptotic signalling in 2D and accelerated differentiation in both the directly irradiated and bystander areas of the 3D model. The signalling pathways utilized by irradiated keratinocytes to induce DNA damage in non-exposed areas of the skin involved the NF-κB transcription factor and its downstream target COX-2.

O trabalho de projeto em ambientes 3D e as aprendizagens de sistemas multimédia : uma prática de ensino com alunos do 12º ano

Relatório da Prática de Ensino Supervisionada, Ensino de Informática, Universidade de Lisboa, 2013

Direct-on-line axial flux permanent magnet synchronous generator static and dynamic performance

In distributed energy production, permanent magnet synchronous generators (PMSG) are often connected to the grid via frequency converters, such as voltage source line converters. The price of the converter may constitute a large part of the costs of a generating set. Some of the permanent magnet synchronous generators with converters and traditional separately excited synchronous generators couldbe replaced by direct-on-line (DOL) non-controlled PMSGs. Small directly networkconnected generators are likely to have large markets in the area of distributed electric energy generation. Typical prime movers could be windmills, watermills and internal combustion engines. DOL PMSGs could also be applied in island networks, such as ships and oil platforms. Also various back-up power generating systems could be carried out with DOL PMSGs. The benefits would be a lower priceof the generating set and the robustness and easy use of the system. The performance of DOL PMSGs is analyzed. The electricity distribution companies have regulations that constrain the design of the generators being connected to the grid. The general guidelines and recommendations are applied in the analysis. By analyzing the results produced by the simulation model for the permanent magnet machine, the guidelines for efficient damper winding parameters for DOL PMSGs are presented. The simulation model is used to simulate grid connections and load transients. The damper winding parameters are calculated by the finite element method (FEM) and determined from experimental measurements. Three-dimensional finite element analysis (3D FEA) is carried out. The results from the simulation model and 3D FEA are compared with practical measurements from two prototype axial flux permanent magnet generators provided with damper windings. The dimensioning of the damper winding parameters is case specific. The damper winding should be dimensioned based on the moment of inertia of the generating set. It is shown that the damper winding has optimal values to reach synchronous operation in the shortest period of time after transient operation. With optimal dimensioning, interferenceon the grid is minimized.

Stereo and motion parallax cues in human 3D vision: can they vanish without a trace?

In an immersive virtual reality environment, subjects fail to notice when a scene expands or contracts around them, despite correct and consistent information from binocular stereopsis and motion parallax, resulting in gross failures of size constancy (A. Glennerster, L. Tcheang, S. J. Gilson, A. W. Fitzgibbon, & A. J. Parker, 2006). We determined whether the integration of stereopsis/motion parallax cues with texture-based cues could be modified through feedback. Subjects compared the size of two objects, each visible when the room was of a different size. As the subject walked, the room expanded or contracted, although subjects failed to notice any change. Subjects were given feedback about the accuracy of their size judgments, where the “correct” size setting was defined either by texture-based cues or (in a separate experiment) by stereo/motion parallax cues. Because of feedback, observers were able to adjust responses such that fewer errors were made. For texture-based feedback, the pattern of responses was consistent with observers weighting texture cues more heavily. However, for stereo/motion parallax feedback, performance in many conditions became worse such that, paradoxically, biases moved away from the point reinforced by the feedback. This can be explained by assuming that subjects remap the relationship between stereo/motion parallax cues and perceived size or that they develop strategies to change their criterion for a size match on different trials. In either case, subjects appear not to have direct access to stereo/motion parallax cues.

Facile production of ordered 3D platinum nanowire networks with “single diamond” bicontinuous cubic morphology

Direct electrochemical templating is carried out using a thin layer of a self-assembled diamond phase (QIID) of phytantriol to create a platinum film with a novel nanostructure. Small-angle X-ray scattering shows that the nanostructured platinum films are asymmetrically templated and exhibit “single diamond” morphology with Fd3m symmetry.

Recorte volumétrico usando técnicas de interação 2D e 3D

A visualização de conjuntos de dados volumétricos é comum em diversas áreas de aplicação e há já alguns anos os diversos aspectos envolvidos nessas técnicas vêm sendo pesquisados. No entanto, apesar dos avanços das técnicas de visualização de volumes, a interação com grandes volumes de dados ainda apresenta desafios devido a questões de percepção (ou isolamento) de estruturas internas e desempenho computacional. O suporte do hardware gráfico para visualização baseada em texturas permite o desenvolvimento de técnicas eficientes de rendering que podem ser combinadas com ferramentas de recorte interativas para possibilitar a inspeção de conjuntos de dados tridimensionais. Muitos estudos abordam a otimização do desempenho de ferramentas de recorte, mas muito poucos tratam das metáforas de interação utilizadas por essas ferramentas. O objetivo deste trabalho é desenvolver ferramentas interativas, intuitivas e fáceis de usar para o recorte de imagens volumétricas. Inicialmente, é apresentado um estudo sobre as principais técnicas de visualização direta de volumes e como é feita a exploração desses volumes utilizando-se recorte volumétrico. Nesse estudo é identificada a solução que melhor se enquadra no presente trabalho para garantir a interatividade necessária. Após, são apresentadas diversas técnicas de interação existentes, suas metáforas e taxonomias, para determinar as possíveis técnicas de interação mais fáceis de serem utilizadas por ferramentas de recorte. A partir desse embasamento, este trabalho apresenta o desenvolvimento de três ferramentas de recorte genéricas implementadas usando-se duas metáforas de interação distintas que são freqüentemente utilizadas por usuários de aplicativos 3D: apontador virtual e mão virtual. A taxa de interação dessas ferramentas é obtida através de programas de fragmentos especiais executados diretamente no hardware gráfico. Estes programas especificam regiões dentro do volume a serem descartadas durante o rendering, com base em predicados geométricos. Primeiramente, o desempenho, precisão e preferência (por parte dos usuários) das ferramentas de recorte volumétrico são avaliados para comparar as metáforas de interação empregadas. Após, é avaliada a interação utilizando-se diferentes dispositivos de entrada para a manipulação do volume e ferramentas. A utilização das duas mãos ao mesmo tempo para essa manipulação também é testada. Os resultados destes experimentos de avaliação são apresentados e discutidos.

tCAD: a 3D modeling application on a depth enhanced tabletop computer

Tabletop computers featuring multi-touch input and object tracking are a common platform for research on Tangible User Interfaces (also known as Tangible Interaction). However, such systems are confined to sensing activity on the tabletop surface, disregarding the rich and relatively unexplored interaction canvas above the tabletop. This dissertation contributes with tCAD, a 3D modeling tool combining fiducial marker tracking, finger tracking and depth sensing in a single system. This dissertation presents the technical details of how these features were integrated, attesting to its viability through the design, development and early evaluation of the tCAD application. A key aspect of this work is a description of the interaction techniques enabled by merging tracked objects with direct user input on and above a table surface.