While uncertainty in scientific data attracts an increasing research interest in the visualization community, two critical issues remain insufficiently studied: (1) visualizing the impact of the uncertainty of a data set on its features and (2) interactively exploring 3D or large 2D data sets with uncertainties. In this study, a suite of feature-based techniques is developed to address these issues. First, a framework of feature-level uncertainty visualization is presented to study the uncertainty of the features in scalar and vector data. The uncertainty in the number and locations of features such as sinks or sources of vector fields are referred to as feature-level uncertainty while the uncertainty in the numerical values of the data is referred to as data-level uncertainty. The features of different ensemble members are indentified and correlated. The feature-level uncertainties are expressed as the transitions between corresponding features through new elliptical glyphs. Second, an interactive visualization tool for exploring scalar data with data-level and two types of feature-level uncertainties — contour-level and topology-level uncertainties — is developed. To avoid visual cluttering and occlusion, the uncertainty information is attached to a contour tree instead of being integrated with the visualization of the data. An efficient contour tree-based interface is designed to reduce users’ workload in viewing and analyzing complicated data with uncertainties and to facilitate a quick and accurate selection of prominent contours. This thesis advances the current uncertainty studies with an in-depth investigation of the feature-level uncertainties and an exploration of topology tools for effective and interactive uncertainty visualizations. With quantified representation and interactive capability, feature-based visualization helps people gain new insights into the uncertainties of their data, especially the uncertainties of extracted features which otherwise would remain unknown with the visualization of only data-level uncertainties.

Glioblastoma (GBM) is the most aggressive and malignant glioma. It accounts for 48.6% of all primary, malignant gliomas with a median survival of 15 months. Infiltration into the surrounding parenchyma is a hallmark of GBM. Radiotherapy is used to address the invasion; however, recent studies have implicated that radiation contributes to increased invasiveness of glioma. Although the effect of radiation on cells has been studied extensively, its effect on the transport of fluid is not well characterized. Transport in the brain which has significant roles in physiology, GBM pathophysiology, and GBM treatment. Thus, understanding the effect of radiation on transport within the lesion and surrounding interstitium will be beneficial in characterizing the effects of radiotherapy in GBM patients. This dissertation seeks to explore the relationship between radiation, transport, and movement of glioma cells and includes the following: 1) Characterizing in vitro motility metrics of glioma stem cell lines in and relating them to in vivo invasion. 2) Studying the effect of radiation on motility, flow-mediated invasion, extracellular matrix components, and transport within the lesion and interstitium. 3) Assessing transport in clinical images and relating transport parameters to progression of GBM. 4) Developing a novel pipeline for applying vector field topology to the study of interstitial fluid flow in glioma. Surprisingly, we found that motility metrics in vitro have a negative correlation trend with in vivo invasion. Next, we found that radiation causes a transient increase in advective flow, and a more sustained decrease in diffusivity in a murine glioma model. Tenascin C was found to correlate significantly with invasion and diffusivity, indicating that it might be a link between radiation, transport, and invasion. Furthermore, interstitial fluid flow was calculated and assessed in clinical images. This showed that interstitial fluid flow velocity magnitude in the tumor correlates with overall survival in GBM patients. Lastly, vector field topology was introduced as a novel method of studying transport that provides more detailed information to identify potential drivers of transport within a flow field. Altogether, this work presents novel insight into the effects of radiation on invasion and transport in GBM. Hopefully, this work can provide a foundation to build upon in efforts of improving treatment planning and clinical outcomes for GBM patients. / Doctor of Philosophy / Glioblastoma (GBM) is the most aggressive glioma. It accounts for 48.6% of all primary, malignant gliomas with a median survival of 15 months. The movement of cancer cells into the surrounding tissue is a defining factor of GBM. Radiotherapy is used after surgery to treat the remaining cancer cells in tissue surrounding the tumor; however, recent studies have implicated that radiation contributes to increased movement of glioma into surrounding tissue. Although the effect of radiation on cells has been studied extensively, its effect on transport of fluid is not well characterized. Interstitial fluid flow in the brain has significant roles in healthy bodily functions, GBM disease state, and GBM treatment. Thus, understanding the effect of radiation on transport within the tumor and surrounding tissue is beneficial in better characterizing the effects of radiotherapy. This dissertation seeks to explore the relationship between radiation, transport, and movement of glioma cells and includes the following: 1) Characterizing in vitro motility metrics of glioma cells in and relating them to in vivo movement into healthy tissue. 2) Studying the effect of radiation on motility, flow-mediated infiltration into healthy tissue, tissue matrix components, and fluid flow within the tumor and surrounding tissue. 3) Assessing transport in clinical images and relating transport parameters to progression of GBM. 4) Developing a novel pipeline for applying vector field topology to the study of interstitial fluid flow in glioma. Surprisingly, we found that motility metrics in vitro have a negative correlation trend with in vivo invasion. Next, we found that radiation causes a transient increase in flow velocity magnitude, and a more sustained decrease in diffusivity in a murine glioma model. Tenascin C, a component of the tissue matrix, was found to correlate significantly with invasion and diffusivity. This indicates that Tenascin C might be a link between radiation, transport, and invasion. Furthermore, interstitial fluid flow was calculated and assessed in clinical images which showed that interstitial fluid flow velocity magnitude in the tumor correlates with survival. Lastly, vector field topology was introduced as a novel method of studying fluid flow in glioma that provides more detailed information regarding the flow field. Altogether, this work presents novel insight into the effects of radiation on fluid flow and cellular movement in GBM. Hopefully, this work can provide a foundation to build upon in efforts of improving treatment planning and clinical outcomes for GBM patients.

In this thesis, we introduce several tools, each coming from a different branch of mathematics, for analyzing real vector fields and their associated flows. Beginning with a discussion about generalized vector field decompositions, that mainly have been derived from the classical Helmholtz-Hodge-decomposition, we decompose a field into a kernel and a rest respectively to an arbitrary vector-valued linear differential operator that allows us to construct decompositions of either toroidal flows or flows obeying differential equations of second (or even fractional) order and a rest. The algorithm is based on the fast Fourier transform and guarantees a rapid processing and an implementation that can be directly derived from the spectral simplifications concerning differentiation used in mathematics. Moreover, we present two combinatorial methods to process 3D steady vector fields, which both use graph algorithms to extract features from the underlying vector field. Combinatorial approaches are known to be less sensitive to noise than extracting individual trajectories. Both of the methods are extensions of an existing 2D technique to 3D fields. We observed that the first technique can generate overly coarse results and therefore we present a second method that works using the same concepts but produces more detailed results. Finally, we discuss several possibilities for categorizing the invariant sets with respect to the flow. Existing methods for analyzing separation of streamlines are often restricted to a finite time or a local area. In the frame of this work, we introduce a new method that complements them by allowing an infinite-time-evaluation of steady planar vector fields. Our algorithm unifies combinatorial and probabilistic methods and introduces the concept of separation in time-discrete Markov chains. We compute particle distributions instead of the streamlines of single particles. We encode the flow into a map and then into a transition matrix for each time direction. Finally, we compare the results of our grid-independent algorithm to the popular Finite-Time-Lyapunov-Exponents and discuss the discrepancies. Gauss\' theorem, which relates the flow through a surface to the vector field inside the surface, is an important tool in flow visualization. We are exploiting the fact that the theorem can be further refined on polygonal cells and construct a process that encodes the particle movement through the boundary facets of these cells using transition matrices. By pure power iteration of transition matrices, various topological features, such as separation and invariant sets, can be extracted without having to rely on the classical techniques, e.g., interpolation, differentiation and numerical streamline integration.

[pt] Nos últimos anos, vários mecanismos permitem medir campos vetoriais reais, provendo uma compreensão melhor de fenômenos importantes, tais como dinâmica de fluidos ou movimentos de fluido cerebral. Isso abre um leque de novos desafios a visualização e análise de campos vetoriais em muitas aplicações de engenharia e de medicina por exemplo. Em particular, dados reais são geralmente corrompidos por ruído, dificultando a compreensão na hora da visualização. Esta informação necessita de uma etapa de remoção de ruído como pré-processamento, no entanto remoção de ruído normalmente remove as descontinuidades e singularidades, que são fundamentais para a análise do campo vetorial. Nesta dissertação é proposto um método inovador para remoção de ruído em campo vetorial baseado em caminhadas aleatórias que preservam certas descontinuidades. O método funciona em um ambiente desestruturado, sendo rápido, simples de implementar e mostra um desempenho melhor do que a tradicional técnica Gaussiana de remoção de ruído. Esta tese propõe também uma metodologia semi-automática para remover ruído, onde o usuário controla a escala visual da filtragem, levando em consideração as mudanças topológicas que ocorrem por causa da filtragem. / [en] In recent years, several devices allow to measure real vector fields, leading to a better understanding of fundamental phenomena such as fluid dynamics or brain water movements. This gives vector field visualization and analysis new challenges in many applications in engineering and in medicine. In particular real data is generally corrupted by noise, puzzling the understanding provided by visualization tools. This data needs a denoising step as preprocessing, however usual denoising removes discontinuities and singularities, which are fundamental for vector field analysis. In this dissertation a novel method for vector field denoising based on random walks is proposed which preserves certain discontinuities. It works in a unstructured setting; being fast, simple to implement, and shows a better performance than the traditional Gaussian denoising technique. This dissertation also proposes a semi-automatic vector field denoising methodology, where the user visually controls the filtering scale by validating topological changes caused by classical vector field filtering.

Topology-related issues are becoming increasingly important in Computer Graphics. This research examines the use of topological analysis for solving two important problems in 3D Graphics: surface parameterization, and vector field design on surfaces. Many applications, such as high-quality and interactive image synthesis, benefit from the solutions to these problems. Surface parameterization refers to segmenting a 3D surface into a number of patches and unfolding them onto a plane. A surface parameterization allows surface properties to be sampled and stored in a texture map for high-quality and interactive display. One of the most important quality measurements for surface parameterization is stretch, which causes an uneven sampling rate across the surface and needs to be avoided whenever possible. In this thesis, I present an automatic parameterization technique that segments the surface according to the handles and large protrusions in the surface. This results in a small number of large patches that can be unfolded with relatively little stretch. To locate the handles and large protrusions, I make use of topological analysis of a distance-based function on the surface. Vector field design refers to creating continuous vector fields on 3D surfaces with control over vector field topology, such as the number and location of the singularities. Many graphics applications make use of an input vector field. The singularities in the input vector field often cause visual artifacts for these applications, such as texture synthesis and non-photorealistic rendering. In this thesis, I describe a vector field design system for both planar domains and 3D mesh surfaces. The system provides topological editing operations that allow the user to control the number and location of the singularities in the vector field. For the system to work for 3D meshes surface, I present a novel piecewise interpolating scheme that produces a continuous vector field based on the vector values defined at the vertices of the mesh. I demonstrate the effectiveness of the system through several graphics applications: painterly rendering of still images, pencil-sketches of surfaces, and texture synthesis.

In this thesis, we introduce several tools, each coming from a different branch of mathematics, for analyzing real vector fields and their associated flows. Beginning with a discussion about generalized vector field decompositions, that mainly have been derived from the classical Helmholtz-Hodge-decomposition, we decompose a field into a kernel and a rest respectively to an arbitrary vector-valued linear differential operator that allows us to construct decompositions of either toroidal flows or flows obeying differential equations of second (or even fractional) order and a rest. The algorithm is based on the fast Fourier transform and guarantees a rapid processing and an implementation that can be directly derived from the spectral simplifications concerning differentiation used in mathematics. Moreover, we present two combinatorial methods to process 3D steady vector fields, which both use graph algorithms to extract features from the underlying vector field. Combinatorial approaches are known to be less sensitive to noise than extracting individual trajectories. Both of the methods are extensions of an existing 2D technique to 3D fields. We observed that the first technique can generate overly coarse results and therefore we present a second method that works using the same concepts but produces more detailed results. Finally, we discuss several possibilities for categorizing the invariant sets with respect to the flow. Existing methods for analyzing separation of streamlines are often restricted to a finite time or a local area. In the frame of this work, we introduce a new method that complements them by allowing an infinite-time-evaluation of steady planar vector fields. Our algorithm unifies combinatorial and probabilistic methods and introduces the concept of separation in time-discrete Markov chains. We compute particle distributions instead of the streamlines of single particles. We encode the flow into a map and then into a transition matrix for each time direction. Finally, we compare the results of our grid-independent algorithm to the popular Finite-Time-Lyapunov-Exponents and discuss the discrepancies. Gauss\'' theorem, which relates the flow through a surface to the vector field inside the surface, is an important tool in flow visualization. We are exploiting the fact that the theorem can be further refined on polygonal cells and construct a process that encodes the particle movement through the boundary facets of these cells using transition matrices. By pure power iteration of transition matrices, various topological features, such as separation and invariant sets, can be extracted without having to rely on the classical techniques, e.g., interpolation, differentiation and numerical streamline integration.

In vielen Forschungsbereichen wie Medizin, Natur- oder Ingenieurwissenschaften spielt die wissenschaftliche Visualisierung eine wichtige Rolle und hilft Wissenschaftlern neue Erkenntnisse zu gewinnen. Der Hauptgrund hierfür ist, dass Visualisierungen das Unsichtbare sichtbar machen können. So können Visualisierungen beispielsweise den Verlauf von Nervenfasern im Gehirn von Probanden oder den Luftstrom um Hindernisse herum darstellen. Diese Arbeit trägt insbesondere zum Teilgebiet der Strömungsvisualisierung bei, welche sich mit der Untersuchung von Prozessen in Flüssigkeiten und Gasen beschäftigt. Eine beliebte Methode, um Einblicke in komplexe Datensätze zu erhalten, besteht darin, einfache und bekannte Strukturen innerhalb eines Datensatzes aufzuspüren. In der Strömungsvisualisierung führt dies zum Konzept der lokalen Linearisierung und Linearität im Allgemeinen. Dies liegt daran, dass lineare Vektorfelder die einfachste Form von nicht-trivialen Feldern darstellen und diese sehr gut verstanden sind. In der Regel werden simulierte Datensätze in einzelne Zellen diskretisiert, welche auf linearer Interpolation basieren. Beispielsweise können auch stationäre Punkte in der Vektorfeldtopologie mittels linearen Strömungsverhaltens charakterisiert werden. Daher ist Linearität allgegenwärtig. Durch das Verständnis von lokalen linearen Strömungsverhalten in Vektorfeldern konnten verschiedene Visualisierungsmethoden erheblich verbessert werden. Ähnliche Erfolge sind auch für andere Methoden zu erwarten. In dieser Arbeit wird das Konzept der Linearität in der Visualisierung weiterentwickelt. Zunächst wird eine bestehende Definition von linearen Nachbarschaften hin zu affin-linearen Nachbarschaften erweitert. Affin-lineare Nachbarschaften sind Regionen mit einem überwiegend linearem Strömungsverhalten. Es wird eine detaillierte Diskussion über die Definition sowie die gewählten Fehlermaße durchgeführt. Weiterhin wird ein Region Growing-Verfahren vorgestellt, welches affin-lineare Nachbarschaften um beliebige Positionen bis zu einem bestimmten, benutzerdefinierten Fehlerschwellwert extrahiert. Um die lokale Linearität in Vektorfeldern zu messen, wird ein komplementärer Ansatz, welcher die Qualität der bestmöglichen linearen Näherung für eine gegebene n-Ring-Nachbarschaft berechnet, diskutiert. In einer ersten Anwendung werden affin-lineare Nachbarschaften an stationären Punkten verwendet, um deren Einflussbereich sowie ihre Wechselwirkung mit der sie umgebenden, nichtlinearen Strömung, aber auch mit sehr nah benachbarten stationären Punkten zu visualisieren. Insbesondere bei sehr großen Datensätzen kann die analytische Beschreibung der Strömung innerhalb eines linearisierten Bereichs verwendet werden, um Vektorfelder zu komprimieren und vorhandene Visualisierungsansätze zu beschleunigen. Insbesondere sollen eine Reihe von Komprimierungsalgorithmen für gitterbasierte Vektorfelder verbessert werden, welche auf der sukzessiven Entfernung einzelner Gitterkanten basieren. Im Gegensatz zu vorherigen Arbeiten sollen affin-lineare Nachbarschaften als Grundlage für eine Segmentierung verwendet werden, um eine obere Fehlergrenze bereitzustellen und somit eine hohe Qualität der Komprimierungsergebnisse zu gewährleisten. Um verschiedene Komprimierungsansätze zu bewerten, werden die Auswirkungen ihrer jeweiligen Approximationsfehler auf die Stromlinienintegration sowie auf integrationsbasierte Visualisierungsmethoden am Beispiel der numerischen Berechnung von Lyapunov-Exponenten diskutiert. Zum Abschluss dieser Arbeit wird eine mögliche Erweiterung des Linearitätbegriffs für Vektorfelder auf zweidimensionalen Mannigfaltigkeiten vorgestellt, welche auf einer adaptiven, atlasbasierten Vektorfeldzerlegung basiert. / In many research areas, such as medicine, natural sciences or engineering, scientific visualization plays an important role and helps scientists to gain new insights. This is because visualizations can make the invisible visible. For example, visualizations can reveal the course of nerve fibers in the brain of test persons or the air flow around obstacles. This thesis in particular contributes to the subfield of flow visualization, which targets the investigation of processes in fluids and gases. A popular way to gain insights into complex datasets is to identify simple and known structures within a dataset. In case of flow visualization, this leads to the concept of local linearizations and linearity in general. This is because linear vector fields represent the most simple class of non-trivial fields and they are extremely well understood. Typically, simulated datasets are discretized into individual cells that are based on linear interpolation. Also, in vector field topology, stationary points can be characterized by considering the local linear flow behavior in their vicinity. Therefore, linearity is ubiquitous. Through the understanding of local linear flow behavior in vector fields by applying the concept of local linearity, some visualization methods have been improved significantly. Similar successes can be expected for other methods. In this thesis, the use of linearity in visualization is investigated. First, an existing definition of linear neighborhoods is extended towards the affine linear neighborhoods. Affine linear neighborhoods are regions of mostly linear flow behavior. A detailed discussion of the definition and of the chosen error measures is provided. Also a region growing algorithm that extracts affine linear neighborhoods around arbitrary positions up to a certain user-defined approximation error threshold is introduced. To measure the local linearity in vector fields, a complementary approach that computes the quality of the best possible linear approximation for a given n-ring neighborhood is discussed. As a first application, the affine linear neighborhoods around stationary points are used to visualize their region of influence, their interaction with the non-linear flow around them as well as their interaction with closely neighbored stationary points. The analytic description of the flow within a linearized region can be used to compress vector fields and accelerate existing visualization approaches, especially in case of very large datasets. In particular, the presented method aims at improving over a series of compression algorithms for grid-based vector fields that are based on edge collapse. In contrast to previous approaches, affine linear neighborhoods serve as the basis for a segmentation in order to provide an upper error bound and also to ensure a high quality of the compression results. To evaluate different compression approaches, the impact of their particular approximation errors on streamline integration as well as on integration-based visualization methods is discussed on the example of Finite-Time Lyapunov Exponent computations. To conclude the thesis, a first possible extension of linearity to fields on two-dimensional manifolds, based on an adaptive atlas-based vector field decomposition, is given.