Applied Visualization in the Neurosciences and the Enhancement of Visualization through Computer Graphics

The complexity and size of measured and simulated data in many fields of science is increasing constantly. The technical evolution allows for capturing smaller features and more complex structures in the data. To make this data accessible by the scientists, efficient and specialized visualization techniques are required. Maximum efficiency and value for the user can only be achieved by adapting visualization to the specific application area and the specific requirements of the scientific field. Part I: In the first part of my work, I address the visualization in the neurosciences. The neuroscience tries to understand the human brain; beginning at its smallest parts, up to its global infrastructure. To achieve this ambitious goal, the neuroscience uses a combination of three-dimensional data from a myriad of sources, like MRI, CT, or functional MRI. To handle this diversity of different data types and sources, the neuroscience need specialized and well evaluated visualization techniques. As a start, I will introduce an extensive software called \"OpenWalnut\". It forms the common base for developing and using visualization techniques with our neuroscientific collaborators. Using OpenWalnut, standard and novel visualization approaches are available to the neuroscientific researchers too. Afterwards, I am introducing a very specialized method to illustrate the causal relation of brain areas, which was, prior to that, only representable via abstract graph models. I will finalize the first part of my work with an evaluation of several standard visualization techniques in the context of simulated electrical fields in the brain. The goal of this evaluation was clarify the advantages and disadvantages of the used visualization techniques to the neuroscientific community. We exemplified these, using clinically relevant scenarios. Part II: Besides the data preprocessing, which plays a tremendous role in visualization, the final graphical representation of the data is essential to understand structure and features in the data. The graphical representation of data can be seen as the interface between the data and the human mind. The second part of my work is focused on the improvement of structural and spatial perception of visualization -- the improvement of the interface. Unfortunately, visual improvements using computer graphics methods of the computer game industry is often seen sceptically. In the second part, I will show that such methods can be applied to existing visualization techniques to improve spatiality and to emphasize structural details in the data. I will use a computer graphics paradigm called \"screen space rendering\". Its advantage, amongst others, is its seamless applicability to nearly every visualization technique. I will start with two methods that improve the perception of mesh-like structures on arbitrary surfaces. Those mesh structures represent second-order tensors and are generated by a method named \"TensorMesh\". Afterwards I show a novel approach to optimally shade line and point data renderings. With this technique it is possible for the first time to emphasize local details and global, spatial relations in dense line and point data.In vielen Bereichen der Wissenschaft nimmt die Größe und Komplexität von gemessenen und simulierten Daten zu. Die technische Entwicklung erlaubt das Erfassen immer kleinerer Strukturen und komplexerer Sachverhalte. Um solche Daten dem Menschen zugänglich zu machen, benötigt man effiziente und spezialisierte Visualisierungswerkzeuge. Nur die Anpassung der Visualisierung auf ein Anwendungsgebiet und dessen Anforderungen erlaubt maximale Effizienz und Nutzen für den Anwender. Teil I: Im ersten Teil meiner Arbeit befasse ich mich mit der Visualisierung im Bereich der Neurowissenschaften. Ihr Ziel ist es, das menschliche Gehirn zu begreifen; von seinen kleinsten Teilen bis hin zu seiner Gesamtstruktur. Um dieses ehrgeizige Ziel zu erreichen nutzt die Neurowissenschaft vor allem kombinierte, dreidimensionale Daten aus vielzähligen Quellen, wie MRT, CT oder funktionalem MRT. Um mit dieser Vielfalt umgehen zu können, benötigt man in der Neurowissenschaft vor allem spezialisierte und evaluierte Visualisierungsmethoden. Zunächst stelle ich ein umfangreiches Softwareprojekt namens \"OpenWalnut\" vor. Es bildet die gemeinsame Basis für die Entwicklung und Nutzung von Visualisierungstechniken mit unseren neurowissenschaftlichen Kollaborationspartnern. Auf dieser Basis sind klassische und neu entwickelte Visualisierungen auch für Neurowissenschaftler zugänglich. Anschließend stelle ich ein spezialisiertes Visualisierungsverfahren vor, welches es ermöglicht, den kausalen Zusammenhang zwischen Gehirnarealen zu illustrieren. Das war vorher nur durch abstrakte Graphenmodelle möglich. Den ersten Teil der Arbeit schließe ich mit einer Evaluation verschiedener Standardmethoden unter dem Blickwinkel simulierter elektrischer Felder im Gehirn ab. Das Ziel dieser Evaluation war es, der neurowissenschaftlichen Gemeinde die Vor- und Nachteile bestimmter Techniken zu verdeutlichen und anhand klinisch relevanter Fälle zu erläutern. Teil II: Neben der eigentlichen Datenvorverarbeitung, welche in der Visualisierung eine enorme Rolle spielt, ist die grafische Darstellung essenziell für das Verständnis der Strukturen und Bestandteile in den Daten. Die grafische Repräsentation von Daten bildet die Schnittstelle zum Gehirn des Menschen. Der zweite Teile meiner Arbeit befasst sich mit der Verbesserung der strukturellen und räumlichen Wahrnehmung in Visualisierungsverfahren -- mit der Verbesserung der Schnittstelle. Leider werden viele visuelle Verbesserungen durch Computergrafikmethoden der Spieleindustrie mit Argwohn beäugt. Im zweiten Teil meiner Arbeit werde ich zeigen, dass solche Methoden in der Visualisierung angewendet werden können um den räumlichen Eindruck zu verbessern und Strukturen in den Daten hervorzuheben. Dazu nutze ich ein in der Computergrafik bekanntes Paradigma: das \"Screen Space Rendering\". Dieses Paradigma hat den Vorteil, dass es auf nahezu jede existierende Visualiserungsmethode als Nachbearbeitunsgschritt angewendet werden kann. Zunächst führe ich zwei Methoden ein, die die Wahrnehmung von gitterartigen Strukturen auf beliebigen Oberflächen verbessern. Diese Gitter repräsentieren die Struktur von Tensoren zweiter Ordnung und wurden durch eine Methode namens \"TensorMesh\" erzeugt. Anschließend zeige ich eine neuartige Technik für die optimale Schattierung von Linien und Punktdaten. Mit dieser Technik ist es erstmals möglich sowohl lokale Details als auch globale räumliche Zusammenhänge in dichten Linien- und Punktdaten zu erfassen

Analysis of the Near-Wall Flow in a Turbine Cascade by Splat Visualization

Turbines are essential components of jet planes and power plants. Therefore, their efficiency and service life are of central engineering interest. In the case of jet planes or thermal power plants, the heating of the turbines due to the hot gas flow is critical. Besides effective cooling, it is a major goal of engineers to minimize heat transfer between gas flow and turbine by design. Since it is known that splat events have a substantial impact on the heat transfer between flow and immersed surfaces, we adapt a splat detection and visualization method to a turbine cascade simulation in this case study. Because splat events are small phenomena, we use a direct numerical simulation resolving the turbulence in the flow as the base of our analysis. The outcome shows promising insights into splat formation and its relation to vortex structures. This may lead to better turbine design in the future.Comment: Accepted at IEEE Scientific Visualization (SciVis) 2019. To appear in IEEE Transactions on Visualization and Computer Graphic

Improving the Tractography Pipeline: on Evaluation, Segmentation, and Visualization

Recent advances in tractography allow for connectomes to be constructed in vivo. These have applications for example in brain tumor surgery and understanding of brain development and diseases. The large size of the data produced by these methods lead to a variety problems, including how to evaluate tractography outputs, development of faster processing algorithms for tractography and clustering, and the development of advanced visualization methods for verification and exploration. This thesis presents several advances in these fields. First, an evaluation is presented for the robustness to noise of multiple commonly used tractography algorithms. It employs a Monte–Carlo simulation of measurement noise on a constructed ground truth dataset. As a result of this evaluation, evidence for obustness of global tractography is found, and algorithmic sources of uncertainty are identified. The second contribution is a fast clustering algorithm for tractography data based on k–means and vector fields for representing the flow of each cluster. It is demonstrated that this algorithm can handle large tractography datasets due to its linear time and memory complexity, and that it can effectively integrate interrupted fibers that would be rejected as outliers by other algorithms. Furthermore, a visualization for the exploration of structural connectomes is presented. It uses illustrative rendering techniques for efficient presentation of connecting fiber bundles in context in anatomical space. Visual hints are employed to improve the perception of spatial relations. Finally, a visualization method with application to exploration and verification of probabilistic tractography is presented, which improves on the previously presented Fiber Stippling technique. It is demonstrated that the method is able to show multiple overlapping tracts in context, and correctly present crossing fiber configurations

Visualizing simulated electrical fields from electroencephalography and transcranial electric brain stimulation: a comparative evaluation

pre-printElectrical activity of neuronal populations is a crucial aspect of brain activity. This activity is not measured directly but recorded as electrical potential changes using head surface electrodes (electroencephalogram - EEG). Head surface electrodes can also be deployed to inject electrical currents in order to modulate brain activity (transcranial electric stimulation techniques) for therapeutic and neuroscientific purposes. In electroencephalography and noninvasive electric brain stimulation, electrical fields mediate between electrical signal sources and regions of interest (ROI). These fields can be very complicated in structure, and are influenced in a complex way by the conductivity profile of the human head. Visualization techniques play a central role to grasp the nature of those fields because such techniques allow for an effective conveyance of complex data and enable quick qualitative and quantitative assessments. The examination of volume conduction effects of particular head model parameterizations (e.g., skull thickness and layering), of brain anomalies (e.g., holes in the skull, tumors), location and extent of active brain areas (e.g., high concentrations of current densities) and around current injecting electrodes can be investigated using visualization. Here, we evaluate a number of widely used visualization techniques, based on either the potential distribution or on the current-flow. In particular, we focus on the extractability of quantitative and qualitative information from the obtained images, their effective integration of anatomical context information, and their interaction. We present illustrative examples from clinically and neuroscientifically relevant cases and discuss the pros and cons of the various visualization techniques

Visual Analysis of High-Dimensional Point Clouds using Topological Abstraction

This thesis is about visualizing a kind of data that is trivial to process by computers but difficult to imagine by humans because nature does not allow for intuition with this type of information: high-dimensional data. Such data often result from representing observations of objects under various aspects or with different properties. In many applications, a typical, laborious task is to find related objects or to group those that are similar to each other. One classic solution for this task is to imagine the data as vectors in a Euclidean space with object variables as dimensions. Utilizing Euclidean distance as a measure of similarity, objects with similar properties and values accumulate to groups, so-called clusters, that are exposed by cluster analysis on the high-dimensional point cloud. Because similar vectors can be thought of as objects that are alike in terms of their attributes, the point cloud\''s structure and individual cluster properties, like their size or compactness, summarize data categories and their relative importance. The contribution of this thesis is a novel analysis approach for visual exploration of high-dimensional point clouds without suffering from structural occlusion. The work is based on implementing two key concepts: The first idea is to discard those geometric properties that cannot be preserved and, thus, lead to the typical artifacts. Topological concepts are used instead to shift away the focus from a point-centered view on the data to a more structure-centered perspective. The advantage is that topology-driven clustering information can be extracted in the data\''s original domain and be preserved without loss in low dimensions. The second idea is to split the analysis into a topology-based global overview and a subsequent geometric local refinement. The occlusion-free overview enables the analyst to identify features and to link them to other visualizations that permit analysis of those properties not captured by the topological abstraction, e.g. cluster shape or value distributions in particular dimensions or subspaces. The advantage of separating structure from data point analysis is that restricting local analysis only to data subsets significantly reduces artifacts and the visual complexity of standard techniques. That is, the additional topological layer enables the analyst to identify structure that was hidden before and to focus on particular features by suppressing irrelevant points during local feature analysis. This thesis addresses the topology-based visual analysis of high-dimensional point clouds for both the time-invariant and the time-varying case. Time-invariant means that the points do not change in their number or positions. That is, the analyst explores the clustering of a fixed and constant set of points. The extension to the time-varying case implies the analysis of a varying clustering, where clusters appear as new, merge or split, or vanish. Especially for high-dimensional data, both tracking---which means to relate features over time---but also visualizing changing structure are difficult problems to solve

Visualisation en imagerie par résonance magnétique de diffusion : tractographie en temps réel des fibres de la matière blanche du cerveau

L'imagerie par résonance magnétique de diffusion est une technique non-invasive permettant de mesurer la diffusion des molécules d'eau selon plusieurs directions. Le résultat d'une telle acquisition contient de l'information implicite sur les structures microbiologiques qui composent le cerveau humain. La tractographie consiste à déterminer et visualiser, en trois dimensions, l'ensemble des connections neuronales de la matière blanche du cerveau en suivant la diffusion préférentielle de l'eau présente en chaque voxel. Les fibres de la matière blanche sont responsables de connecter les différentes aires fonctionnelles du cerveau entre-elles. En présence d'une tumeur, elles peuvent se réorganiser de multiples façons et refaire des connections pour assurer le suivi des fonctions importantes. L'imagerie du câblage cérébral est utilisée lors d'interventions neurochirurgicales afin d'aider le neurochirurgien à planifier son angle d'attaque pour réséquer le maximum de la tumeur sans léser la fonction du patient. La tractographie prend donc tout son sens pour le neurochirurgien avant et pendant l'opération. Dans ce mémoire, il sera question de tractographie en temps réel. La plupart des algorithmes de tractographie utilisent des paramètres fixes et prédéfinis pour l'ensemble du cerveau. Nous croyons que ces paramètres devraient être accessibles et modifiables afin de voir l'impact que ceux-ci ont sur la reconstruction des connections cérébrales. Nous proposons une méthode de visualisation de fibres en temps réel, permettant de calculer et d'afficher instantanément le résultat d'un nouvel algorithme de tractographie qui sera confronté aux méthodes existantes. Le nouveau module permet d'effectuer la tractographie des fibres de la matière blanche de manière interactive en offrant la possibilité d'ajuster les paramètres impliqués dans le processus de tractographie. Il a notamment été introduit plus d'une vingtaine de fois lors d'interventions neurochirurgicales au Centre Hospitalier Universitaire de Sherbrooke, grâce à la supervision du Dr. David Fortin. La tractographie en temps réel a changé la manière dont les données sont préparées en vue d'une intervention en bloc opératoire. Dans un contexte où le temps entre le traitement des données et l'intervention chirurgicale est une contrainte majeure, l'élimination de l'étape de tractographie du processus de prétraitement est un avantage non-négligeable

Jornadas Nacionales de Investigación en Ciberseguridad: actas de las VIII Jornadas Nacionales de Investigación en ciberseguridad: Vigo, 21 a 23 de junio de 2023

Jornadas Nacionales de Investigación en Ciberseguridad (8ª. 2023. Vigo)atlanTTicAMTEGA: Axencia para a modernización tecnolóxica de GaliciaINCIBE: Instituto Nacional de Cibersegurida