Development and Application of Computer Graphics Techniques for the Visualization of Large Geo-Related Data-Sets

Ziel dieser Arbeit war es, Algorithmen zu entwickeln und zu verbessern, die es gestatten, grosse geographische und andere geo-bezogene Datensätze mithilfe computergraphischer Techniken visualisieren zu können. Ein Schwerpunkt war dabei die Entwicklung neuer kamera-adaptiver Datenstrukturen für digitale Höhenmodelle und Rasterbilder. In der Arbeit wird zunächst ein neuartiges Multiresolutionmodell für Höhenfelder definiert. Dieses Modell braucht nur sehr wenig zusätzlichen Speicherplatz und ist geeignet, interaktive Anpassungsraten zu gewährleisten. Weiterhin werden Ansätze zur schnellen Bestimmung sichtbarer und verdeckter Teile einer computergraphischen Szene diskutiert, um die Bewegung in grossen und ausgedehnten Szenen wie Stadtmodellen oder Gebäuden zu beschleunigen. Im Anschluss daran werden einige Problemstellungen im Zusammenhang mit Texture Mapping erörtert, so werden zum Beispiel eine neue beobachterabhängige Datenstruktur für Texturdaten und ein neuer Ansatz zur Texturfilterung vorgestellt. Die meisten dieser Algorithmen und Verfahren wurden in ein interaktives System zur Geländevisualisierung integriert, das den Projektnamen 'FlyAway' hat und im letzten Kapitel der Arbeit beschrieben wird

New techniques for the automatic registration of microwave and optical remotely sensed images

Remote sensing is a remarkable tool for monitoring and mapping the land and ocean surfaces of the Earth. Recently, with the launch of many new Earth observation satellites, there has been an increase in the amount of data that is being acquired, and the potential for mapping is greater than ever before. Furthermore, sensors which are currently operational are acquiring data in many different parts of the electromagnetic spectrum. It has long been known that by combining images that have been acquired at different wavelengths, or at different times, the ability to detect and recognise features on the ground is greatly increased. This thesis investigates the possibilities for automatically combining radar and optical remotely sensed images. The process of combining images, known as data integration, is a two step procedure: geometric integration (image registration) and radiometric integration (data fusion). Data fusion is essentially an automatic procedure, but the problems associated with automatic registration of multisource images have not, in general, been resolved. This thesis proposes a method of automatic image registration based on the extraction and matching of common features which are visible in both images. The first stage of the registration procedure uses patches as the matching primitives in order to determine the approximate alignment of the images. The second stage refines the registration results by matching edge features. Throughout the development of the proposed registration algorithm, reliability, robustness and automation were always considered priorities. Tests with both small images (512x512 pixels) and full scene images showed that the algorithm could successfully register images to an acceptable level of accuracy

On the popularization of digital close-range photogrammetry: a handbook for new users.

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Γεωπληροφορική

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

Perceptually Optimized Visualization on Autostereoscopic 3D Displays

The family of displays, which aims to visualize a 3D scene with realistic depth, are known as "3D displays". Due to technical limitations and design decisions, such displays create visible distortions, which are interpreted by the human vision as artefacts. In absence of visual reference (e.g. the original scene is not available for comparison) one can improve the perceived quality of the representations by making the distortions less visible. This thesis proposes a number of signal processing techniques for decreasing the visibility of artefacts on 3D displays. The visual perception of depth is discussed, and the properties (depth cues) of a scene which the brain uses for assessing an image in 3D are identified. Following the physiology of vision, a taxonomy of 3D artefacts is proposed. The taxonomy classifies the artefacts based on their origin and on the way they are interpreted by the human visual system. The principles of operation of the most popular types of 3D displays are explained. Based on the display operation principles, 3D displays are modelled as a signal processing channel. The model is used to explain the process of introducing distortions. It also allows one to identify which optical properties of a display are most relevant to the creation of artefacts. A set of optical properties for dual-view and multiview 3D displays are identified, and a methodology for measuring them is introduced. The measurement methodology allows one to derive the angular visibility and crosstalk of each display element without the need for precision measurement equipment. Based on the measurements, a methodology for creating a quality profile of 3D displays is proposed. The quality profile can be either simulated using the angular brightness function or directly measured from a series of photographs. A comparative study introducing the measurement results on the visual quality and position of the sweet-spots of eleven 3D displays of different types is presented. Knowing the sweet-spot position and the quality profile allows for easy comparison between 3D displays. The shape and size of the passband allows depth and textures of a 3D content to be optimized for a given 3D display. Based on knowledge of 3D artefact visibility and an understanding of distortions introduced by 3D displays, a number of signal processing techniques for artefact mitigation are created. A methodology for creating anti-aliasing filters for 3D displays is proposed. For multiview displays, the methodology is extended towards so-called passband optimization which addresses Moiré, fixed-pattern-noise and ghosting artefacts, which are characteristic for such displays. Additionally, design of tuneable anti-aliasing filters is presented, along with a framework which allows the user to select the so-called 3d sharpness parameter according to his or her preferences. Finally, a set of real-time algorithms for view-point-based optimization are presented. These algorithms require active user-tracking, which is implemented as a combination of face and eye-tracking. Once the observer position is known, the image on a stereoscopic display is optimised for the derived observation angle and distance. For multiview displays, the combination of precise light re-direction and less-precise face-tracking is used for extending the head parallax. For some user-tracking algorithms, implementation details are given, regarding execution of the algorithm on a mobile device or on desktop computer with graphical accelerator

Image Registration Workshop Proceedings

Automatic image registration has often been considered as a preliminary step for higher-level processing, such as object recognition or data fusion. But with the unprecedented amounts of data which are being and will continue to be generated by newly developed sensors, the very topic of automatic image registration has become and important research topic. This workshop presents a collection of very high quality work which has been grouped in four main areas: (1) theoretical aspects of image registration; (2) applications to satellite imagery; (3) applications to medical imagery; and (4) image registration for computer vision research

GPU data structures for graphics and vision

Graphics hardware has in recent years become increasingly programmable, and its programming APIs use the stream processor model to expose massive parallelization to the programmer. Unfortunately, the inherent restrictions of the stream processor model, used by the GPU in order to maintain high performance, often pose a problem in porting CPU algorithms for both video and volume processing to graphics hardware. Serial data dependencies which accelerate CPU processing are counterproductive for the data-parallel GPU. This thesis demonstrates new ways for tackling well-known problems of large scale video/volume analysis. In some instances, we enable processing on the restricted hardware model by re-introducing algorithms from early computer graphics research. On other occasions, we use newly discovered, hierarchical data structures to circumvent the random-access read/fixed write restriction that had previously kept sophisticated analysis algorithms from running solely on graphics hardware. For 3D processing, we apply known game graphics concepts such as mip-maps, projective texturing, and dependent texture lookups to show how video/volume processing can benefit algorithmically from being implemented in a graphics API. The novel GPU data structures provide drastically increased processing speed, and lift processing heavy operations to real-time performance levels, paving the way for new and interactive vision/graphics applications.Graphikhardware wurde in den letzen Jahren immer weiter programmierbar. Ihre APIs verwenden das Streamprozessor-Modell, um die massive Parallelisierung auch für den Programmierer verfügbar zu machen. Leider folgen aus dem strikten Streamprozessor-Modell, welches die GPU für ihre hohe Rechenleistung benötigt, auch Hindernisse in der Portierung von CPU-Algorithmen zur Video- und Volumenverarbeitung auf die GPU. Serielle Datenabhängigkeiten beschleunigen zwar CPU-Verarbeitung, sind aber für die daten-parallele GPU kontraproduktiv . Diese Arbeit präsentiert neue Herangehensweisen für bekannte Probleme der Video- und Volumensverarbeitung. Teilweise wird die Verarbeitung mit Hilfe von modifizierten Algorithmen aus der frühen Computergraphik-Forschung an das beschränkte Hardwaremodell angepasst. Anderswo helfen neu entdeckte, hierarchische Datenstrukturen beim Umgang mit den Schreibzugriff-Restriktionen die lange die Portierung von komplexeren Bildanalyseverfahren verhindert hatten. In der 3D-Verarbeitung nutzen wir bekannte Konzepte aus der Computerspielegraphik wie Mipmaps, projektive Texturierung, oder verkettete Texturzugriffe, und zeigen auf welche Vorteile die Video- und Volumenverarbeitung aus hardwarebeschleunigter Graphik-API-Implementation ziehen kann. Die präsentierten GPU-Datenstrukturen bieten drastisch schnellere Verarbeitung und heben rechenintensive Operationen auf Echtzeit-Niveau. Damit werden neue, interaktive Bildverarbeitungs- und Graphik-Anwendungen möglich