Real-time Shadows for Gigapixel Displacement Maps

Shadows portray helpful information in scenes. From a scientific visualization standpoint, they help to add data without unnecessary clutter. In video games they add realism and depth. In common graphics pipelines, due to the independent and parallel rendering of geometric primitives, shadows are difficult to achieve. Objects require knowledge of each other and therefore multiple renders are needed to collect the necessary data. The collection of this data comes with its own set of trade offs. Our research involves adding shadows into a lunar rendering framework developed by Dr. Robert Kooima. The NASA-collected data contains a multi-gigapixel displacement map describing the lunar topology. This map does not fit entirely into main memory and therefore out-of-core paging is utilized to achieve real-time speeds. Current shadow techniques do not attempt to generate occluder data on such a scale, and therefore we have developed a novel approach to fit this situation. By using a chain of pre-processing steps, we analyze the structure of the displacement map and calculate horizon lines at each vertex. This information is saved into several images and used to generate shadows in a single pass, maintaining real-time speeds. The algorithm is even capable of generating soft shadows without extra information or loss of speed. We compare our algorithm with common approaches in the field as well as two forms of ground truth; one from ray tracing and the other from the gigapixel lunar texture data, showing real shadows at the time it was collected

Exploratory visualizations and statistical analysis of large, heterogeneous epigenetic datasets

Epigenetic marks, such as DNA methylation and histone modifications, are important regulatory mechanisms that allow a single genomic sequence to give rise to a complex multicellular organism. When studying mechanisms of epigenetic regulation, the analyses depend on the experimental technologies and the available data. Recent advancements in sequencing technologies allow for the efficient extraction of genome-wide maps of epigenetic marks. A number of large-scale mapping projects, such as ENCODE and IHEC, intensively produce data for different tissues and cell cultures. The increasing quantity of data highlights a major bottleneck in bioinformatic research, namely the lack of bioinformatic tools for analyzing these data. To date, there are bioinformatics tools for detailed (mostly visual) inspection of single genomic loci, allowing biologists to focus research on regions of interest. Also, efficient tools for manipulation and analysis of the data have been published, but often they require computer science abilities. Furthermore, the available tools provide solutions to only already well formulated biological questions. What is missing, in our opinion, are tools (or pipelines of tools) to explore the data interactively, in a process that would facilitate a trained biologist to recognize interesting aspects and pursue them further until concrete hypotheses are formulated. A possible solution stems from the best practices in the fields of information retrieval and exploratory search. In this thesis, I propose EpiExplorer, a paradigm for integration of state-of-the-art information retrieval methods and indexing structures, applied to offer instant interactive exploration of large epigenetic datasets. The algorithms we use are developed for semi-structured text data, but we apply them on bioinformatic data through clever textual mapping of biological properties. We demonstrate the power of EpiExplorer in a series of studies that address interesting biological problems. We also present in this manuscript EpiGRAPH, a bioinformatic software that we developed with colleagues. EpiGRAPH helps identify and model significant biological associations among epigenetic and genetic properties for sets of regions. Using EpiExplorer and EpiGRAPH, independently or in a pipeline, provides the bioinformatic community with access to large databases of annotations, allows for exploratory visualizations or statistical analysis and facilitates reproduction and sharing of results.Epigenetische Signaturen wie die Methylierung der DNS oder posttranslationale Modifikationen der Histonproteine stellen wichtige regulatorische Mechanismen dar. Diese ermöglichen es, dass ein komplexer, multizellulärer Organismus aus einer einzelnen genomische Sequenz hervorgeht. Adequate Analysemethoden hängen von den verwendeten experimentellen Technologien und den verfügbaren Daten ab. Jüngste Fortschritte in der DNS-Sequenzierungstechnologie ermöglichen die effiziente Erstellung genomweiter Karten epigenetischer Informationen. Diese Epigenomkarten werden von einigen Projekten und Initiativen wie ENCODE und IHEC im grossen Massstab für diverse Gewebe- und Zelltypen erstellt. Hierbei stellt der Mangel an effizienten bioinformatischen Softwarewerkzeugen einen wesentlichen Engpass in der Analyse dieser stetig wachsenden Datenflut dar. Experimentelle Biologen können heute einzelne genomische Loci mithilfe benutzerfreundlicher (meist visueller) bioinformatischer Software im Detail inspizieren. Des Weiteren existieren effiziente Werkzeuge für die Manipulation und Analyse dieser Datensätze, die jedoch ein gewisses Mass informatischer Expertise erfordern und sich zumeist auf die Lösung bereits wohldefinierter biologischer Fragestellungen fokussieren. Unserer Ansicht nach fehlen Werkzeuge und Softwarepipelines mithilfe derer ein Benutzer, der über ein fundiertes Wissen der biologischen Grundlagen, jedoch nicht unbedingt über informatische Kenntnisse verfügt, die verfügbaren Datensätze interaktiv durchstöbern und darauf aufbauend weiterführende Hypothesen entwickeln kann. Eine möglichen Ansatz hierfür bieten Methoden aus den Bereichen Information Retrieval und der explorativen Suche. Diese Arbeit beschreibt EpiExplorer, eine Software, die auf dem Paradigma der Integration von modernen Information Retrieval und Indexstrukturen basiert und darauf ausgelegt ist eine Vielzahl von (epi-)genomweiten Datensätzen in Echtzeit zu explorieren. Die verwendeten Algorithmen wurden ursprünglich für die Suche in semistrukturierten, textuellen Datensätzen entwickelt. EpiExplorer ermöglicht ihre Verwendung durch eine systematische Umwandlung biologischer Eigenschaften in Textdukumente. Ausserdem demonstriert diese Arbeit EpiExplorers Leistungsfähigkeit und Nützlichkeit durch relevante Anwendungsbeispiele biologisch interessanter Fragestellungen. Komplementär zu EpiExplorer wurde in Kollaboration mit Kollegen EpiGRAPH entwickelt, mithilfe dessen signifikante biologische Assoziationen zwischen genetischen und epigenetischen Eigenschaften regionsbasiert identifiziert und modelliert werden können. EpiExplorer und EpiGRAPH stellen - unabhängig voneinander oder im Verbund miteinander - nützliche Ressourcen dar. In einer bioinformatischen Softwarepipeline ermöglichen sie den Datenbank-basierten Zugriff auf eine Vielzahl (epi-)genomischer Datensätze, deren explorative Visualisierung oder statistische Analyse sowie die Reproduzierbarkeit und den Austausch von Analyseergebnissen

Development of a Multiband Remote Sensing System for Determination of Unsaturated Soil Properties

A multiband system including active microwave sensing and visible-near infrared reflectance spectroscopy was developed to measure unsaturated soil properties in both field and laboratory environments. Remote measurements of soil volumetric water content (θv), soil water matric potential (ψ), and soil index properties (liquid limit [LL], plastic limit [PL], and clay fraction [CF]) were conducted. Field-based measurement of θv was conducted using a ground-based radar system and field measurements within 10 percentage points of measurements acquired with traditional sampling techniques were obtained. Laboratory-based, visible and near infrared spectroscopy was found to be capable of obtaining empirical, soil specific regression functions (partial least squares [PLS]) with coefficient of determination (R2) values greater than 0.9 for the LL, PL, and CF. A silt sized granite material, a silt sized illite clay, and a silt sized kaolinite clay were optically characterized within the visible to near-infrared wavelength range and were found to have absorption coefficient values of 0.81 to 78.8cm-1, 0.93 to 150.0cm-1, and 0.12 to 4.02cm-1, respectively. Measurements of θv and ψ using an analytical solution based on the Kubelka-Munk color theory were found not to provide viable results. Soil water characteristic curves (SWCC) were fitted to both laboratory-obtained and remotely-sensed data between -10 and -1500kPa. θv for the laboratory-obtained SWCC (SWCC-L) and remotely-obtained SWCC (SWCC-R) for the granite silt were within 1 percentage points for ψ values less than -100kPa. The SWCC-L and SWCC-R values for the silt sized illite clay were within 2 percentage points for values of ψ greater than 400kPa. The SWCC-L and SWCC-R for the silt sized kaolinite clay were within 8 percentage points for all ψ values. For the Donna Fill and illite soil types ψ values within 150kPa of the applied pressure were obtained. Specific contributions of this research project were the evaluation of remote and proximal (active microwave and diffuse reflectance spectroscopy) sensing techniques as a means of acquiring measurements of soil properties. Microwave measurements of field θv were demonstrated for ground based systems. Additional areas of research in both laboratory- and field-scale measurements of soil hydraulic and index properties are identified and discussed