Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Traffic Scene Perception for Automated Driving with Top-View Grid Maps

Ein automatisiertes Fahrzeug muss sichere, sinnvolle und schnelle Entscheidungen auf Basis seiner Umgebung treffen. Dies benötigt ein genaues und recheneffizientes Modell der Verkehrsumgebung. Mit diesem Umfeldmodell sollen Messungen verschiedener Sensoren fusioniert, gefiltert und nachfolgenden Teilsysteme als kompakte, aber aussagekräftige Information bereitgestellt werden. Diese Arbeit befasst sich mit der Modellierung der Verkehrsszene auf Basis von Top-View Grid Maps. Im Vergleich zu anderen Umfeldmodellen ermöglichen sie eine frühe Fusion von Distanzmessungen aus verschiedenen Quellen mit geringem Rechenaufwand sowie eine explizite Modellierung von Freiraum. Nach der Vorstellung eines Verfahrens zur Bodenoberflächenschätzung, das die Grundlage der Top-View Modellierung darstellt, werden Methoden zur Belegungs- und Elevationskartierung für Grid Maps auf Basis von mehreren, verrauschten, teilweise widersprüchlichen oder fehlenden Distanzmessungen behandelt. Auf der resultierenden, sensorunabhängigen Repräsentation werden anschließend Modelle zur Detektion von Verkehrsteilnehmern sowie zur Schätzung von Szenenfluss, Odometrie und Tracking-Merkmalen untersucht. Untersuchungen auf öffentlich verfügbaren Datensätzen und einem Realfahrzeug zeigen, dass Top-View Grid Maps durch on-board LiDAR Sensorik geschätzt und verlässlich sicherheitskritische Umgebungsinformationen wie Beobachtbarkeit und Befahrbarkeit abgeleitet werden können. Schließlich werden Verkehrsteilnehmer als orientierte Bounding Boxen mit semantischen Klassen, Geschwindigkeiten und Tracking-Merkmalen aus einem gemeinsamen Modell zur Objektdetektion und Flussschätzung auf Basis der Top-View Grid Maps bestimmt

Geo-rectification and cloud-cover correction of multi-temporal Earth observation imagery

Over the past decades, improvements in remote sensing technology have led to mass proliferation of aerial imagery. This, in turn, opened vast new possibilities relating to land cover classification, cartography, and so forth. As applications in these fields became increasingly more complex, the amount of data required also rose accordingly and so, to satisfy these new needs, automated systems had to be developed. Geometric distortions in raw imagery must be rectified, otherwise the high accuracy requirements of the newest applications will not be attained. This dissertation proposes an automated solution for the pre-stages of multi-spectral satellite imagery classification, focusing on Fast Fourier Shift theorem based geo-rectification and multi-temporal cloud-cover correction. By automatizing the first stages of image processing, automatic classifiers can take advantage of a larger supply of image data, eventually allowing for the creation of semi-real-time mapping applications

Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D

Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.Comment: 49 pages, 10 figure

Structureless Camera Motion Estimation of Unordered Omnidirectional Images

This work aims at providing a novel camera motion estimation pipeline from large collections of unordered omnidirectional images. In oder to keep the pipeline as general and flexible as possible, cameras are modelled as unit spheres, allowing to incorporate any central camera type. For each camera an unprojection lookup is generated from intrinsics, which is called P2S-map (Pixel-to-Sphere-map), mapping pixels to their corresponding positions on the unit sphere. Consequently the camera geometry becomes independent of the underlying projection model. The pipeline also generates P2S-maps from world map projections with less distortion effects as they are known from cartography. Using P2S-maps from camera calibration and world map projection allows to convert omnidirectional camera images to an appropriate world map projection in oder to apply standard feature extraction and matching algorithms for data association. The proposed estimation pipeline combines the flexibility of SfM (Structure from Motion) - which handles unordered image collections - with the efficiency of PGO (Pose Graph Optimization), which is used as back-end in graph-based Visual SLAM (Simultaneous Localization and Mapping) approaches to optimize camera poses from large image sequences. SfM uses BA (Bundle Adjustment) to jointly optimize camera poses (motion) and 3d feature locations (structure), which becomes computationally expensive for large-scale scenarios. On the contrary PGO solves for camera poses (motion) from measured transformations between cameras, maintaining optimization managable. The proposed estimation algorithm combines both worlds. It obtains up-to-scale transformations between image pairs using two-view constraints, which are jointly scaled using trifocal constraints. A pose graph is generated from scaled two-view transformations and solved by PGO to obtain camera motion efficiently even for large image collections. Obtained results can be used as input data to provide initial pose estimates for further 3d reconstruction purposes e.g. to build a sparse structure from feature correspondences in an SfM or SLAM framework with further refinement via BA. The pipeline also incorporates fixed extrinsic constraints from multi-camera setups as well as depth information provided by RGBD sensors. The entire camera motion estimation pipeline does not need to generate a sparse 3d structure of the captured environment and thus is called SCME (Structureless Camera Motion Estimation).:1 Introduction 1.1 Motivation 1.1.1 Increasing Interest of Image-Based 3D Reconstruction 1.1.2 Underground Environments as Challenging Scenario 1.1.3 Improved Mobile Camera Systems for Full Omnidirectional Imaging 1.2 Issues 1.2.1 Directional versus Omnidirectional Image Acquisition 1.2.2 Structure from Motion versus Visual Simultaneous Localization and Mapping 1.3 Contribution 1.4 Structure of this Work 2 Related Work 2.1 Visual Simultaneous Localization and Mapping 2.1.1 Visual Odometry 2.1.2 Pose Graph Optimization 2.2 Structure from Motion 2.2.1 Bundle Adjustment 2.2.2 Structureless Bundle Adjustment 2.3 Corresponding Issues 2.4 Proposed Reconstruction Pipeline 3 Cameras and Pixel-to-Sphere Mappings with P2S-Maps 3.1 Types 3.2 Models 3.2.1 Unified Camera Model 3.2.2 Polynomal Camera Model 3.2.3 Spherical Camera Model 3.3 P2S-Maps - Mapping onto Unit Sphere via Lookup Table 3.3.1 Lookup Table as Color Image 3.3.2 Lookup Interpolation 3.3.3 Depth Data Conversion 4 Calibration 4.1 Overview of Proposed Calibration Pipeline 4.2 Target Detection 4.3 Intrinsic Calibration 4.3.1 Selected Examples 4.4 Extrinsic Calibration 4.4.1 3D-2D Pose Estimation 4.4.2 2D-2D Pose Estimation 4.4.3 Pose Optimization 4.4.4 Uncertainty Estimation 4.4.5 PoseGraph Representation 4.4.6 Bundle Adjustment 4.4.7 Selected Examples 5 Full Omnidirectional Image Projections 5.1 Panoramic Image Stitching 5.2 World Map Projections 5.3 World Map Projection Generator for P2S-Maps 5.4 Conversion between Projections based on P2S-Maps 5.4.1 Proposed Workflow 5.4.2 Data Storage Format 5.4.3 Real World Example 6 Relations between Two Camera Spheres 6.1 Forward and Backward Projection 6.2 Triangulation 6.2.1 Linear Least Squares Method 6.2.2 Alternative Midpoint Method 6.3 Epipolar Geometry 6.4 Transformation Recovery from Essential Matrix 6.4.1 Cheirality 6.4.2 Standard Procedure 6.4.3 Simplified Procedure 6.4.4 Improved Procedure 6.5 Two-View Estimation 6.5.1 Evaluation Strategy 6.5.2 Error Metric 6.5.3 Evaluation of Estimation Algorithms 6.5.4 Concluding Remarks 6.6 Two-View Optimization 6.6.1 Epipolar-Based Error Distances 6.6.2 Projection-Based Error Distances 6.6.3 Comparison between Error Distances 6.7 Two-View Translation Scaling 6.7.1 Linear Least Squares Estimation 6.7.2 Non-Linear Least Squares Optimization 6.7.3 Comparison between Initial and Optimized Scaling Factor 6.8 Homography to Identify Degeneracies 6.8.1 Homography for Spherical Cameras 6.8.2 Homography Estimation 6.8.3 Homography Optimization 6.8.4 Homography and Pure Rotation 6.8.5 Homography in Epipolar Geometry 7 Relations between Three Camera Spheres 7.1 Three View Geometry 7.2 Crossing Epipolar Planes Geometry 7.3 Trifocal Geometry 7.4 Relation between Trifocal, Three-View and Crossing Epipolar Planes 7.5 Translation Ratio between Up-To-Scale Two-View Transformations 7.5.1 Structureless Determination Approaches 7.5.2 Structure-Based Determination Approaches 7.5.3 Comparison between Proposed Approaches 8 Pose Graphs 8.1 Optimization Principle 8.2 Solvers 8.2.1 Additional Graph Solvers 8.2.2 False Loop Closure Detection 8.3 Pose Graph Generation 8.3.1 Generation of Synthetic Pose Graph Data 8.3.2 Optimization of Synthetic Pose Graph Data 9 Structureless Camera Motion Estimation 9.1 SCME Pipeline 9.2 Determination of Two-View Translation Scale Factors 9.3 Integration of Depth Data 9.4 Integration of Extrinsic Camera Constraints 10 Camera Motion Estimation Results 10.1 Directional Camera Images 10.2 Omnidirectional Camera Images 11 Conclusion 11.1 Summary 11.2 Outlook and Future Work Appendices A.1 Additional Extrinsic Calibration Results A.2 Linear Least Squares Scaling A.3 Proof Rank Deficiency A.4 Alternative Derivation Midpoint Method A.5 Simplification of Depth Calculation A.6 Relation between Epipolar and Circumferential Constraint A.7 Covariance Estimation A.8 Uncertainty Estimation from Epipolar Geometry A.9 Two-View Scaling Factor Estimation: Uncertainty Estimation A.10 Two-View Scaling Factor Optimization: Uncertainty Estimation A.11 Depth from Adjoining Two-View Geometries A.12 Alternative Three-View Derivation A.12.1 Second Derivation Approach A.12.2 Third Derivation Approach A.13 Relation between Trifocal Geometry and Alternative Midpoint Method A.14 Additional Pose Graph Generation Examples A.15 Pose Graph Solver Settings A.16 Additional Pose Graph Optimization Examples Bibliograph

Three-dimensional morphanalysis of the face.

The aim of the work reported in this thesis was to determine the extent to which orthogonal two-dimensional morphanalytic (universally relatable) craniofacial imaging methods can be extended into the realm of computer-based three-dimensional imaging. New methods are presented for capturing universally relatable laser-video surface data, for inter-relating facial surface scans and for constructing probabilistic facial averages. Universally relatable surface scans are captured using the fixed relations principle com- bined with a new laser-video scanner calibration method. Inter- subject comparison of facial surface scans is achieved using inter- active feature labelling and warping methods. These methods have been extended to groups of subjects to allow the construction of three-dimensional probabilistic facial averages. The potential of universally relatable facial surface data for applications such as growth studies and patient assessment is demonstrated. In addition, new methods for scattered data interpolation, for controlling overlap in image warping and a fast, high-resolution method for simulating craniofacial surgery are described. The results demonstrate that it is not only possible to extend universally relatable imaging into three dimensions, but that the extension also enhances the established methods, providing a wide range of new applications

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