Distributed scene reconstruction from multiple mobile platforms

Recent research on mobile robotics has produced new designs that provide house-hold robots with omnidirectional motion. The image sensor embedded in these devices motivates the application of 3D vision techniques on them for navigation and mapping purposes. In addition to this, distributed cheapsensing systems acting as unitary entity have recently been discovered as an efficient alternative to expensive mobile equipment. In this work we present an implementation of a visual reconstruction method, structure from motion (SfM), on a low-budget, omnidirectional mobile platform, and extend this method to distributed 3D scene reconstruction with several instances of such a platform. Our approach overcomes the challenges yielded by the plaform. The unprecedented levels of noise produced by the image compression typical of the platform is processed by our feature filtering methods, which ensure suitable feature matching populations for epipolar geometry estimation by means of a strict quality-based feature selection. The robust pose estimation algorithms implemented, along with a novel feature tracking system, enable our incremental SfM approach to novelly deal with ill-conditioned inter-image configurations provoked by the omnidirectional motion. The feature tracking system developed efficiently manages the feature scarcity produced by noise and outputs quality feature tracks, which allow robust 3D mapping of a given scene even if - due to noise - their length is shorter than what it is usually assumed for performing stable 3D reconstructions. The distributed reconstruction from multiple instances of SfM is attained by applying loop-closing techniques. Our multiple reconstruction system merges individual 3D structures and resolves the global scale problem with minimal overlaps, whereas in the literature 3D mapping is obtained by overlapping stretches of sequences. The performance of this system is demonstrated in the 2-session case. The management of noise, the stability against ill-configurations and the robustness of our SfM system is validated on a number of experiments and compared with state-of-the-art approaches. Possible future research areas are also discussed

Integration and visualisation of clinical-omics datasets for medical knowledge discovery

In recent decades, the rise of various omics fields has flooded life sciences with unprecedented amounts of high-throughput data, which have transformed the way biomedical research is conducted. This trend will only intensify in the coming decades, as the cost of data acquisition will continue to decrease. Therefore, there is a pressing need to find novel ways to turn this ocean of raw data into waves of information and finally distil those into drops of translational medical knowledge. This is particularly challenging because of the incredible richness of these datasets, the humbling complexity of biological systems and the growing abundance of clinical metadata, which makes the integration of disparate data sources even more difficult. Data integration has proven to be a promising avenue for knowledge discovery in biomedical research. Multi-omics studies allow us to examine a biological problem through different lenses using more than one analytical platform. These studies not only present tremendous opportunities for the deep and systematic understanding of health and disease, but they also pose new statistical and computational challenges. The work presented in this thesis aims to alleviate this problem with a novel pipeline for omics data integration. Modern omics datasets are extremely feature rich and in multi-omics studies this complexity is compounded by a second or even third dataset. However, many of these features might be completely irrelevant to the studied biological problem or redundant in the context of others. Therefore, in this thesis, clinical metadata driven feature selection is proposed as a viable option for narrowing down the focus of analyses in biomedical research. Our visual cortex has been fine-tuned through millions of years to become an outstanding pattern recognition machine. To leverage this incredible resource of the human brain, we need to develop advanced visualisation software that enables researchers to explore these vast biological datasets through illuminating charts and interactivity. Accordingly, a substantial portion of this PhD was dedicated to implementing truly novel visualisation methods for multi-omics studies.Open Acces

Model-Based Environmental Visual Perception for Humanoid Robots

The visual perception of a robot should answer two fundamental questions: What? and Where? In order to properly and efficiently reply to these questions, it is essential to establish a bidirectional coupling between the external stimuli and the internal representations. This coupling links the physical world with the inner abstraction models by sensor transformation, recognition, matching and optimization algorithms. The objective of this PhD is to establish this sensor-model coupling

Inferring Geodesic Cerebrovascular Graphs: Image Processing, Topological Alignment and Biomarkers Extraction

A vectorial representation of the vascular network that embodies quantitative features - location, direction, scale, and bifurcations - has many potential neuro-vascular applications. Patient-specific models support computer-assisted surgical procedures in neurovascular interventions, while analyses on multiple subjects are essential for group-level studies on which clinical prediction and therapeutic inference ultimately depend. This first motivated the development of a variety of methods to segment the cerebrovascular system. Nonetheless, a number of limitations, ranging from data-driven inhomogeneities, the anatomical intra- and inter-subject variability, the lack of exhaustive ground-truth, the need for operator-dependent processing pipelines, and the highly non-linear vascular domain, still make the automatic inference of the cerebrovascular topology an open problem. In this thesis, brain vessels’ topology is inferred by focusing on their connectedness. With a novel framework, the brain vasculature is recovered from 3D angiographies by solving a connectivity-optimised anisotropic level-set over a voxel-wise tensor field representing the orientation of the underlying vasculature. Assuming vessels joining by minimal paths, a connectivity paradigm is formulated to automatically determine the vascular topology as an over-connected geodesic graph. Ultimately, deep-brain vascular structures are extracted with geodesic minimum spanning trees. The inferred topologies are then aligned with similar ones for labelling and propagating information over a non-linear vectorial domain, where the branching pattern of a set of vessels transcends a subject-specific quantized grid. Using a multi-source embedding of a vascular graph, the pairwise registration of topologies is performed with the state-of-the-art graph matching techniques employed in computer vision. Functional biomarkers are determined over the neurovascular graphs with two complementary approaches. Efficient approximations of blood flow and pressure drop account for autoregulation and compensation mechanisms in the whole network in presence of perturbations, using lumped-parameters analog-equivalents from clinical angiographies. Also, a localised NURBS-based parametrisation of bifurcations is introduced to model fluid-solid interactions by means of hemodynamic simulations using an isogeometric analysis framework, where both geometry and solution profile at the interface share the same homogeneous domain. Experimental results on synthetic and clinical angiographies validated the proposed formulations. Perspectives and future works are discussed for the group-wise alignment of cerebrovascular topologies over a population, towards defining cerebrovascular atlases, and for further topological optimisation strategies and risk prediction models for therapeutic inference. Most of the algorithms presented in this work are available as part of the open-source package VTrails

Exploring space situational awareness using neuromorphic event-based cameras

The orbits around earth are a limited natural resource and one that hosts a vast range of vital space-based systems that support international systems use by both commercial industries, civil organisations, and national defence. The availability of this space resource is rapidly depleting due to the ever-growing presence of space debris and rampant overcrowding, especially in the limited and highly desirable slots in geosynchronous orbit. The field of Space Situational Awareness encompasses tasks aimed at mitigating these hazards to on-orbit systems through the monitoring of satellite traffic. Essential to this task is the collection of accurate and timely observation data. This thesis explores the use of a novel sensor paradigm to optically collect and process sensor data to enhance and improve space situational awareness tasks. Solving this issue is critical to ensure that we can continue to utilise the space environment in a sustainable way. However, these tasks pose significant engineering challenges that involve the detection and characterisation of faint, highly distant, and high-speed targets. Recent advances in neuromorphic engineering have led to the availability of high-quality neuromorphic event-based cameras that provide a promising alternative to the conventional cameras used in space imaging. These cameras offer the potential to improve the capabilities of existing space tracking systems and have been shown to detect and track satellites or ‘Resident Space Objects’ at low data rates, high temporal resolutions, and in conditions typically unsuitable for conventional optical cameras. This thesis presents a thorough exploration of neuromorphic event-based cameras for space situational awareness tasks and establishes a rigorous foundation for event-based space imaging. The work conducted in this project demonstrates how to enable event-based space imaging systems that serve the goals of space situational awareness by providing accurate and timely information on the space domain. By developing and implementing event-based processing techniques, the asynchronous operation, high temporal resolution, and dynamic range of these novel sensors are leveraged to provide low latency target acquisition and rapid reaction to challenging satellite tracking scenarios. The algorithms and experiments developed in this thesis successfully study the properties and trade-offs of event-based space imaging and provide comparisons with traditional observing methods and conventional frame-based sensors. The outcomes of this thesis demonstrate the viability of event-based cameras for use in tracking and space imaging tasks and therefore contribute to the growing efforts of the international space situational awareness community and the development of the event-based technology in astronomy and space science applications

Computer Vision and Kinematic Sensing in Robotics

To use vision in a robotic setting it is important to achieve realtime performance. Real-time vision may be used to directly steer robots using for instance visual servoing techniques. In this thesis, an experimental vision setup using a stereo rig mounted on an industrial robot (ABB Irb-6) was built from ground up and then used to perform two experiments; visual servoing and collection of data for calibration of stereo rig and positioning of second robot (ABB Irb-2000) using visual feedback. The system is currently capable of achieving a ~15Hz visual feedback rate which could be easily extended into the 20Hz domain

Hardward and algorithm architectures for real-time additive synthesis

Additive synthesis is a fundamental computer music synthesis paradigm tracing its origins to the work of Fourier and Helmholtz. Rudimentary implementation linearly combines harmonic sinusoids (or partials) to generate tones whose perceived timbral characteristics are a strong function of the partial amplitude spectrum. Having evolved over time, additive synthesis describes a collection of algorithms each characterised by the time-varying linear combination of basis components to generate temporal evolution of timbre. Basis components include exactly harmonic partials, inharmonic partials with time-varying frequency or non-sinusoidal waveforms each with distinct spectral characteristics. Additive synthesis of polyphonic musical instrument tones requires a large number of independently controlled partials incurring a large computational overhead whose investigation and reduction is a key motivator for this work. The thesis begins with a review of prevalent synthesis techniques setting additive synthesis in context and introducing the spectrum modelling paradigm which provides baseline spectral data to the additive synthesis process obtained from the analysis of natural sounds. We proceed to investigate recursive and phase accumulating digital sinusoidal oscillator algorithms, defining specific metrics to quantify relative performance. The concepts of phase accumulation, table lookup phase-amplitude mapping and interpolated fractional addressing are introduced and developed and shown to underpin an additive synthesis subclass - wavetable lookup synthesis (WLS). WLS performance is simulated against specific metrics and parameter conditions peculiar to computer music requirements. We conclude by presenting processing architectures which accelerate computational throughput of specific WLS operations and the sinusoidal additive synthesis model. In particular, we introduce and investigate the concept of phase domain processing and present several “pipeline friendly” arithmetic architectures using this technique which implement the additive synthesis of sinusoidal partials

Analysis of large-scale molecular biological data using self-organizing maps

Modern high-throughput technologies such as microarrays, next generation sequencing and mass spectrometry provide huge amounts of data per measurement and challenge traditional analyses. New strategies of data processing, visualization and functional analysis are inevitable. This thesis presents an approach which applies a machine learning technique known as self organizing maps (SOMs). SOMs enable the parallel sample- and feature-centered view of molecular phenotypes combined with strong visualization and second-level analysis capabilities. We developed a comprehensive analysis and visualization pipeline based on SOMs. The unsupervised SOM mapping projects the initially high number of features, such as gene expression profiles, to meta-feature clusters of similar and hence potentially co-regulated single features. This reduction of dimension is attained by the re-weighting of primary information and does not entail a loss of primary information in contrast to simple filtering approaches. The meta-data provided by the SOM algorithm is visualized in terms of intuitive mosaic portraits. Sample-specific and common properties shared between samples emerge as a handful of localized spots in the portraits collecting groups of co-regulated and co-expressed meta-features. This characteristic color patterns reflect the data landscape of each sample and promote immediate identification of (meta-)features of interest. It will be demonstrated that SOM portraits transform large and heterogeneous sets of molecular biological data into an atlas of sample-specific texture maps which can be directly compared in terms of similarities and dissimilarities. Spot-clusters of correlated meta-features can be extracted from the SOM portraits in a subsequent step of aggregation. This spot-clustering effectively enables reduction of the dimensionality of the data in two subsequent steps towards a handful of signature modules in an unsupervised fashion. Furthermore we demonstrate that analysis techniques provide enhanced resolution if applied to the meta-features. The improved discrimination power of meta-features in downstream analyses such as hierarchical clustering, independent component analysis or pairwise correlation analysis is ascribed to essentially two facts: Firstly, the set of meta-features better represents the diversity of patterns and modes inherent in the data and secondly, it also possesses the better signal-to-noise characteristics as a comparable collection of single features. Additionally to the pattern-driven feature selection in the SOM portraits, we apply statistical measures to detect significantly differential features between sample classes. Implementation of scoring measurements supplements the basal SOM algorithm. Further, two variants of functional enrichment analyses are introduced which link sample specific patterns of the meta-feature landscape with biological knowledge and support functional interpretation of the data based on the ‘guilt by association’ principle. Finally, case studies selected from different ‘OMIC’ realms are presented in this thesis. In particular, molecular phenotype data derived from expression microarrays (mRNA, miRNA), sequencing (DNA methylation, histone modification patterns) or mass spectrometry (proteome), and also genotype data (SNP-microarrays) is analyzed. It is shown that the SOM analysis pipeline implies strong application capabilities and covers a broad range of potential purposes ranging from time series and treatment-vs.-control experiments to discrimination of samples according to genotypic, phenotypic or taxonomic classifications