Robust Modular Feature-Based Terrain-Aided Visual Navigation and Mapping

The visual feature-based Terrain-Aided Navigation (TAN) system presented in this thesis addresses the problem of constraining inertial drift introduced into the location estimate of Unmanned Aerial Vehicles (UAVs) in GPS-denied environment. The presented TAN system utilises salient visual features representing semantic or human-interpretable objects (roads, forest and water boundaries) from onboard aerial imagery and associates them to a database of reference features created a-priori, through application of the same feature detection algorithms to satellite imagery. Correlation of the detected features with the reference features via a series of the robust data association steps allows a localisation solution to be achieved with a finite absolute bound precision defined by the certainty of the reference dataset. The feature-based Visual Navigation System (VNS) presented in this thesis was originally developed for a navigation application using simulated multi-year satellite image datasets. The extension of the system application into the mapping domain, in turn, has been based on the real (not simulated) flight data and imagery. In the mapping study the full potential of the system, being a versatile tool for enhancing the accuracy of the information derived from the aerial imagery has been demonstrated. Not only have the visual features, such as road networks, shorelines and water bodies, been used to obtain a position ’fix’, they have also been used in reverse for accurate mapping of vehicles detected on the roads into an inertial space with improved precision. Combined correction of the geo-coding errors and improved aircraft localisation formed a robust solution to the defense mapping application. A system of the proposed design will provide a complete independent navigation solution to an autonomous UAV and additionally give it object tracking capability

DH-PTAM: A Deep Hybrid Stereo Events-Frames Parallel Tracking And Mapping System

This paper presents a robust approach for a visual parallel tracking and mapping (PTAM) system that excels in challenging environments. Our proposed method combines the strengths of heterogeneous multi-modal visual sensors, including stereo event-based and frame-based sensors, in a unified reference frame through a novel spatio-temporal synchronization of stereo visual frames and stereo event streams. We employ deep learning-based feature extraction and description for estimation to enhance robustness further. We also introduce an end-to-end parallel tracking and mapping optimization layer complemented by a simple loop-closure algorithm for efficient SLAM behavior. Through comprehensive experiments on both small-scale and large-scale real-world sequences of VECtor and TUM-VIE benchmarks, our proposed method (DH-PTAM) demonstrates superior performance compared to state-of-the-art methods in terms of robustness and accuracy in adverse conditions. Our implementation's research-based Python API is publicly available on GitHub for further research and development: https://github.com/AbanobSoliman/DH-PTAM.Comment: Submitted for publication in IEEE RA-

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

Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated

Panoramic Video Stitching

Digital camera and smartphone technologies have made high quality images and video pervasive and abundant. Combining or stitching collections of images from a variety of viewpoints into an extended panoramic image is a common and popular function for such devices. Extending this functionality to video however, poses many new challenges due to the demand for both spatial and temporal continuity. Multi-view video stitching (also called panoramic video stitching) is an emerging, common research area in computer vision, image/video processing and computer graphics and has wide applications in virtual reality, virtual tourism, surveillance, and human computer interaction. In this thesis, I will explore the technical and practical problems in the complete process of stitching a high-resolution multiview video into a high-resolution panoramic video. The challenges addressed include video stabilization, efficient multi-view video alignment and panoramic video stitching, color correction, and blurred frame detection and repair. Specifically, I propose a continuity aware Kalman filtering scheme for rotation angles for video stabilization and jitter removal. For efficient stitching of long, high-resolution panoramic videos, I propose constrained and multigrid SIFT matching schemes, concatenated image projection and warping and min-space feathering. These three approaches together can greatly reduce the computational time and memory requirement in panoramic video stitching, which makes it feasible to stitch high-resolution (e.g., 1920x1080 pixels) and long panoramic video sequences using standard workstations. Color correction is the emphasis of my research. On this topic I first performed a systematic survey and performance evaluation of nine state of the art color correction approaches in the context of two-view image stitching. My evaluation work not only gives useful insights and conclusions about the relative performance of these approaches, but also points out the remaining challenges and possible directions for future color correction research. Based on the conclusions from this evaluation work, I proposed a hybrid and scalable color correction approach for general n-view image stitching, and designed a two-view video color correction approach for panoramic video stitching. For blurred frame detection and repair, I have completed preliminary work on image partial blur detection and classification, in which I proposed a SVM-based blur block classifier using improved and new local blur features. Then, based on partial blur classification results, I designed a statistical thresholding scheme for blurred frame identification. For the detected blurred frames, I repaired them using polynomial data fitting from neighboring unblurred frames. Many of the techniques and ideas in this thesis are novel and general solutions to the technical or practical problems in panoramic video stitching. At the end of this thesis, I conclude the contributions made by this thesis to the research and popularization of panoramic video stitching, and describe those open research issues

Towards an efficient segmentation of small rodents brain: a short critical review

One of the most common tasks in small rodents MRI pipelines is the voxel-wise segmentation of the volume in multiple classes. While many segmentation schemes have been developed for the human brain, fewer are available for rodent MRI, often by adaptation from human neuroimaging. Common methods include atlas-based and clustering schemes. The former labels the target volume by registering one or more pre-labeled atlases using a deformable registration method, in which case the result depends on the quality of the reference volumes, the registration algorithm and the label fusion approach, if more than one atlas is employed. The latter is based on an expectation maximization procedure to maximize the variance between voxel categories, and is often combined with Markov Random Fields and the atlas based approach to include spatial information, priors, and improve the classification accuracy. Our primary goal is to critically review the state of the art of rat and mouse segmentation of neuro MRI volumes and compare the available literature on popular, readily and freely available MRI toolsets, including SPM, FSL and ANTs, when applied to this task in the context of common pre-processing steps. Furthermore, we will briefly address the emerging Deep Learning methods for the segmentation of medical imaging, and the perspectives for applications to small rodents

Digital video moving object segmentation using tensor voting: A non-causal, accurate approach

Motion based video segmentation is important in many video processing applications such as MPEG4. This thesis presents an exhaustive, non-causal method to estimate boundaries between moving objects in a video clip. It make use of tensor voting principles. The tensor voting is adapted to allow image structure to manifest in the tangential plane of the saliency map. The technique allows direct estimation of motion vectors from second-order tensor analysis. The tensors make maximal and direct use of the available information by encoding it into the dimensionality of the tensor. The tensor voting methodology introduces a non-symmetrical voting kernel to allow a measure of voting skewness to be inferred. Skewness is found in the third-order tensor in the direction of the tangential first eigenvector. This new concept is introduced as the Tensor Skewness Map or TS map. The TS map gives further information about whether an object is occluding or disoccluding another object. The information can be used to infer the layering order of the moving objects in the video clip. Matched filtering and detection are applied to reduce the TS map into occluding and disoccluding detections. The technique is computationally exhaustive, but may find use in off-line video object segmentation processes. The use of commercial-off-the-shelf Graphic Processor Units is demonstrated to scale well to the tensor voting framework, providing the computational speed improvement required to make the framework realisable on a larger scale and to handle tensor dimensionalities higher than before

Robust whole-brain segmentation: Application to traumatic brain injury

We propose a framework for the robust and fully-automatic segmentation of magnetic resonance (MR) brain images called "Multi-Atlas Label Propagation with Expectation-Maximisation based refinement" (MALP-EM). The presented approach is based on a robust registration approach (MAPER), highly performant label fusion (joint label fusion) and intensity-based label refinement using EM. We further adapt this framework to be applicable for the segmentation of brain images with gross changes in anatomy. We propose to account for consistent registration errors by relaxing anatomical priors obtained by multi-atlas propagation and a weighting scheme to locally combine anatomical atlas priors and intensity-refined posterior probabilities. The method is evaluated on a benchmark dataset used in a recent MICCAI segmentation challenge. In this context we show that MALP-EM is competitive for the segmentation of MR brain scans of healthy adults when compared to state-of-the-art automatic labelling techniques. To demonstrate the versatility of the proposed approach, we employed MALP-EM to segment 125 MR brain images into 134 regions from subjects who had sustained traumatic brain injury (TBI). We employ a protocol to assess segmentation quality if no manual reference labels are available. Based on this protocol, three independent, blinded raters confirmed on 13 MR brain scans with pathology that MALP-EM is superior to established label fusion techniques. We visually confirm the robustness of our segmentation approach on the full cohort and investigate the potential of derived symmetry-based imaging biomarkers that correlate with and predict clinically relevant variables in TBI such as the Marshall Classification (MC) or Glasgow Outcome Score (GOS). Specifically, we show that we are able to stratify TBI patients with favourable outcomes from non-favourable outcomes with 64.7% accuracy using acute-phase MR images and 66.8% accuracy using follow-up MR images. Furthermore, we are able to differentiate subjects with the presence of a mass lesion or midline shift from those with diffuse brain injury with 76.0% accuracy. The thalamus, putamen, pallidum and hippocampus are particularly affected. Their involvement predicts TBI disease progression.This work was partially funded under the 7th Framework Programme by the European Commission (http://cordis.europa.eu/ist/, TBIcare: http://www.tbicare.eu/, last accessed: 8 December 2014). The research was further supported by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London. AH is supported by the Department of Health via the NIHR comprehensive BRC award to Guy’s & St Thomas’ NHS Foundation Trust in partnership with King’s College London and Kings College Hospital NHS Foundation Trust. This work was further supported by a Medical Research Council (UK) Program Grant (Acute brain injury: heterogeneity of mechanisms, therapeutic targets and outcome effects [G9439390 ID 65883]), the UK National Institute of Health Research Biomedical Research Centre at Cambridge, the Technology Platform funding provided by the UK Department of Health and an EPSRC Pathways to Impact award. VFJN is supported by a Health Foundation/Academy of Medical Sciences Clinician Scientist Fellowship. DKM is supported by an NIHR Senior Investigator Award. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. The funders had no role in study design, data collection and analyses, decision to publish, or preparation of the manuscript