Automated Strategies in Multimodal and Multidimensional Ultrasound Image-based Diagnosis

Medical ultrasonography is an effective technique in traditional anatomical and functional diagnosis. However, it requires the visual examination by experienced clinicians, which is a laborious, time consuming and highly subjective procedure. Computer-aided diagnosis (CADx) have been extensively used in clinical practice to support the interpretation of images; nevertheless, current ultrasound CADx still entails a substantial user-dependency and are unable to extract image data for prediction modelling. The aim of this thesis is to propose a set of fully automated strategies to overcome the limitations of ultrasound CADx. These strategies are addressed to multiple modalities (B-Mode, Contrast-Enhanced Ultrasound-CEUS, Power Doppler-PDUS and Acoustic Angiography-AA) and dimensions (2-D and 3-D imaging). The enabling techniques presented in this work are designed, developed and quantitively validated to efficiently improve the overall patients’ diagnosis. This work is subdivided in 2 macro-sections: in the first part, two fully automated algorithms for the reliable quantification of 2-D B-Mode ultrasound skeletal muscle architecture and morphology are proposed. In the second part, two fully automated algorithms for the objective assessment and characterization of tumors’ vasculature in 3-D CEUS and PDUS thyroid tumors and preclinical AA cancer growth are presented. In the first part, the MUSA (Muscle UltraSound Analysis) algorithm is designed to measure the muscle thickness, the fascicles length and the pennation angle; the TRAMA (TRAnsversal Muscle Analysis) algorithm is proposed to extract and analyze the Visible Cross-Sectional Area (VCSA). MUSA and TRAMA algorithms have been validated on two datasets of 200 images; automatic measurements have been compared with expert operators’ manual measurements. A preliminary statistical analysis was performed to prove the ability of texture analysis on automatic VCSA in the distinction between healthy and pathological muscles. In the second part, quantitative assessment on tumor vasculature is proposed in two automated algorithms for the objective characterization of 3-D CEUS/Power Doppler thyroid nodules and the evolution study of fibrosarcoma invasion in preclinical 3-D AA imaging. Vasculature analysis relies on the quantification of architecture and vessels tortuosity. Vascular features obtained from CEUS and PDUS images of 20 thyroid nodules (10 benign, 10 malignant) have been used in a multivariate statistical analysis supported by histopathological results. Vasculature parametric maps of implanted fibrosarcoma are extracted from 8 rats investigated with 3-D AA along four time points (TPs), in control and tumors areas; results have been compared with manual previous findings in a longitudinal tumor growth study. Performance of MUSA and TRAMA algorithms results in 100% segmentation success rate. Absolute difference between manual and automatic measurements is below 2% for the muscle thickness and 4% for the VCSA (values between 5-10% are acceptable in clinical practice), suggesting that automatic and manual measurements can be used interchangeably. The texture features extraction on the automatic VCSAs reveals that texture descriptors can distinguish healthy from pathological muscles with a 100% success rate for all the four muscles. Vascular features extracted of 20 thyroid nodules in 3-D CEUS and PDUS volumes can be used to distinguish benign from malignant tumors with 100% success rate for both ultrasound techniques. Malignant tumors present higher values of architecture and tortuosity descriptors; 3-D CEUS and PDUS imaging present the same accuracy in the differentiation between benign and malignant nodules. Vascular parametric maps extracted from the 8 rats along the 4 TPs in 3-D AA imaging show that parameters extracted from the control area are statistically different compared to the ones within the tumor volume. Tumor angiogenetic vessels present a smaller diameter and higher tortuosity. Tumor evolution is characterized by the significant vascular trees growth and a constant value of vessel diameter along the four TPs, confirming the previous findings. In conclusion, the proposed automated strategies are highly performant in segmentation, features extraction, muscle disease detection and tumor vascular characterization. These techniques can be extended in the investigation of other organs, diseases and embedded in ultrasound CADx, providing a user-independent reliable diagnosis

Map-Based Localization for Unmanned Aerial Vehicle Navigation

Unmanned Aerial Vehicles (UAVs) require precise pose estimation when navigating in indoor and GNSS-denied / GNSS-degraded outdoor environments. The possibility of crashing in these environments is high, as spaces are confined, with many moving obstacles. There are many solutions for localization in GNSS-denied environments, and many different technologies are used. Common solutions involve setting up or using existing infrastructure, such as beacons, Wi-Fi, or surveyed targets. These solutions were avoided because the cost should be proportional to the number of users, not the coverage area. Heavy and expensive sensors, for example a high-end IMU, were also avoided. Given these requirements, a camera-based localization solution was selected for the sensor pose estimation. Several camera-based localization approaches were investigated. Map-based localization methods were shown to be the most efficient because they close loops using a pre-existing map, thus the amount of data and the amount of time spent collecting data are reduced as there is no need to re-observe the same areas multiple times. This dissertation proposes a solution to address the task of fully localizing a monocular camera onboard a UAV with respect to a known environment (i.e., it is assumed that a 3D model of the environment is available) for the purpose of navigation for UAVs in structured environments. Incremental map-based localization involves tracking a map through an image sequence. When the map is a 3D model, this task is referred to as model-based tracking. A by-product of the tracker is the relative 3D pose (position and orientation) between the camera and the object being tracked. State-of-the-art solutions advocate that tracking geometry is more robust than tracking image texture because edges are more invariant to changes in object appearance and lighting. However, model-based trackers have been limited to tracking small simple objects in small environments. An assessment was performed in tracking larger, more complex building models, in larger environments. A state-of-the art model-based tracker called ViSP (Visual Servoing Platform) was applied in tracking outdoor and indoor buildings using a UAVs low-cost camera. The assessment revealed weaknesses at large scales. Specifically, ViSP failed when tracking was lost, and needed to be manually re-initialized. Failure occurred when there was a lack of model features in the cameras field of view, and because of rapid camera motion. Experiments revealed that ViSP achieved positional accuracies similar to single point positioning solutions obtained from single-frequency (L1) GPS observations standard deviations around 10 metres. These errors were considered to be large, considering the geometric accuracy of the 3D model used in the experiments was 10 to 40 cm. The first contribution of this dissertation proposes to increase the performance of the localization system by combining ViSP with map-building incremental localization, also referred to as simultaneous localization and mapping (SLAM). Experimental results in both indoor and outdoor environments show sub-metre positional accuracies were achieved, while reducing the number of tracking losses throughout the image sequence. It is shown that by integrating model-based tracking with SLAM, not only does SLAM improve model tracking performance, but the model-based tracker alleviates the computational expense of SLAMs loop closing procedure to improve runtime performance. Experiments also revealed that ViSP was unable to handle occlusions when a complete 3D building model was used, resulting in large errors in its pose estimates. The second contribution of this dissertation is a novel map-based incremental localization algorithm that improves tracking performance, and increases pose estimation accuracies from ViSP. The novelty of this algorithm is the implementation of an efficient matching process that identifies corresponding linear features from the UAVs RGB image data and a large, complex, and untextured 3D model. The proposed model-based tracker improved positional accuracies from 10 m (obtained with ViSP) to 46 cm in outdoor environments, and improved from an unattainable result using VISP to 2 cm positional accuracies in large indoor environments. The main disadvantage of any incremental algorithm is that it requires the camera pose of the first frame. Initialization is often a manual process. The third contribution of this dissertation is a map-based absolute localization algorithm that automatically estimates the camera pose when no prior pose information is available. The method benefits from vertical line matching to accomplish a registration procedure of the reference model views with a set of initial input images via geometric hashing. Results demonstrate that sub-metre positional accuracies were achieved and a proposed enhancement of conventional geometric hashing produced more correct matches - 75% of the correct matches were identified, compared to 11%. Further the number of incorrect matches was reduced by 80%

Feature detection algorithms in computed images

The problem of sensing a medium by several sensors and retrieving interesting features is a very general one. The basic framework of the problem is generally the same for applications from MRI, tomography, Radar SAR imaging to subsurface imaging, even though the data acquisition processes, sensing geometries and sensed properties are different. In this thesis we introduced a new perspective to the problem of remote sensing and information retrieval by studying the problem of subsurface imaging using GPR and seismic sensors. We have shown that if the sensed medium is sparse in some domain then it can be imaged using many fewer measurements than required by the standard methods. This leads to much lower data acquisition times and better images representing the medium. We have used the ideas from Compressive Sensing, which show that a small number of random measurements about a signal is sufficient to completely characterize it, if the signal is sparse or compressible in some domain. Although we have applied our ideas to the subsurface imaging problem, our results are general and can be extended to other remote sensing applications. A second objective in remote sensing is information retrieval which involves searching for important features in the computed image of the medium. In this thesis we focus on detecting buried structures like pipes, and tunnels in computed GPR or seismic images. The problem of finding these structures in high clutter and noise conditions, and finding them faster than the standard shape detecting methods like the Hough transform is analyzed. One of the most important contributions of this thesis is, where the sensing and the information retrieval stages are unified in a single framework using compressive sensing. Instead of taking lots of standard measurements to compute the image of the medium and search the necessary information in the computed image, a much smaller number of measurements as random projections are taken. The data acquisition and information retrieval stages are unified by using a data model dictionary that connects the information to the sensor data.Ph.D.Committee Chair: McClellan, James H.; Committee Member: Romberg, Justin K.; Committee Member: Scott, Waymond R. Jr.; Committee Member: Vela, Patricio A.; Committee Member: Vidakovic, Bran

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

Medical image processing: applications in ophthalmology and total hip replacement

Medical imaging tools technologically supported by the recent advances in the areas of computer vision can provide systems that aid medical professionals to carry out their expert diagnostics and investigations more effectively and efficiently. Two medical application domains that can benefit by such tools are ophthalmology and Total Hip Replacement (THR). Although a literature review conducted within the research context of this thesis revealed a number of existing solutions these are either very much limited by their application scope, robustness or scope of the extensiveness of the functionality made available. Therefore this thesis focuses on initially investigating a number of requirements defined by leading experts in the respective specialisms and providing practical solutions, well supported by the theoretical advances of computer vision and pattern recognition. This thesis provides three novel algorithms/systems for use within image analysis in the areas of Ophthalmology and THR. The first approach uses Contourlet Transform to analyse and quantify corneal neovascularization. Experimental results are provided to prove that the proposed approach provides improved robustness in the presence of noise, non-uniform illumination and reflections, common problems that exist in captured corneal images. The second approach uses a colour based segmentation approach to segment, measure and analyse corneal ulcers using the HVS colour space. Literature review conducted within the research context of this thesis revealed that there is no such system available for analysis and measurement of corneal ulcers. Finally the thesis provides a robust approach towards detecting and analysing possible dislocations and misalignments in THR X-ray images. The algorithm uses localised histogram equalisation to enhance the quality of X-ray images first prior to using Hough Transforms and filtered back projections to locate and recognise key points of the THR x-ray images. These key points are then used to measure the possible presence of dislocations and misalignments. The thesis further highlights possible extensions and improvements to the proposed algorithms and systems

Biometric iris image segmentation and feature extraction for iris recognition

PhD ThesisThe continued threat to security in our interconnected world today begs for urgent solution. Iris biometric like many other biometric systems provides an alternative solution to this lingering problem. Although, iris recognition have been extensively studied, it is nevertheless, not a fully solved problem which is the factor inhibiting its implementation in real world situations today. There exists three main problems facing the existing iris recognition systems: 1) lack of robustness of the algorithm to handle non-ideal iris images, 2) slow speed of the algorithm and 3) the applicability to the existing systems in real world situation. In this thesis, six novel approaches were derived and implemented to address these current limitation of existing iris recognition systems. A novel fast and accurate segmentation approach based on the combination of graph-cut optimization and active contour model is proposed to define the irregular boundaries of the iris in a hierarchical 2-level approach. In the first hierarchy, the approximate boundary of the pupil/iris is estimated using a method based on Hough’s transform for the pupil and adapted starburst algorithm for the iris. Subsequently, in the second hierarchy, the final irregular boundary of the pupil/iris is refined and segmented using graph-cut based active contour (GCBAC) model proposed in this work. The segmentation is performed in two levels, whereby the pupil is segmented first before the iris. In order to detect and eliminate noise and reflection artefacts which might introduce errors to the algorithm, a preprocessing technique based on adaptive weighted edge detection and high-pass filtering is used to detect reflections on the high intensity areas of the image while exemplar based image inpainting is used to eliminate the reflections. After the segmentation of the iris boundaries, a post-processing operation based on combination of block classification method and statistical prediction approach is used to detect any super-imposed occluding eyelashes/eyeshadows. The normalization of the iris image is achieved though the rubber sheet model. In the second stage, an approach based on construction of complex wavelet filters and rotation of the filters to the direction of the principal texture direction is used for the extraction of important iris information while a modified particle swam optimization (PSO) is used to select the most prominent iris features for iris encoding. Classification of the iriscode is performed using adaptive support vector machines (ASVM). Experimental results demonstrate that the proposed approach achieves accuracy of 98.99% and is computationally about 2 times faster than the best existing approach.Ebonyi State University and Education Task Fund, Nigeri

Digital Multispectral Map Reconstruction Using Aerial Imagery

Advances made in the computer vision field allowed for the establishment of faster and more accurate photogrammetry techniques. Structure from Motion(SfM) is a photogrammetric technique focused on the digital spatial reconstruction of objects based on a sequence of images. The benefit of Unmanned Aerial Vehicle (UAV) platforms allowed the ability to acquire high fidelity imagery intended for environmental mapping. This way, UAV platforms became a heavily adopted method of survey. The combination of SfM and the recent improvements of Unmanned Aerial Vehicle (UAV) platforms granted greater flexibility and applicability, opening a new path for a new remote sensing technique aimed to replace more traditional and laborious approaches often associated with high monetary costs. The continued development of digital reconstruction software and advances in the field of computer processing allowed for a more affordable and higher resolution solution when compared to the traditional methods. The present work proposed a digital reconstruction algorithm based on images taken by a UAV platform inspired by the work made available by the open-source project OpenDroneMap. The aerial images are inserted in the computer vision program and several operations are applied to them, including detection and matching of features, point cloud reconstruction, meshing, and texturing, which results in a final product that represents the surveyed site. Additionally, from the study, it was concluded that an implementation which addresses the processing of thermal images was not integrated in the works of OpenDroneMap. By this point, their work was altered to allow for the reconstruction of thermal maps without sacrificing the resolution of the final model. Standard methods to process thermal images required a larger image footprint (or area of ground capture in a frame), the reason for this is that these types of images lack the presence of invariable features and by increasing the image’s footprint, the number of features present in each frame also rises. However, this method of image capture results in a lower resolution of the final product. The algorithm was developed using open-source libraries. In order to validate the obtained results, this model was compared to data obtained from commercial products, like Pix4D. Furthermore, due to circumstances brought about by the current pandemic, it was not possible to conduct a field study for the comparison and assessment of our results, as such the validation of the models was performed by verifying if the geographic location of the model was performed correctly and by visually assessing the generated maps.Avanços no campo da visão computacional permitiu o desenvolvimento de algoritmos mais eficientes de fotogrametria. Structure from Motion (SfM) é uma técnica de fotogrametria que tem como objetivo a reconstrução digital de objectos no espaço derivados de uma sequência de imagens. A característica importante que os Veículos Aérios não-tripulados (UAV) conseguem fornecer, a nível de mapeamento, é a sua capacidade de obter um conjunto de imagens de alta resolução. Devido a isto, UAV tornaram-se num dos métodos adotados no estudo de topografia. A combinação entre SfM e recentes avanços nos UAV permitiram uma melhor flexibilidade e aplicabilidade, permitindo deste modo desenvolver um novo método de Remote Sensing. Este método pretende substituir técnicas tradicionais, as quais estão associadas a mão-de-obra intensiva e a custos monetários elevados. Avanços contínuos feitos em softwares de reconstrução digital e no poder de processamento resultou em modelos de maior resolução e menos dispendiosos comparando a métodos tradicionais. O presente estudo propõe um algoritmo de reconstrução digital baseado em imagens obtidas através de UAV inspiradas no estudo disponibilizado pela OpenDroneMap. Estas imagens são inseridas no programa de visão computacional, onde várias operações são realizadas, incluindo: deteção e correspondência de caracteristicas, geração da point cloud, meshing e texturação dos quais resulta o produto final que representa o local em estudo. De forma complementar, concluiu-se que o trabalho da OpenDroneMap não incluia um processo de tratamento de imagens térmicas. Desta forma, alterações foram efetuadas que permitissem a criação de mapas térmicos sem sacrificar resolução do produto final, pois métodos típicos para processamento de imagens térmicas requerem uma área de captura maior, devido à falta de características invariantes neste tipo de imagens, o que leva a uma redução de resolução. Desta forma, o programa proposto foi desenvolvido através de bibliotecas open-source e os resultados foram comparados com modelos gerados através de software comerciais. Além do mais, devido à situação pandémica atual, não foi possível efetuar um estudo de campo para validar os modelos obtidos, como tal esta verificação foi feita através da correta localização geográfica do modelo, bem como avaliação visual dos modelos criados