Ensemble learning based on classifier prediction confidence and comprehensive learning particle swarm optimisation for medical image segmentation.

Segmentation, a process of partitioning an image into multiple segments to locate objects and boundaries, is considered one of the most essential medical imaging process. In recent years, Deep Neural Networks (DNN) have achieved many notable successes in medical image analysis, including image segmentation. Due to the fact that medical imaging applications require robust, reliable results, it is necessary to devise effective DNN models for medical applications. One solution is to combine multiple DNN models in an ensemble system to obtain better results than using each single DNN model. Ensemble learning is a popular machine learning technique in which multiple models are combined to improve the final results and has been widely used in medical image analysis. In this paper, we propose to measure the confidence in the prediction of each model in the ensemble system and then use an associate threshold to determine whether the confidence is acceptable or not. A segmentation model is selected based on the comparison between the confidence and its associated threshold. The optimal threshold for each segmentation model is found by using Comprehensive Learning Particle Swarm Optimisation (CLPSO), a swarm intelligence algorithm. The Dice coefficient, a popular performance metric for image segmentation, is used as the fitness criteria. The experimental results on three medical image segmentation datasets confirm that our ensemble achieves better results compared to some well-known segmentation models

A pilot study on discriminative power of features of superficial venous pattern in the hand

The goal of the project is to develop an automatic way to identify, represent the superficial vasculature of the back hand and investigate its discriminative power as biometric feature. A prototype of a system that extracts the superficial venous pattern of infrared images of back hands will be described. Enhancement algorithms are used to solve the lack of contrast of the infrared images. To trace the veins, a vessel tracking technique is applied, obtaining binary masks of the superficial venous tree. Successively, a method to estimate the blood vessels calibre, length, the location and angles of vessel junctions, will be presented. The discriminative power of these features will be studied, independently and simultaneously, considering two features vector. Pattern matching of two vasculature maps will be performed, to investigate the uniqueness of the vessel network / L’obiettivo del progetto è di sviluppare un metodo automatico per identificare e rappresentare la rete vascolare superficiale presente nel dorso della mano ed investigare sul suo potere discriminativo come caratteristica biometrica. Un prototipo di sistema che estrae l’albero superficiale delle vene da immagini infrarosse del dorso della mano sarà descritto. Algoritmi per il miglioramento del contrasto delle immagini infrarosse saranno applicati. Per tracciare le vene, una tecnica di tracking verrà utilizzata per ottenere una maschera binaria della rete vascolare. Successivamente, un metodo per stimare il calibro e la lunghezza dei vasi sanguigni, la posizione e gli angoli delle giunzioni sarà trattato. Il potere discriminativo delle precedenti caratteristiche verrà studiato ed una tecnica di pattern matching di due modelli vascolari sarà presentata per verificare l’unicità di quest

NON-RIGID BODY MECHANICAL PROPERTY RECOVERY FROM IMAGES AND VIDEOS

Material property has great importance in surgical simulation and virtual reality. The mechanical properties of the human soft tissue are critical to characterize the tissue deformation of each patient. Studies have shown that the tissue stiffness described by the tissue properties may indicate abnormal pathological process. The (recovered) elasticity parameters can assist surgeons to perform better pre-op surgical planning and enable medical robots to carry out personalized surgical procedures. Traditional elasticity parameters estimation methods rely largely on known external forces measured by special devices and strain field estimated by landmarks on the deformable bodies. Or they are limited to mechanical property estimation for quasi-static deformation. For virtual reality applications such as virtual try-on, garment material capturing is of equal significance as the geometry reconstruction. In this thesis, I present novel approaches for automatically estimating the material properties of soft bodies from images or from a video capturing the motion of the deformable body. I use a coupled simulation-optimization-identification framework to deform one soft body at its original, non-deformed state to match the deformed geometry of the same object in its deformed state. The optimal set of material parameters is thereby determined by minimizing the error metric function. This method can simultaneously recover the elasticity parameters of multiple regions of soft bodies using Finite Element Method-based simulation (of either linear or nonlinear materials undergoing large deformation) and particle-swarm optimization methods. I demonstrate the effectiveness of this approach on real-time interaction with virtual organs in patient-specific surgical simulation, using parameters acquired from low-resolution medical images. With the recovered elasticity parameters and the age of the prostate cancer patients as features, I build a cancer grading and staging classifier. The classifier achieves up to 91% for predicting cancer T-Stage and 88% for predicting Gleason score. To recover the mechanical properties of soft bodies from a video, I propose a method which couples statistical graphical model with FEM simulation. Using this method, I can recover the material properties of a soft ball from a high-speed camera video that captures the motion of the ball. Furthermore, I extend the material recovery framework to fabric material identification. I propose a novel method for garment material extraction from a single-view image and a learning based cloth material recovery method from a video recording the motion of the cloth. Most recent garment capturing techniques rely on acquiring multiple views of clothing, which may not always be readily available, especially in the case of pre-existing photographs from the web. As an alternative, I propose a method that can compute a 3D model of a human body and its outfit from a single photograph with little human interaction. My proposed learning-based cloth material type recovery method exploits simulated data-set and deep neural network. I demonstrate the effectiveness of my algorithms by re-purposing the reconstructed garments for virtual try-on, garment transfer, and cloth animation on digital characters. With the recovered mechanical properties, one can construct a virtual world with soft objects exhibiting real-world behaviors.Doctor of Philosoph

Automatic Construction of Immobilisation Masks for use in Radiotherapy Treatment of Head-and-Neck Cancer

Current clinical practice for immobilisation for patients undergoing brain or head and neck radiotherapy is normally achieved using Perspex or thermoplastic shells that are moulded to patient anatomy during a visit to the mould room. The shells are “made to measure” and the methods currently employed to make them require patients to visit the mould room. The mould room visit can be depressing and some patients find this process particularly unpleasant. In some cases, as treatment progresses, the tumour may shrink and therefore there may be a need for a further mould room visits. With modern manufacturing and rapid prototyping comes the possibility of determining the shape of the shells from the CT-scan of the patient directly, alleviating the need for making physical moulds from the patients’ head. However, extracting such a surface model remains a challenge and is the focus of this thesis. The aim of the work in this thesis is to develop an automatic pipeline capable of creating physical models of immobilisation shells directly from CT scans. The work includes an investigation of a number of image segmentation techniques to segment the skin/air interface from CT images. To enable the developed pipeline to be quantitatively evaluated we compared the 3D model generated from the CT data to ground truth obtained by 3D laser scans of masks produced by the mould room in the frame of a clinical trial. This involved automatically removing image artefacts due to fixations from CT imagery, automatic alignment (registration) between two meshes, measuring the degree of similarity between two 3D volumes, and automatic approach to evaluate the accuracy of segmentation. This thesis has raised and addressed many challenges within this pipeline. We have examined and evaluated each stage of the pipeline separately. The outcomes of the pipeline as a whole are currently being evaluated by a clinical trial (IRAS ID:209119, REC Ref.:16/YH/0485). Early results from the trial indicate that the approach is viable

Development of registration methods for cardiovascular anatomy and function using advanced 3T MRI, 320-slice CT and PET imaging

Different medical imaging modalities provide complementary anatomical and functional information. One increasingly important use of such information is in the clinical management of cardiovascular disease. Multi-modality data is helping improve diagnosis accuracy, and individualize treatment. The Clinical Research Imaging Centre at the University of Edinburgh, has been involved in a number of cardiovascular clinical trials using longitudinal computed tomography (CT) and multi-parametric magnetic resonance (MR) imaging. The critical image processing technique that combines the information from all these different datasets is known as image registration, which is the topic of this thesis. Image registration, especially multi-modality and multi-parametric registration, remains a challenging field in medical image analysis. The new registration methods described in this work were all developed in response to genuine challenges in on-going clinical studies. These methods have been evaluated using data from these studies. In order to gain an insight into the building blocks of image registration methods, the thesis begins with a comprehensive literature review of state-of-the-art algorithms. This is followed by a description of the first registration method I developed to help track inflammation in aortic abdominal aneurysms. It registers multi-modality and multi-parametric images, with new contrast agents. The registration framework uses a semi-automatically generated region of interest around the aorta. The aorta is aligned based on a combination of the centres of the regions of interest and intensity matching. The method achieved sub-voxel accuracy. The second clinical study involved cardiac data. The first framework failed to register many of these datasets, because the cardiac data suffers from a common artefact of magnetic resonance images, namely intensity inhomogeneity. Thus I developed a new preprocessing technique that is able to correct the artefacts in the functional data using data from the anatomical scans. The registration framework, with this preprocessing step and new particle swarm optimizer, achieved significantly improved registration results on the cardiac data, and was validated quantitatively using neuro images from a clinical study of neonates. Although on average the new framework achieved accurate results, when processing data corrupted by severe artefacts and noise, premature convergence of the optimizer is still a common problem. To overcome this, I invented a new optimization method, that achieves more robust convergence by encoding prior knowledge of registration. The registration results from this new registration-oriented optimizer are more accurate than other general-purpose particle swarm optimization methods commonly applied to registration problems. In summary, this thesis describes a series of novel developments to an image registration framework, aimed to improve accuracy, robustness and speed. The resulting registration framework was applied to, and validated by, different types of images taken from several ongoing clinical trials. In the future, this framework could be extended to include more diverse transformation models, aided by new machine learning techniques. It may also be applied to the registration of other types and modalities of imaging data

Dense RGB-D SLAM and object localisation for robotics and industrial applications

Dense reconstruction and object localisation are two critical steps in robotic and industrial applications. The former entails a joint estimation of camera egomotion and the structure of the surrounding environment, also known as Simultaneous Localisation and Mapping (SLAM), and the latter aims to locate the object in the reconstructed scenes. This thesis addresses the challenges of dense SLAM with RGB-D cameras and object localisation towards robotic and industrial applications. Camera drift is an essential issue in camera egomotion estimation. Due to the accumulated error in camera pose estimation, the estimated camera trajectory is inaccurate, and the reconstruction of the environment is inconsistent. This thesis analyses camera drift in SLAM under the probabilistic inference framework and proposes an online map fusion strategy with standard deviation estimation based on frame-to-model camera tracking. The camera pose is estimated by aligning the input image with the global map model, and the global map merges the information in the images by weighted fusion with standard deviation modelling. In addition, a pre-screening step is applied before map fusion to preclude the adverse effect of accumulated errors and noises on camera egomotion estimation. Experimental results indicated that the proposed method mitigates camera drift and improves the global consistency of camera trajectories. Another critical challenge for dense RGB-D SLAM in industrial scenarios is to handle mechanical and plastic components that usually have reflective and shiny surfaces. Photometric alignment in frame-to-model camera tracking tends to fail on such objects due to the inconsistency in intensity patterns of the images and the global map model. This thesis addresses this problem and proposes RSO-SLAM, namely a SLAM approach to reflective and shiny object reconstruction. RSO-SLAM adopts frame-to-model camera tracking and combines local photometric alignment and global geometric registration. This study revealed the effectiveness and excellent performance of the proposed RSO-SLAM on both plastic and metallic objects. In addition, a case study involving the cover of a electric vehicle battery with metallic surface demonstrated the superior performance of the RSO-SLAM approach in the reconstruction of a common industrial product. With the reconstructed point cloud model of the object, the problem of object localisation is tackled as point cloud registration in the thesis. Iterative Closest Point (ICP) is arguably the best-known method for point cloud registration, but it is susceptible to sub-optimal convergence due to the multimodal solution space. This thesis proposes the Bees Algorithm (BA) enhanced with the Singular Value Decomposition (SVD) procedure for point cloud registration. SVD accelerates the speed of the local search of the BA, helping the algorithm to rapidly identify the local optima. It also enhances the precision of the obtained solutions. At the same time, the global outlook of the BA ensures adequate exploration of the whole solution space. Experimental results demonstrated the remarkable performance of the SVD-enhanced BA in terms of consistency and precision. Additional tests on noisy datasets demonstrated the robustness of the proposed procedure to imprecision in the models

An Evaluation of Performance Enhancements to Particle Swarm Optimisation on Real-World Data

Swarm Computation is a relatively new optimisation paradigm. The basic premise is to model the collective behaviour of self-organised natural phenomena such as swarms, flocks and shoals, in order to solve optimisation problems. Particle Swarm Optimisation (PSO) is a type of swarm computation inspired by bird flocks or swarms of bees by modelling their collective social influence as they search for optimal solutions. In many real-world applications of PSO, the algorithm is used as a data pre-processor for a neural network or similar post processing system, and is often extensively modified to suit the application. The thesis introduces techniques that allow unmodified PSO to be applied successfully to a range of problems, specifically three extensions to the basic PSO algorithm: solving optimisation problems by training a hyperspatial matrix, using a hierarchy of swarms to coordinate optimisation on several data sets simultaneously, and dynamic neighbourhood selection in swarms. Rather than working directly with candidate solutions to an optimisation problem, the PSO algorithm is adapted to train a matrix of weights, to produce a solution to the problem from the inputs. The search space is abstracted from the problem data. A single PSO swarm optimises a single data set and has difficulties where the data set comprises disjoint parts (such as time series data for different days). To address this problem, we introduce a hierarchy of swarms, where each child swarm optimises one section of the data set whose gbest particle is a member of the swarm above in the hierarchy. The parent swarm(s) coordinate their children and encourage more exploration of the solution space. We show that hierarchical swarms of this type perform better than single swarm PSO optimisers on the disjoint data sets used. PSO relies on interaction between particles within a neighbourhood to find good solutions. In many PSO variants, possible interactions are arbitrary and fixed on initialisation. Our third contribution is a dynamic neighbourhood selection: particles can modify their neighbourhood, based on the success of the candidate neighbour particle. As PSO is intended to reflect the social interaction of agents, this change significantly increases the ability of the swarm to find optimal solutions. Applied to real-world medical and cosmological data, this modification is and shows improvements over standard PSO approaches with fixed neighbourhoods

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

Automated liver tissues delineation based on machine learning techniques: A survey, current trends and future orientations

There is no denying how machine learning and computer vision have grown in the recent years. Their highest advantages lie within their automation, suitability, and ability to generate astounding results in a matter of seconds in a reproducible manner. This is aided by the ubiquitous advancements reached in the computing capabilities of current graphical processing units and the highly efficient implementation of such techniques. Hence, in this paper, we survey the key studies that are published between 2014 and 2020, showcasing the different machine learning algorithms researchers have used to segment the liver, hepatic-tumors, and hepatic-vasculature structures. We divide the surveyed studies based on the tissue of interest (hepatic-parenchyma, hepatic-tumors, or hepatic-vessels), highlighting the studies that tackle more than one task simultaneously. Additionally, the machine learning algorithms are classified as either supervised or unsupervised, and further partitioned if the amount of works that fall under a certain scheme is significant. Moreover, different datasets and challenges found in literature and websites, containing masks of the aforementioned tissues, are thoroughly discussed, highlighting the organizers original contributions, and those of other researchers. Also, the metrics that are used excessively in literature are mentioned in our review stressing their relevancy to the task at hand. Finally, critical challenges and future directions are emphasized for innovative researchers to tackle, exposing gaps that need addressing such as the scarcity of many studies on the vessels segmentation challenge, and why their absence needs to be dealt with in an accelerated manner.Comment: 41 pages, 4 figures, 13 equations, 1 table. A review paper on liver tissues segmentation based on automated ML-based technique