Ensemble classification and signal image processing for genus Gyrodactylus (Monogenea)

This thesis presents an investigation into Gyrodactylus species recognition, making use of machine learning classification and feature selection techniques, and explores image feature extraction to demonstrate proof of concept for an envisaged rapid, consistent and secure initial identification of pathogens by field workers and non-expert users. The design of the proposed cognitively inspired framework is able to provide confident discrimination recognition from its non-pathogenic congeners, which is sought in order to assist diagnostics during periods of a suspected outbreak. Accurate identification of pathogens is a key to their control in an aquaculture context and the monogenean worm genus Gyrodactylus provides an ideal test-bed for the selected techniques. In the proposed algorithm, the concept of classification using a single model is extended to include more than one model. In classifying multiple species of Gyrodactylus, experiments using 557 specimens of nine different species, two classifiers and three feature sets were performed. To combine these models, an ensemble based majority voting approach has been adopted. Experimental results with a database of Gyrodactylus species show the superior performance of the ensemble system. Comparison with single classification approaches indicates that the proposed framework produces a marked improvement in classification performance. The second contribution of this thesis is the exploration of image processing techniques. Active Shape Model (ASM) and Complex Network methods are applied to images of the attachment hooks of several species of Gyrodactylus to classify each species according to their true species type. ASM is used to provide landmark points to segment the contour of the image, while the Complex Network model is used to extract the information from the contour of an image. The current system aims to confidently classify species, which is notifiable pathogen of Atlantic salmon, to their true class with high degree of accuracy. Finally, some concluding remarks are made along with proposal for future work

A neuro-genetic hybrid approach to automatic identification of plant leaves

Plants are essential for the existence of most living things on this planet. Plants are used for providing food, shelter, and medicine. The ability to identify plants is very important for several applications, including conservation of endangered plant species, rehabilitation of lands after mining activities and differentiating crop plants from weeds. In recent times, many researchers have made attempts to develop automated plant species recognition systems. However, the current computer-based plants recognition systems have limitations as some plants are naturally complex, thus it is difficult to extract and represent their features. Further, natural differences of features within the same plant and similarities between plants of different species cause problems in classification. This thesis developed a novel hybrid intelligent system based on a neuro-genetic model for automatic recognition of plants using leaf image analysis based on novel approach of combining several image descriptors with Cellular Neural Networks (CNN), Genetic Algorithm (GA), and Probabilistic Neural Networks (PNN) to address classification challenges in plant computer-based plant species identification using the images of plant leaves. A GA-based feature selection module was developed to select the best of these leaf features. Particle Swam Optimization (PSO) and Principal Component Analysis (PCA) were also used sideways for comparison and to provide rigorous feature selection and analysis. Statistical analysis using ANOVA and correlation techniques confirmed the effectiveness of the GA-based and PSO-based techniques as there were no redundant features, since the subset of features selected by both techniques correlated well. The number of principal components (PC) from the past were selected by conventional method associated with PCA. However, in this study, GA was used to select a minimum number of PC from the original PC space. This reduced computational cost with respect to time and increased the accuracy of the classifier used. The algebraic nature of the GA’s fitness function ensures good performance of the GA. Furthermore, GA was also used to optimize the parameters of a CNN (CNN for image segmentation) and then uniquely combined with PNN to improve and stabilize the performance of the classification system. The CNN (being an ordinary differential equation (ODE)) was solved using Runge-Kutta 4th order algorithm in order to minimize descritisation errors associated with edge detection. This study involved the extraction of 112 features from the images of plant species found in the Flavia dataset (publically available) using MATLAB programming environment. These features include Zernike Moments (20 ZMs), Fourier Descriptors (21 FDs), Legendre Moments (20 LMs), Hu 7 Moments (7 Hu7Ms), Texture Properties (22 TP) , Geometrical Properties (10 GP), and Colour features (12 CF). With the use of GA, only 14 features were finally selected for optimal accuracy. The PNN was genetically optimized to ensure optimal accuracy since it is not the best practise to fix the tunning parameters for the PNN arbitrarily. Two separate GA algorithms were implemented to optimize the PNN, that is, the GA provided by MATLAB Optimization Toolbox (GA1) and a separately implemented GA (GA2). The best chromosome (PNN spread) for GA1 was 0.035 with associated classification accuracy of 91.3740% while a spread value of 0.06 was obtained from GA2 giving rise to improved classification accuracy of 92.62%. The PNN-based classifier used in this study was benchmarked against other classifiers such as Multi-layer perceptron (MLP), K Nearest Neigbhour (kNN), Naive Bayes Classifier (NBC), Radial Basis Function (RBF), Ensemble classifiers (Adaboost). The best candidate among these classifiers was the genetically optimized PNN. Some computational theoretic properties on PNN are also presented

GuavaNet: A deep neural network architecture for automatic sensory evaluation to predict degree of acceptability for Guava by a consumer

This thesis is divided into two parts:Part I: Analysis of Fruits, Vegetables, Cheese and Fish based on Image Processing using Computer Vision and Deep Learning: A Review. It consists of a comprehensive review of image processing, computer vision and deep learning techniques applied to carry out analysis of fruits, vegetables, cheese and fish.This part also serves as a literature review for Part II.Part II: GuavaNet: A deep neural network architecture for automatic sensory evaluation to predict degree of acceptability for Guava by a consumer. This part introduces to an end-to-end deep neural network architecture that can predict the degree of acceptability by the consumer for a guava based on sensory evaluation

Machine learning-based automated segmentation with a feedback loop for 3D synchrotron micro-CT

Die Entwicklung von Synchrotronlichtquellen der dritten Generation hat die Grundlage für die Untersuchung der 3D-Struktur opaker Proben mit einer Auflösung im Mikrometerbereich und höher geschaffen. Dies führte zur Entwicklung der Röntgen-Synchrotron-Mikro-Computertomographie, welche die Schaffung von Bildgebungseinrichtungen zur Untersuchung von Proben verschiedenster Art förderte, z.B. von Modellorganismen, um die Physiologie komplexer lebender Systeme besser zu verstehen. Die Entwicklung moderner Steuerungssysteme und Robotik ermöglichte die vollständige Automatisierung der Röntgenbildgebungsexperimente und die Kalibrierung der Parameter des Versuchsaufbaus während des Betriebs. Die Weiterentwicklung der digitalen Detektorsysteme führte zu Verbesserungen der Auflösung, des Dynamikbereichs, der Empfindlichkeit und anderer wesentlicher Eigenschaften. Diese Verbesserungen führten zu einer beträchtlichen Steigerung des Durchsatzes des Bildgebungsprozesses, aber auf der anderen Seite begannen die Experimente eine wesentlich größere Datenmenge von bis zu Dutzenden von Terabyte zu generieren, welche anschließend manuell verarbeitet wurden. Somit ebneten diese technischen Fortschritte den Weg für die Durchführung effizienterer Hochdurchsatzexperimente zur Untersuchung einer großen Anzahl von Proben, welche Datensätze von besserer Qualität produzierten. In der wissenschaftlichen Gemeinschaft besteht daher ein hoher Bedarf an einem effizienten, automatisierten Workflow für die Röntgendatenanalyse, welcher eine solche Datenlast bewältigen und wertvolle Erkenntnisse für die Fachexperten liefern kann. Die bestehenden Lösungen für einen solchen Workflow sind nicht direkt auf Hochdurchsatzexperimente anwendbar, da sie für Ad-hoc-Szenarien im Bereich der medizinischen Bildgebung entwickelt wurden. Daher sind sie nicht für Hochdurchsatzdatenströme optimiert und auch nicht in der Lage, die hierarchische Beschaffenheit von Proben zu nutzen. Die wichtigsten Beiträge der vorliegenden Arbeit sind ein neuer automatisierter Analyse-Workflow, der für die effiziente Verarbeitung heterogener Röntgendatensätze hierarchischer Natur geeignet ist. Der entwickelte Workflow basiert auf verbesserten Methoden zur Datenvorverarbeitung, Registrierung, Lokalisierung und Segmentierung. Jede Phase eines Arbeitsablaufs, die eine Trainingsphase beinhaltet, kann automatisch feinabgestimmt werden, um die besten Hyperparameter für den spezifischen Datensatz zu finden. Für die Analyse von Faserstrukturen in Proben wurde eine neue, hochgradig parallelisierbare 3D-Orientierungsanalysemethode entwickelt, die auf einem neuartigen Konzept der emittierenden Strahlen basiert und eine präzisere morphologische Analyse ermöglicht. Alle entwickelten Methoden wurden gründlich an synthetischen Datensätzen validiert, um ihre Anwendbarkeit unter verschiedenen Abbildungsbedingungen quantitativ zu bewerten. Es wurde gezeigt, dass der Workflow in der Lage ist, eine Reihe von Datensätzen ähnlicher Art zu verarbeiten. Darüber hinaus werden die effizienten CPU/GPU-Implementierungen des entwickelten Workflows und der Methoden vorgestellt und der Gemeinschaft als Module für die Sprache Python zur Verfügung gestellt. Der entwickelte automatisierte Analyse-Workflow wurde erfolgreich für Mikro-CT-Datensätze angewandt, die in Hochdurchsatzröntgenexperimenten im Bereich der Entwicklungsbiologie und Materialwissenschaft gewonnen wurden. Insbesondere wurde dieser Arbeitsablauf für die Analyse der Medaka-Fisch-Datensätze angewandt, was eine automatisierte Segmentierung und anschließende morphologische Analyse von Gehirn, Leber, Kopfnephronen und Herz ermöglichte. Darüber hinaus wurde die entwickelte Methode der 3D-Orientierungsanalyse bei der morphologischen Analyse von Polymergerüst-Datensätzen eingesetzt, um einen Herstellungsprozess in Richtung wünschenswerter Eigenschaften zu lenken

Image processing techniques to identify predatory birds in aquacultural settings

Bird predation is a major problem in aquaculture. A novel method for dispersing birds is the use of a vehicle that can sense and chase birds. Image recognition software can improve their efficiency in chasing birds. Three recognition techniques were tested to identify birds 1) image morphology 2) artificial neural networks, and 3) template matching have been tested. A study was conducted on three species of birds 1) pelicans, 2) egrets, and 3) cormorants. Images were divided into 3 types 1) Type 1, 2) Type 2, and 3) Type 3 depending upon difficulty to separate from the others in the images. These types were clear, medium clear and unclear respectively. Image morphology resulted in 57.1% to 97.7%, 73.0% to 100%, and 46.1% to 95.5% correct classification rates (CCR) respectively on images of pelicans, cormorants and egrets before size thresholding. The artificial neural network model achieved 100% CCR while testing type 1 images and its classification success ranged from 63.5% to 70.0%, and 57.1% to 67.7% while testing type 2 and type 3 images respectively. The template matching algorithm succeeded in classifying 90%, 80%, and 60% of Type 1, Type 2 and Type 3 images of pelicans and egrets. This technique recognized 80%, 91.7%, and 80% of Type 1, Type 2, and Type 3 images of cormorants. We developed a real time recognition algorithm that could capture images from a camera, process them, and send output to the autonomous boat in regular intervals of time. Future research will focus on testing the recognition algorithms in natural or aquacultural settings on autonomous boats

Image Processing and Analysis for Preclinical and Clinical Applications

Radiomics is one of the most successful branches of research in the field of image processing and analysis, as it provides valuable quantitative information for the personalized medicine. It has the potential to discover features of the disease that cannot be appreciated with the naked eye in both preclinical and clinical studies. In general, all quantitative approaches based on biomedical images, such as positron emission tomography (PET), computed tomography (CT) and magnetic resonance imaging (MRI), have a positive clinical impact in the detection of biological processes and diseases as well as in predicting response to treatment. This Special Issue, “Image Processing and Analysis for Preclinical and Clinical Applications”, addresses some gaps in this field to improve the quality of research in the clinical and preclinical environment. It consists of fourteen peer-reviewed papers covering a range of topics and applications related to biomedical image processing and analysis

Offshore oil spill detection using synthetic aperture radar

Among the different types of marine pollution, oil spill has been considered as a major threat to the sea ecosystems. The source of the oil pollution can be located on the mainland or directly at sea. The sources of oil pollution at sea are discharges coming from ships, offshore platforms or natural seepage from sea bed. Oil pollution from sea-based sources can be accidental or deliberate. Different sensors to detect and monitor oil spills could be onboard vessels, aircraft, or satellites. Vessels equipped with specialised radars, can detect oil at sea but they can cover a very limited area. One of the established ways to monitor sea-based oil pollution is the use of satellites equipped with Synthetic Aperture Radar (SAR).The aim of the work presented in this thesis is to identify optimum set of feature extracted parameters and implement methods at various stages for oil spill detection from Synthetic Aperture Radar (SAR) imagery. More than 200 images of ERS-2, ENVSAT and RADARSAT 2 SAR sensor have been used to assess proposed feature vector for oil spill detection methodology, which involves three stages: segmentation for dark spot detection, feature extraction and classification of feature vector. Unfortunately oil spill is not only the phenomenon that can create a dark spot in SAR imagery. There are several others meteorological and oceanographic and wind induced phenomena which may lead to a dark spot in SAR imagery. Therefore, these dark objects also appear similar to the dark spot due to oil spill and are called as look-alikes. These look-alikes thus cause difficulty in detecting oil spill spots as their primary characteristic similar to oil spill spots. To get over this difficulty, feature extraction becomes important; a stage which may involve selection of appropriate feature extraction parameters. The main objective of this dissertation is to identify the optimum feature vector in order to segregate oil spill and ‘look-alike’ spots. A total of 44 Feature extracted parameters have been studied. For segmentation, four methods; based on edge detection, adaptive theresholding, artificial neural network (ANN) segmentation and the other on contrast split segmentation have been implemented. Spot features are extracted from both the dark spots themselves and their surroundings. Classification stage was performed using two different classification techniques, first one is based on ANN and the other based on a two-stage processing that combines classification tree analysis and fuzzy logic. A modified feature vector, including both new and improved features, is suggested for better description of different types of dark spots. An ANN classifier using full spectrum of feature parameters has also been developed and evaluated. The implemented methodology appears promising in detecting dark spots and discriminating oil spills from look-alikes and processing time is well below any operational service requirements

Intelligent X-ray imaging inspection system for the food industry.

The inspection process of a product is an important stage of a modern production factory. This research presents a generic X-ray imaging inspection system with application for the detection of foreign bodies in a meat product for the food industry. The most important modules in the system are the image processing module and the high-level detection system. This research discusses the use of neural networks for image processing and fuzzy-logic for the detection of potential foreign bodies found in x-ray images of chicken breast meat after the de-boning process. The meat product is passed under a solid-state x-ray sensor that acquires a dual-band two-dimensional image of the meat (a low- and a high energy image). A series of image processing operations are applied to the acquired image (pre-processing, noise removal, contrast enhancement). The most important step of the image processing is the segmentation of the image into meaningful objects. The segmentation task is a difficult one due to the lack of clarity of the acquired X-ray images and the resulting segmented image represents not only correctly identified foreign bodies but also areas caused by overlapping muscle regions in the meat which appear very similar to foreign bodies in the resulting x-ray image. A Hopfield neural network architecture was proposed for the segmentation of a X-ray dual-band image. A number of image processing measurements were made on each object (geometrical and grey-level based statistical features) and these features were used as the input into a fuzzy logic based high-level detection system whose function was to differentiate between bones and non-bone segmented regions. The results show that system's performance is considerably improved over non-fuzzy or crisp methods. Possible noise affecting the system is also investigated. The proposed system proved to be robust and flexible while achieving a high level of performance. Furthermore, it is possible to use the same approach when analysing images from other applications areas from the automotive industry to medicine

Intelligent X-ray imaging inspection system for the food industry.

The inspection process of a product is an important stage of a modern production factory. This research presents a generic X-ray imaging inspection system with application for the detection of foreign bodies in a meat product for the food industry. The most important modules in the system are the image processing module and the high-level detection system. This research discusses the use of neural networks for image processing and fuzzy-logic for the detection of potential foreign bodies found in x-ray images of chicken breast meat after the de-boning process. The meat product is passed under a solid-state x-ray sensor that acquires a dual-band two-dimensional image of the meat (a low- and a high energy image). A series of image processing operations are applied to the acquired image (pre-processing, noise removal, contrast enhancement). The most important step of the image processing is the segmentation of the image into meaningful objects. The segmentation task is a difficult one due to the lack of clarity of the acquired X-ray images and the resulting segmented image represents not only correctly identified foreign bodies but also areas caused by overlapping muscle regions in the meat which appear very similar to foreign bodies in the resulting x-ray image. A Hopfield neural network architecture was proposed for the segmentation of a X-ray dual-band image. A number of image processing measurements were made on each object (geometrical and grey-level based statistical features) and these features were used as the input into a fuzzy logic based high-level detection system whose function was to differentiate between bones and non-bone segmented regions. The results show that system's performance is considerably improved over non-fuzzy or crisp methods. Possible noise affecting the system is also investigated. The proposed system proved to be robust and flexible while achieving a high level of performance. Furthermore, it is possible to use the same approach when analysing images from other applications areas from the automotive industry to medicine