Texture and Colour in Image Analysis

Research in colour and texture has experienced major changes in the last few years. This book presents some recent advances in the field, specifically in the theory and applications of colour texture analysis. This volume also features benchmarks, comparative evaluations and reviews

Organising and structuring a visual diary using visual interest point detectors

As wearable cameras become more popular, researchers are increasingly focusing on novel applications to manage the large volume of data these devices produce. One such application is the construction of a Visual Diary from an individual’s photographs. Microsoft’s SenseCam, a device designed to passively record a Visual Diary and cover a typical day of the user wearing the camera, is an example of one such device. The vast quantity of images generated by these devices means that the management and organisation of these collections is not a trivial matter. We believe wearable cameras, such as SenseCam, will become more popular in the future and the management of the volume of data generated by these devices is a key issue. Although there is a significant volume of work in the literature in the object detection and recognition and scene classification fields, there is little work in the area of setting detection. Furthermore, few authors have examined the issues involved in analysing extremely large image collections (like a Visual Diary) gathered over a long period of time. An algorithm developed for setting detection should be capable of clustering images captured at the same real world locations (e.g. in the dining room at home, in front of the computer in the office, in the park, etc.). This requires the selection and implementation of suitable methods to identify visually similar backgrounds in images using their visual features. We present a number of approaches to setting detection based on the extraction of visual interest point detectors from the images. We also analyse the performance of two of the most popular descriptors - Scale Invariant Feature Transform (SIFT) and Speeded Up Robust Features (SURF).We present an implementation of a Visual Diary application and evaluate its performance via a series of user experiments. Finally, we also outline some techniques to allow the Visual Diary to automatically detect new settings, to scale as the image collection continues to grow substantially over time, and to allow the user to generate a personalised summary of their data

Machine Learning

Machine Learning can be defined in various ways related to a scientific domain concerned with the design and development of theoretical and implementation tools that allow building systems with some Human Like intelligent behavior. Machine learning addresses more specifically the ability to improve automatically through experience

Automatic Segmentation of Cells of Different Types in Fluorescence Microscopy Images

Recognition of different cell compartments, types of cells, and their interactions is a critical aspect of quantitative cell biology. This provides a valuable insight for understanding cellular and subcellular interactions and mechanisms of biological processes, such as cancer cell dissemination, organ development and wound healing. Quantitative analysis of cell images is also the mainstay of numerous clinical diagnostic and grading procedures, for example in cancer, immunological, infectious, heart and lung disease. Computer automation of cellular biological samples quantification requires segmenting different cellular and sub-cellular structures in microscopy images. However, automating this problem has proven to be non-trivial, and requires solving multi-class image segmentation tasks that are challenging owing to the high similarity of objects from different classes and irregularly shaped structures. This thesis focuses on the development and application of probabilistic graphical models to multi-class cell segmentation. Graphical models can improve the segmentation accuracy by their ability to exploit prior knowledge and model inter-class dependencies. Directed acyclic graphs, such as trees have been widely used to model top-down statistical dependencies as a prior for improved image segmentation. However, using trees, a few inter-class constraints can be captured. To overcome this limitation, polytree graphical models are proposed in this thesis that capture label proximity relations more naturally compared to tree-based approaches. Polytrees can effectively impose the prior knowledge on the inclusion of different classes by capturing both same-level and across-level dependencies. A novel recursive mechanism based on two-pass message passing is developed to efficiently calculate closed form posteriors of graph nodes on polytrees. Furthermore, since an accurate and sufficiently large ground truth is not always available for training segmentation algorithms, a weakly supervised framework is developed to employ polytrees for multi-class segmentation that reduces the need for training with the aid of modeling the prior knowledge during segmentation. Generating a hierarchical graph for the superpixels in the image, labels of nodes are inferred through a novel efficient message-passing algorithm and the model parameters are optimized with Expectation Maximization (EM). Results of evaluation on the segmentation of simulated data and multiple publicly available fluorescence microscopy datasets indicate the outperformance of the proposed method compared to state-of-the-art. The proposed method has also been assessed in predicting the possible segmentation error and has been shown to outperform trees. This can pave the way to calculate uncertainty measures on the resulting segmentation and guide subsequent segmentation refinement, which can be useful in the development of an interactive segmentation framework

A picture is worth a thousand words : content-based image retrieval techniques

In my dissertation I investigate techniques for improving the state of the art in content-based image retrieval. To place my work into context, I highlight the current trends and challenges in my field by analyzing over 200 recent articles. Next, I propose a novel paradigm called __artificial imagination__, which gives the retrieval system the power to imagine and think along with the user in terms of what she is looking for. I then introduce a new user interface for visualizing and exploring image collections, empowering the user to navigate large collections based on her own needs and preferences, while simultaneously providing her with an accurate sense of what the database has to offer. In the later chapters I present work dealing with millions of images and focus in particular on high-performance techniques that minimize memory and computational use for both near-duplicate image detection and web search. Finally, I show early work on a scene completion-based image retrieval engine, which synthesizes realistic imagery that matches what the user has in mind.LEI Universiteit LeidenNWOImagin

Machine learning for particle identification in the LHCb detector

LHCb experiment is a specialised b-physics experiment at the Large Hadron Collider at CERN. It has a broad physics program with the primary objective being the search for CP violations that would explain the matter-antimatter asymmetry of the Universe. LHCb studies very rare phenomena, making it necessary to process millions of collision events per second to gather enough data in a reasonable time frame. Thus software and data analysis tools are essential for the success of the experiment. Particle identification (PID) is a crucial ingredient of most of the LHCb results. The quality of the particle identification depends a lot on the data processing algorithms. This dissertation aims to leverage the recent advances in machine learning field to improve the PID at LHCb. The thesis contribution consists of four essential parts related to LHCb internal projects. Muon identification aims to quickly separate muons from the other charged particles using only information from the Muon subsystem. The second contribution is a method that takes into account a priori information on label noise and improves the accuracy of a machine learning model for classification of this data. Such data are common in high-energy physics and, in particular, is used to develop the data-driven muon identification methods. Global PID combines information from different subdetectors into a single set of PID variables. Cherenkov detector fast simulation aims to improve the speed of the PID variables simulation in Monte-Carlo

Distance-based methods for the analysis of Next-Generation sequencing data

Die Analyse von NGS Daten ist ein zentraler Aspekt der modernen genomischen Forschung. Bei der Extraktion von Daten aus den beiden am häufigsten verwendeten Quellorganismen bestehen jedoch vielfältige Problemstellungen. Im ersten Kapitel wird ein neuartiger Ansatz vorgestellt welcher einen Abstand zwischen Krebszellinienkulturen auf Grundlage ihrer kleinen genomischen Varianten bestimmt um die Kulturen zu identifizieren. Eine Voll-Exom sequenzierte Kultur wird durch paarweise Vergleiche zu Referenzdatensätzen identifiziert so ein gemessener Abstand geringer ist als dies bei nicht verwandten Kulturen zu erwarten wäre. Die Wirksamkeit der Methode wurde verifiziert, jedoch verbleiben Einschränkung da nur das Sequenzierformat des Voll-Exoms unterstützt wird. Daher wird im zweiten Kapitel eine publizierte Modifikation des Ansatzes vorgestellt welcher die Unterstützung der weitläufig genutzten Bulk RNA sowie der Panel-Sequenzierung ermöglicht. Die Ausweitung der Technologiebasis führt jedoch zu einer Verstärkung von Störeffekten welche zu Verletzungen der mathematischen Konditionen einer Abstandsmetrik führen. Daher werden die entstandenen Verletzungen durch statistische Verfahren zuerst quantifiziert und danach durch dynamische Schwellwertanpassungen erfolgreich kompensiert. Das dritte Kapitel stellt eine neuartige Daten-Aufwertungsmethode (Data-Augmentation) vor welche das Trainieren von maschinellen Lernmodellen in Abwesenheit von neoplastischen Trainingsdaten ermöglicht. Ein abstraktes Abstandsmaß wird zwischen neoplastischen Entitäten sowie Entitäten gesundem Ursprungs mittels einer transkriptomischen Dekonvolution hergestellt. Die Ausgabe der Dekonvolution erlaubt dann das effektive Vorhersagen von klinischen Eigenschaften von seltenen jedoch biologisch vielfältigen Krebsarten wobei die prädiktive Kraft des Verfahrens der des etablierten Goldstandard ebenbürtig ist.The analysis of NGS data is a central aspect of modern Molecular Genetics and Oncology. The first scientific contribution is the development of a method which identifies Whole-exome-sequenced CCL via the quantification of a distance between their sets of small genomic variants. A distinguishing aspect of the method is that it was designed for the computer-based identification of NGS-sequenced CCL. An identification of an unknown CCL occurs when its abstract distance to a known CCL is smaller than is expected due to chance. The method performed favorably during benchmarks but only supported the Whole-exome-sequencing technology. The second contribution therefore extended the identification method by additionally supporting the Bulk mRNA-sequencing technology and Panel-sequencing format. However, the technological extension incurred predictive biases which detrimentally affected the quantification of abstract distances. Hence, statistical methods were introduced to quantify and compensate for confounding factors. The method revealed a heterogeneity-robust benchmark performance at the trade-off of a slightly reduced sensitivity compared to the Whole-exome-sequencing method. The third contribution is a method which trains Machine-Learning models for rare and diverse cancer types. Machine-Learning models are subsequently trained on these distances to predict clinically relevant characteristics. The performance of such-trained models was comparable to that of models trained on both the substituted neoplastic data and the gold-standard biomarker Ki-67. No proliferation rate-indicative features were utilized to predict clinical characteristics which is why the method can complement the proliferation rate-oriented pathological assessment of biopsies. The thesis revealed that the quantification of an abstract distance can address sources of erroneous NGS data analysis