Modelling Neuron Morphology: Automated Reconstruction from Microscopy Images

Understanding how the brain works is, beyond a shadow of doubt, one of the greatest challenges for modern science. Achieving a deep knowledge about the structure, function and development of the nervous system at the molecular, cellular and network levels is crucial in this attempt, as processes at all these scales are intrinsically linked with higher-order cognitive functions. The research in the various areas of neuroscience deals with advanced imaging techniques, collecting an increasing amounts of heterogeneous and complex data at different scales. Then, computational tools and neuroinformatics solutions are required in order to integrate and analyze the massive quantity of acquired information. Within this context, the development of automaticmethods and tools for the study of neuronal anatomy has a central role. The morphological properties of the soma and of the axonal and dendritic arborizations constitute a key discriminant for the neuronal phenotype and play a determinant role in network connectivity. A quantitative analysis allows the study of possible factors influencing neuronal development, the neuropathological abnormalities related to specific syndromes, the relationships between neuronal shape and function, the signal transmission and the network connectivity. Therefore, three-dimensional digital reconstructions of soma, axons and dendrites are indispensable for exploring neural networks. This thesis proposes a novel and completely automatic pipeline for neuron reconstruction with operations ranging from the detection and segmentation of the soma to the dendritic arborization tracing. The pipeline can deal with different datasets and acquisitions both at the network and at the single scale level without any user interventions or manual adjustment. We developed an ad hoc approach for the localization and segmentation of neuron bodies. Then, various methods and research lines have been investigated for the reconstruction of the whole dendritic arborization of each neuron, which is solved both in 2D and in 3D images

Biological model representation and analysis

In this thesis, we discuss solutions of phenotype description based on the microscopy image analysis to deal with biological problems both in 2D and 3D space. Our description of patterns goes beyond conventional features and helps to visualize the unseen in feature dataset. These solutions share several common processes which are based on similar principles. Furthermore, we notice that advanced features and classier strategies can help us improve the performance of the solutions. The biological problems that we have studied include the endocytosis routing using high-throughput screening in 2D and time and 3D geometrical representation from biological structures.China Scholarship CouncilComputer Systems, Imagery and Medi

Shape analysis and description based on the isometric invariances of topological skeletonization

ilustracionesIn this dissertation, we explore the problem of how to describe the shape of an object in 2D and 3D with a set of features that are invariant to isometric transformations. We focus to based our approach on the well-known Medial Axis Transform and its topological properties. We aim to study two problems. The first is how to find a shape representation of a segmented object that exhibits rotation, translation, and reflection invariance. The second problem is how to build a machine learning pipeline that uses the isometric invariance of the shape representation to do both classification and retrieval. Our proposed solution demonstrates competitive results compared to state-of-the-art approaches. We based our shape representation on the medial axis transform (MAT), sometimes called the topological skeleton. Accepted and well-studied properties of the medial axis include: homotopy preservation, rotation invariance, mediality, one pixel thickness, and the ability to fully reconstruct the object. These properties make the MAT a suitable input to create shape features; however, several problems arise because not all skeletonization methods satisfy all the above-mentioned properties at the same time. In general, skeletons based on thinning approaches preserve topology but are noise sensitive and do not allow a proper reconstruction. They are also not invariant to rotations. Voronoi skeletons also preserve topology and are rotation invariant, but do not have information about the thickness of the object, making reconstruction impossible. The Voronoi skeleton is an approximation of the real skeleton. The denser the sampling of the boundary, the better the approximation; however, a denser sampling makes the Voronoi diagram more computationally expensive. In contrast, distance transform methods allow the reconstruction of the original object by providing the distance from every pixel in the skeleton to the boundary. Moreover, they exhibit an acceptable degree of the properties listed above, but noise sensitivity remains an issue. Therefore, we selected distance transform medial axis methods as our skeletonization strategy, and focused on creating a new noise-free approach to solve the contour noise problem. To effectively classify an object, or perform any other task with features based on its shape, the descriptor needs to be a normalized, compact form: $\Phi$ should map every shape $\Omega$ to the same vector space $\mathrm{R}^{n}$. This is not possible with skeletonization methods because the skeletons of different objects have different numbers of branches and different numbers of points, even when they belong to the same category. Consequently, we developed a strategy to extract features from the skeleton through the map $\Phi$, which we used as an input to a machine learning approach. After developing our method for robust skeletonization, the next step is to use such skeleton into the machine learning pipeline to classify object into previously defined categories. We developed a set of skeletal features that were used as input data to the machine learning architectures. We ran experiments on MPEG7 and ModelNet40 dataset to test our approach in both 2D and 3D. Our experiments show results comparable with the state-of-the-art in shape classification and retrieval. Our experiments also show that our pipeline and our skeletal features exhibit some degree of invariance to isometric transformations. In this study, we sought to design an isometric invariant shape descriptor through robust skeletonization enforced by a feature extraction pipeline that exploits such invariance through a machine learning methodology. We conducted a set of classification and retrieval experiments over well-known benchmarks to validate our proposed method. (Tomado de la fuente)En esta disertación se explora el problema de cómo describir la forma de un objeto en 2D y 3D con un conjunto de características que sean invariantes a transformaciones isométricas. La metodología propuesta en este documento se enfoca en la Transformada del Eje Medio (Medial Axis Transform) y sus propiedades topológicas. Nuestro objetivo es estudiar dos problemas. El primero es encontrar una representación matemática de la forma de un objeto que exhiba invarianza a las operaciones de rotación, translación y reflexión. El segundo problema es como construir un modelo de machine learning que use esas invarianzas para las tareas de clasificación y consulta de objetos a través de su forma. El método propuesto en esta tesis muestra resultados competitivos en comparación con otros métodos del estado del arte. En este trabajo basamos nuestra representación de forma en la transformada del eje medio, a veces llamada esqueleto topológico. Algunas propiedades conocidas y bien estudiadas de la transformada del eje medio son: conservación de la homotopía, invarianza a la rotación, su grosor consiste en un solo pixel (1D), y la habilidad para reconstruir el objeto original a través de ella. Estas propiedades hacen de la transformada del eje medio un punto de partida adecuado para crear características de forma. Sin embargo, en este punto surgen varios problemas dado que no todos los métodos de esqueletización satisfacen, al mismo tiempo, todas las propiedades mencionadas anteriormente. En general, los esqueletos basados en enfoques de erosión morfológica conservan la topología del objeto, pero son sensibles al ruido y no permiten una reconstrucción adecuada. Además, no son invariantes a las rotaciones. Otro método de esqueletización son los esqueletos de Voronoi. Los esqueletos de Voronoi también conservan la topología y son invariantes a la rotación, pero no tienen información sobre el grosor del objeto, lo que hace imposible su reconstrucción. Cuanto más denso sea el muestreo del contorno del objeto, mejor será la aproximación. Sin embargo, un muestreo más denso hace que el diagrama de Voronoi sea más costoso computacionalmente. Por el contrario, los métodos basados en la transformada de la distancia permiten la reconstrucción del objeto original, ya que proporcionan la distancia desde cada píxel del esqueleto hasta su punto más cercano en el contorno. Además, exhiben un grado aceptable de las propiedades enumeradas anteriormente, aunque la sensibilidad al ruido sigue siendo un problema. Por lo tanto, en este documento seleccionamos los métodos basados en la transformada de la distancia como nuestra estrategia de esqueletización, y nos enfocamos en crear un nuevo enfoque que resuelva el problema del ruido en el contorno. Para clasificar eficazmente un objeto o realizar cualquier otra tarea con características basadas en su forma, el descriptor debe ser compacto y estar normalizado: $\Phi$ debe relacionar cada forma $\Omega$ al mismo espacio vectorial $\mathrm{R}^{n}$. Esto no es posible con los métodos de esqueletización en el estado del arte, porque los esqueletos de diferentes objetos tienen diferentes números de ramas y diferentes números de puntos incluso cuando pertenecen a la misma categoría. Consecuentemente, en nuestra propuesta desarrollamos una estrategia para extraer características del esqueleto a través de la función $\Phi$, que usamos como entrada para un enfoque de aprendizaje automático. % TODO completar con resultados. Después de desarrollar nuestro método de esqueletización robusta, el siguiente paso es usar dicho esqueleto en un modelo de aprendizaje de máquina para clasificar el objeto en categorías previamente definidas. Para ello se desarrolló un conjunto de características basadas en el eje medio que se utilizaron como datos de entrada para la arquitectura de aprendizaje automático. Realizamos experimentos en los conjuntos de datos: MPEG7 y ModelNet40 para probar nuestro enfoque tanto en 2D como en 3D. Nuestros experimentos muestran resultados comparables con el estado del arte en clasificación y consulta de formas (retrieval). Nuestros experimentos también muestran que el modelo desarrollado junto con nuestras características basadas en el eje medio son invariantes a las transformaciones isométricas. (Tomado de la fuente)Beca para Doctorados Nacionales de Colciencias, convocatoria 725 de 2015DoctoradoDoctor en IngenieríaVisión por computadora y aprendizaje automátic

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

Proceedings of Abstracts Engineering and Computer Science Research Conference 2019

© 2019 The Author(s). This is an open-access work distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. For further details please see https://creativecommons.org/licenses/by/4.0/. Note: Keynote: Fluorescence visualisation to evaluate effectiveness of personal protective equipment for infection control is © 2019 Crown copyright and so is licensed under the Open Government Licence v3.0. Under this licence users are permitted to copy, publish, distribute and transmit the Information; adapt the Information; exploit the Information commercially and non-commercially for example, by combining it with other Information, or by including it in your own product or application. Where you do any of the above you must acknowledge the source of the Information in your product or application by including or linking to any attribution statement specified by the Information Provider(s) and, where possible, provide a link to this licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/This book is the record of abstracts submitted and accepted for presentation at the Inaugural Engineering and Computer Science Research Conference held 17th April 2019 at the University of Hertfordshire, Hatfield, UK. This conference is a local event aiming at bringing together the research students, staff and eminent external guests to celebrate Engineering and Computer Science Research at the University of Hertfordshire. The ECS Research Conference aims to showcase the broad landscape of research taking place in the School of Engineering and Computer Science. The 2019 conference was articulated around three topical cross-disciplinary themes: Make and Preserve the Future; Connect the People and Cities; and Protect and Care

Cued Speech Gesture Recognition: A First Prototype Based on Early Reduction

International audienceCued Speech is a specific linguistic code for hearing-impaired people. It is based on both lip reading and manual gestures. In the context of THIMP (Telephony for the Hearing-IMpaired Project), we work on automatic cued speech translation. In this paper, we only address the problem of automatic cued speech manual gesture recognition. Such a gesture recognition issue is really common from a theoretical point of view, but we approach it with respect to its particularities in order to derive an original method. This method is essentially built around a bioinspired method called early reduction. Prior to a complete analysis of each image of a sequence, the early reduction process automatically extracts a restricted number of key images which summarize the whole sequence. Only the key images are studied from a temporal point of view with lighter computation than the complete sequenc

An investigation into common challenges of 3D scene understanding in visual surveillance

Nowadays, video surveillance systems are ubiquitous. Most installations simply consist of CCTV cameras connected to a central control room and rely on human operators to interpret what they see on the screen in order to, for example, detect a crime (either during or after an event). Some modern computer vision systems aim to automate the process, at least to some degree, and various algorithms have been somewhat successful in certain limited areas. However, such systems remain inefficient in general circumstances and present real challenges yet to be solved. These challenges include the ability to recognise and ultimately predict and prevent abnormal behaviour or even reliably recognise objects, for example in order to detect left luggage or suspicious objects. This thesis first aims to study the state-of-the-art and identify the major challenges and possible requirements of future automated and semi-automated CCTV technology in the field. This thesis presents the application of a suite of 2D and highly novel 3D methodologies that go some way to overcome current limitations.The methods presented here are based on the analysis of object features directly extracted from the geometry of the scene and start with a consideration of mainly existing techniques, such as the use of lines, vanishing points (VPs) and planes, applied to real scenes. Then, an investigation is presented into the use of richer 2.5D/3D surface normal data. In all cases the aim is to combine both 2D and 3D data to obtain a better understanding of the scene, aimed ultimately at capturing what is happening within the scene in order to be able to move towards automated scene analysis. Although this thesis focuses on the widespread application of video surveillance, an example case of the railway station environment is used to represent typical real-world challenges, where the principles can be readily extended elsewhere, such as to airports, motorways, the households, shopping malls etc. The context of this research work, together with an overall presentation of existing methods used in video surveillance and their challenges are described in chapter 1.Common computer vision techniques such as VP detection, camera calibration, 3D reconstruction, segmentation etc., can be applied in an effort to extract meaning to video surveillance applications. According to the literature, these methods have been well researched and their use will be assessed in the context of current surveillance requirements in chapter 2. While existing techniques can perform well in some contexts, such as an architectural environment composed of simple geometrical elements, their robustness and performance in feature extraction and object recognition tasks is not sufficient to solve the key challenges encountered in general video surveillance context. This is largely due to issues such as variable lighting, weather conditions, and shadows and in general complexity of the real-world environment. Chapter 3 presents the research and contribution on those topics – methods to extract optimal features for a specific CCTV application – as well as their strengths and weaknesses to highlight that the proposed algorithm obtains better results than most due to its specific design.The comparison of current surveillance systems and methods from the literature has shown that 2D data are however almost constantly used for many applications. Indeed, industrial systems as well as the research community have been improving intensively 2D feature extraction methods since image analysis and Scene understanding has been of interest. The constant progress on 2D feature extraction methods throughout the years makes it almost effortless nowadays due to a large variety of techniques. Moreover, even if 2D data do not allow solving all challenges in video surveillance or other applications, they are still used as starting stages towards scene understanding and image analysis. Chapter 4 will then explore 2D feature extraction via vanishing point detection and segmentation methods. A combination of most common techniques and a novel approach will be then proposed to extract vanishing points from video surveillance environments. Moreover, segmentation techniques will be explored in the aim to determine how they can be used to complement vanishing point detection and lead towards 3D data extraction and analysis. In spite of the contribution above, 2D data is insufficient for all but the simplest applications aimed at obtaining an understanding of a scene, where the aim is for a robust detection of, say, left luggage or abnormal behaviour; without significant a priori information about the scene geometry. Therefore, more information is required in order to be able to design a more automated and intelligent algorithm to obtain richer information from the scene geometry and so a better understanding of what is happening within. This can be overcome by the use of 3D data (in addition to 2D data) allowing opportunity for object “classification” and from this to infer a map of functionality, describing feasible and unfeasible object functionality in a given environment. Chapter 5 presents how 3D data can be beneficial for this task and the various solutions investigated to recover 3D data, as well as some preliminary work towards plane extraction.It is apparent that VPs and planes give useful information about a scene’s perspective and can assist in 3D data recovery within a scene. However, neither VPs nor plane detection techniques alone allow the recovery of more complex generic object shapes - for example composed of spheres, cylinders etc - and any simple model will suffer in the presence of non-Manhattan features, e.g. introduced by the presence of an escalator. For this reason, a novel photometric stereo-based surface normal retrieval methodology is introduced to capture the 3D geometry of the whole scene or part of it. Chapter 6 describes how photometric stereo allows recovery of 3D information in order to obtain a better understanding of a scene, as well as also partially overcoming some current surveillance challenges, such as difficulty in resolving fine detail, particularly at large standoff distances, and in isolating and recognising more complex objects in real scenes. Here items of interest may be obscured by complex environmental factors that are subject to rapid change, making, for example, the detection of suspicious objects and behaviour highly problematic. Here innovative use is made of an untapped latent capability offered within modern surveillance environments to introduce a form of environmental structuring to good advantage in order to achieve a richer form of data acquisition. This chapter also goes on to explore the novel application of photometric stereo in such diverse applications, how our algorithm can be incorporated into an existing surveillance system and considers a typical real commercial application.One of the most important aspects of this research work is its application. Indeed, while most of the research literature has been based on relatively simple structured environments, the approach here has been designed to be applied to real surveillance environments, such as railway stations, airports, waiting rooms, etc, and where surveillance cameras may be fixed or in the future form part of a mobile robotic free roaming surveillance device, that must continually reinterpret its changing environment. So, as mentioned previously, while the main focus has been to apply this algorithm to railway station environments, the work has been approached in a way that allows adaptation to many other applications, such as autonomous robotics, and in motorway, shopping centre, street and home environments. All of these applications require a better understanding of the scene for security or safety purposes. Finally, chapter 7 presents a global conclusion and what will be achieved in the future

Dynamically reconfigurable architecture for embedded computer vision systems

The objective of this research work is to design, develop and implement a new architecture which integrates on the same chip all the processing levels of a complete Computer Vision system, so that the execution is efficient without compromising the power consumption while keeping a reduced cost. For this purpose, an analysis and classification of different mathematical operations and algorithms commonly used in Computer Vision are carried out, as well as a in-depth review of the image processing capabilities of current-generation hardware devices. This permits to determine the requirements and the key aspects for an efficient architecture. A representative set of algorithms is employed as benchmark to evaluate the proposed architecture, which is implemented on an FPGA-based system-on-chip. Finally, the prototype is compared to other related approaches in order to determine its advantages and weaknesses