Doctor of Philosophy

dissertationConfocal microscopy has become a popular imaging technique in biology research in recent years. It is often used to study three-dimensional (3D) structures of biological samples. Confocal data are commonly multichannel, with each channel resulting from a different fluorescent staining. This technique also results in finely detailed structures in 3D, such as neuron fibers. Despite the plethora of volume rendering techniques that have been available for many years, there is a demand from biologists for a flexible tool that allows interactive visualization and analysis of multichannel confocal data. Together with biologists, we have designed and developed FluoRender. It incorporates volume rendering techniques such as a two-dimensional (2D) transfer function and multichannel intermixing. Rendering results can be enhanced through tone-mappings and overlays. To facilitate analyses of confocal data, FluoRender provides interactive operations for extracting complex structures. Furthermore, we developed the Synthetic Brainbow technique, which takes advantage of the asynchronous behavior in Graphics Processing Unit (GPU) framebuffer loops and generates random colorizations for different structures in single-channel confocal data. The results from our Synthetic Brainbows, when applied to a sequence of developing cells, can then be used for tracking the movements of these cells. Finally, we present an application of FluoRender in the workflow of constructing anatomical atlases

Image Segmentation using PDE, Variational, Morphological and Probabilistic Methods

The research in this dissertation has focused upon image segmentation and its related areas, using the techniques of partial differential equations, variational methods, mathematical morphological methods and probabilistic methods. An integrated segmentation method using both curve evolution and anisotropic diffusion is presented that utilizes both gradient and region information in images. A bottom-up image segmentation method is proposed to minimize the Mumford-Shah functional. Preferential image segmentation methods are presented that are based on the tree of shapes in mathematical morphologies and the Kullback-Leibler distance in information theory. A thorough evaluation of the morphological preferential image segmentation method is provided, and a web interface is described. A probabilistic model is presented that is based on particle filters for image segmentation. These methods may be incorporated as components of an integrated image processed system. The system utilizes Internet Protocol (IP) cameras for data acquisition. It utilizes image databases to provide prior information and store image processing results. Image preprocessing, image segmentation and object recognition are integrated in one stage in the system, using various methods developed in several areas. Interactions between data acquisition, integrated image processing and image databases are handled smoothly. A framework of the integrated system is implemented using Perl, C++, MySQL and CGI. The integrated system works for various applications such as video tracking, medical image processing and facial image processing. Experimental results on this applications are provided in the dissertation. Efficient computations such as multi-scale computing and parallel computing using graphic processors are also presented

A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Image Filtering Using Morphological Amoebas

International audienceThis article presents the use of anisotropic dynamic structuring elements, or amoebas, in order to build content-aware noise reduction filters. The amoeba is the ball defined by a special geodesic distance computed for each pixel, and can be used as a kernel for many kinds of filters and morphological operators. 1. Introduction Noise is possibly the most annoying problem in the field of image processing. There are two ways to work around it: either design particularly robust algorithms that can work in noisy environments, or try to eliminate the noise in a first step while losing as little relevant information as possible and consequently use a normally robust algorithm. There are of course many algorithms that aim at reducing the amount of noise in images. In mathematical morphology filters can be, broadly-speaking, divided into two groups: 1 alternate sequential filters based on morphological openings and clos-ings, that are quite effective but also remove thin elements such as canals or peninsulas. Even worse, they can displace the contours and thus create additional problems in a segmentation application

Machine Learning And Image Processing For Noise Removal And Robust Edge Detection In The Presence Of Mixed Noise

The central goal of this dissertation is to design and model a smoothing filter based on the random single and mixed noise distribution that would attenuate the effect of noise while preserving edge details. Only then could robust, integrated and resilient edge detection methods be deployed to overcome the ubiquitous presence of random noise in images. Random noise effects are modeled as those that could emanate from impulse noise, Gaussian noise and speckle noise. In the first step, evaluation of methods is performed based on an exhaustive review on the different types of denoising methods which focus on impulse noise, Gaussian noise and their related denoising filters. These include spatial filters (linear, non-linear and a combination of them), transform domain filters, neural network-based filters, numerical-based filters, fuzzy based filters, morphological filters, statistical filters, and supervised learning-based filters. In the second step, switching adaptive median and fixed weighted mean filter (SAMFWMF) which is a combination of linear and non-linear filters, is introduced in order to detect and remove impulse noise. Then, a robust edge detection method is applied which relies on an integrated process including non-maximum suppression, maximum sequence, thresholding and morphological operations. The results are obtained on MRI and natural images. In the third step, a combination of transform domain-based filter which is a combination of dual tree – complex wavelet transform (DT-CWT) and total variation, is introduced in order to detect and remove Gaussian noise as well as mixed Gaussian and Speckle noise. Then, a robust edge detection is applied in order to track the true edges. The results are obtained on medical ultrasound and natural images. In the fourth step, a smoothing filter, which is a feed-forward convolutional network (CNN) is introduced to assume a deep architecture, and supported through a specific learning algorithm, l2 loss function minimization, a regularization method, and batch normalization all integrated in order to detect and remove impulse noise as well as mixed impulse and Gaussian noise. Then, a robust edge detection is applied in order to track the true edges. The results are obtained on natural images for both specific and non-specific noise-level

Curvature-driven PDE methods for matrix-valued images

Matrix-valued data sets arise in a number of applications including diffusion tensor magnetic resonance imaging (DT-MRI) and physical measurements of anisotropic behaviour. Consequently, there arises the need to filter and segment such tensor fields. In order to detect edgelike structures in tensor fields, we first generalise Di Zenzo\u27s concept of a structure tensor for vector-valued images to tensor-valued data. This structure tensor allows us to extend scalar-valued mean curvature motion and self-snakes to the tensor setting. We present both two-dimensional and three-dimensional formulations, and we prove that these filters maintain positive semidefiniteness if the initial matrix data are positive semidefinite. We give an interpretation of tensorial mean curvature motion as a process for which the corresponding curve evolution of each generalised level line is the gradient descent of its total length. Moreover, we propose a geodesic active contour model for segmenting tensor fields and interpret it as a minimiser of a suitable energy functional with a metric induced by the tensor image. Since tensorial active contours incorporate information from all channels, they give a contour representation that is highly robust under noise. Experiments on three-dimensional DT-MRI data and an indefinite tensor field from fluid dynamics show that the proposed methods inherit the essential properties of their scalar-valued counterparts

High-ISO long-exposure image denoising based on quantitative blob characterization

Blob detection and image denoising are fundamental, sometimes related tasks in computer vision. In this paper, we present a computational method to quantitatively measure blob characteristics using normalized unilateral second-order Gaussian kernels. This method suppresses non-blob structures while yielding a quantitative measurement of the position, prominence and scale of blobs, which can facilitate the tasks of blob reconstruction and blob reduction. Subsequently, we propose a denoising scheme to address high-ISO long-exposure noise, which sometimes spatially shows a blob appearance, employing a blob reduction procedure as a cheap preprocessing for conventional denoising methods. We apply the proposed denoising methods to real-world noisy images as well as standard images that are corrupted by real noise. The experimental results demonstrate the superiority of the proposed methods over state-of-the-art denoising methods

Automatic segmentation of the lumen of the carotid artery in ultrasound B-mode images

A new algorithm is proposed for the segmentation of the lumen and bifurcation boundaries of the carotid artery in B-mode ultrasound images. It uses the hipoechogenic characteristics of the lumen for the identification of the carotid boundaries and the echogenic characteristics for the identification of the bifurcation boundaries. The image to be segmented is processed with the application of an anisotropic diffusion filter for speckle removal and morphologic operators are employed in the detection of the artery. The obtained information is then used in the definition of two initial contours, one corresponding to the lumen and the other to the bifurcation boundaries, for the posterior application of the Chan-vese level set segmentation model. A set of longitudinal B-mode images of the common carotid artery (CCA) was acquired with a GE Healthcare Vivid-e ultrasound system (GE Healthcare, United Kingdom). All the acquired images include a part of the CCA and of the bifurcation that separates the CCA into the internal and external carotid arteries. In order to achieve the uppermost robustness in the imaging acquisition process, i.e., images with high contrast and low speckle noise, the scanner was adjusted differently for each acquisition and according to the medical exam. The obtained results prove that we were able to successfully apply a carotid segmentation technique based on cervical ultrasonography. The main advantage of the new segmentation method relies on the automatic identification of the carotid lumen, overcoming the limitations of the traditional methods