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

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd

On generalized adaptive neural filter

Linear filters have historically been used in the past as the most useful tools for suppressing noise in signal processing. It has been shown that the optimal filter which minimizes the mean square error (MSE) between the filter output and the desired output is a linear filter provided that the noise is additive white Gaussian noise (AWGN). However, in most signal processing applications, the noise in the channel through which a signal is transmitted is not AWGN; it is not stationary, and it may have unknown characteristics. To overcome the shortcomings of linear filters, nonlinear filters ranging from the median filters to stack filters have been developed. They have been successfully used in a number of applications, such as enhancing the signal-to-noise ratio of the telecommunication receivers, modeling the human vocal tract to synthesize speech in speech processing, and separating out the maternal and fetal electrocardiogram signals to diagnose prenatal ailments. In particular, stack filters have been shown to provide robust noise suppression, and are easily implementable in hardware, but configuring an optimal stack filter remains a challenge. This dissertation takes on this challenge by extending stack filters to a new class of nonlinear adaptive filters called generalized adaptive neural filters (GANFs). The objective of this work is to investigate their performance in terms of the mean absolute error criterion, to evaluate and predict the generalization of various discriminant functions employed for GANFs, and to address issues regarding their applications and implementation. It is shown that GANFs not only extend the class of stack filters, but also have better performance in terms of suppressing non-additive white Gaussian noise. Several results are drawn from the theoretical and experimental work: stack filters can be adaptively configured by neural networks; GANFs encompass a large class of nonlinear sliding-window filters which include stack filters; the mean absolute error (MAE) of the optimal GANF is upper-bounded by that of the optimal stack filter; a suitable class of discriminant functions can be determined before a training scheme is executed; VC dimension (VCdim) theory can be applied to determine the number of training samples; the algorithm presented in configuring GANFs is effective and robust

Biomimetic Design for Efficient Robotic Performance in Dynamic Aquatic Environments - Survey

This manuscript is a review over the published articles on edge detection. At first, it provides theoretical background, and then reviews wide range of methods of edge detection in different categorizes. The review also studies the relationship between categories, and presents evaluations regarding to their application, performance, and implementation. It was stated that the edge detection methods structurally are a combination of image smoothing and image differentiation plus a post-processing for edge labelling. The image smoothing involves filters that reduce the noise, regularize the numerical computation, and provide a parametric representation of the image that works as a mathematical microscope to analyze it in different scales and increase the accuracy and reliability of edge detection. The image differentiation provides information of intensity transition in the image that is necessary to represent the position and strength of the edges and their orientation. The edge labelling calls for post-processing to suppress the false edges, link the dispread ones, and produce a uniform contour of objects

Fast space-variant elliptical filtering using box splines

The efficient realization of linear space-variant (non-convolution) filters is a challenging computational problem in image processing. In this paper, we demonstrate that it is possible to filter an image with a Gaussian-like elliptic window of varying size, elongation and orientation using a fixed number of computations per pixel. The associated algorithm, which is based on a family of smooth compactly supported piecewise polynomials, the radially-uniform box splines, is realized using pre-integration and local finite-differences. The radially-uniform box splines are constructed through the repeated convolution of a fixed number of box distributions, which have been suitably scaled and distributed radially in an uniform fashion. The attractive features of these box splines are their asymptotic behavior, their simple covariance structure, and their quasi-separability. They converge to Gaussians with the increase of their order, and are used to approximate anisotropic Gaussians of varying covariance simply by controlling the scales of the constituent box distributions. Based on the second feature, we develop a technique for continuously controlling the size, elongation and orientation of these Gaussian-like functions. Finally, the quasi-separable structure, along with a certain scaling property of box distributions, is used to efficiently realize the associated space-variant elliptical filtering, which requires O(1) computations per pixel irrespective of the shape and size of the filter.Comment: 12 figures; IEEE Transactions on Image Processing, vol. 19, 201

SAR Image Edge Detection: Review and Benchmark Experiments

Edges are distinct geometric features crucial to higher level object detection and recognition in remote-sensing processing, which is a key for surveillance and gathering up-to-date geospatial intelligence. Synthetic aperture radar (SAR) is a powerful form of remote-sensing. However, edge detectors designed for optical images tend to have low performance on SAR images due to the presence of the strong speckle noise-causing false-positives (type I errors). Therefore, many researchers have proposed edge detectors that are tailored to deal with the SAR image characteristics specifically. Although these edge detectors might achieve effective results on their own evaluations, the comparisons tend to include a very limited number of (simulated) SAR images. As a result, the generalized performance of the proposed methods is not truly reflected, as real-world patterns are much more complex and diverse. From this emerges another problem, namely, a quantitative benchmark is missing in the field. Hence, it is not currently possible to fairly evaluate any edge detection method for SAR images. Thus, in this paper, we aim to close the aforementioned gaps by providing an extensive experimental evaluation for SAR images on edge detection. To that end, we propose the first benchmark on SAR image edge detection methods established by evaluating various freely available methods, including methods that are considered to be the state of the art