A novel neural network approach to cDNA microarray image segmentation

This is the post-print version of the Article. The official published version can be accessed from the link below. Copyright @ 2013 Elsevier.Microarray technology has become a great source of information for biologists to understand the workings of DNA which is one of the most complex codes in nature. Microarray images typically contain several thousands of small spots, each of which represents a different gene in the experiment. One of the key steps in extracting information from a microarray image is the segmentation whose aim is to identify which pixels within an image represent which gene. This task is greatly complicated by noise within the image and a wide degree of variation in the values of the pixels belonging to a typical spot. In the past there have been many methods proposed for the segmentation of microarray image. In this paper, a new method utilizing a series of artificial neural networks, which are based on multi-layer perceptron (MLP) and Kohonen networks, is proposed. The proposed method is applied to a set of real-world cDNA images. Quantitative comparisons between the proposed method and commercial software GenePix(®) are carried out in terms of the peak signal-to-noise ratio (PSNR). This method is shown to not only deliver results comparable and even superior to existing techniques but also have a faster run time.This work was funded in part by the National Natural Science Foundation of China under Grants 61174136 and 61104041, the Natural Science Foundation of Jiangsu Province of China under Grant BK2011598, the International Science and Technology Cooperation Project of China under Grant No. 2011DFA12910, the Engineering and Physical Sciences Research Council (EPSRC) of the U.K. under Grant GR/S27658/01, the Royal Society of the U.K., and the Alexander von Humboldt Foundation of Germany

Color image segmentation using a self-initializing EM algorithm

This paper presents a new method based on the Expectation-Maximization (EM) algorithm that we apply for color image segmentation. Since this algorithm partitions the data based on an initial set of mixtures, the color segmentation provided by the EM algorithm is highly dependent on the starting condition (initialization stage). Usually the initialization procedure selects the color seeds randomly and often this procedure forces the EM algorithm to converge to numerous local minima and produce inappropriate results. In this paper we propose a simple and yet effective solution to initialize the EM algorithm with relevant color seeds. The resulting self initialised EM algorithm has been included in the development of an adaptive image segmentation scheme that has been applied to a large number of color images. The experimental data indicates that the refined initialization procedure leads to improved color segmentation

Automatic segmentation of skin cancer images using adaptive color clustering

This paper presents the development of an adaptive image segmentation algorithm designed for the identification of the skin cancer and pigmented lesions in dermoscopy images. The key component of the developed algorithm is the Adaptive Spatial K-Means (A-SKM) clustering technique that is applied to extract the color features from skin cancer images. Adaptive-SKM is a novel technique that includes the primary features that describe the color smoothness and texture complexity in the process of pixel assignment. The A-SKM has been included in the development of a flexible color-texture image segmentation scheme and the experimental data indicates that the developed algorithm is able to produce accurate segmentation when applied to a large number of skin cancer (melanoma) images

Development of retinal blood vessel segmentation methodology using wavelet transforms for assessment of diabetic retinopathy

Automated image processing has the potential to assist in the early detection of diabetes, by detecting changes in blood vessel diameter and patterns in the retina. This paper describes the development of segmentation methodology in the processing of retinal blood vessel images obtained using non-mydriatic colour photography. The methods used include wavelet analysis, supervised classifier probabilities and adaptive threshold procedures, as well as morphology-based techniques. We show highly accurate identification of blood vessels for the purpose of studying changes in the vessel network that can be utilized for detecting blood vessel diameter changes associated with the pathophysiology of diabetes. In conjunction with suitable feature extraction and automated classification methods, our segmentation method could form the basis of a quick and accurate test for diabetic retinopathy, which would have huge benefits in terms of improved access to screening people for risk or presence of diabetes

Medical image enhancement using threshold decomposition driven adaptive morphological filter

One of the most common degradations in medical images is their poor contrast quality. This suggests the use of contrast enhancement methods as an attempt to modify the intensity distribution of the image. In this paper, a new edge detected morphological filter is proposed to sharpen digital medical images. This is done by detecting the positions of the edges and then applying a class of morphological filtering. Motivated by the success of threshold decomposition, gradientbased operators are used to detect the locations of the edges. A morphological filter is used to sharpen these detected edges. Experimental results demonstrate that the detected edge deblurring filter improved the visibility and perceptibility of various embedded structures in digital medical images. Moreover, the performance of the proposed filter is superior to that of other sharpener-type filters

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

Perceptually-Driven Video Coding with the Daala Video Codec

The Daala project is a royalty-free video codec that attempts to compete with the best patent-encumbered codecs. Part of our strategy is to replace core tools of traditional video codecs with alternative approaches, many of them designed to take perceptual aspects into account, rather than optimizing for simple metrics like PSNR. This paper documents some of our experiences with these tools, which ones worked and which did not. We evaluate which tools are easy to integrate into a more traditional codec design, and show results in the context of the codec being developed by the Alliance for Open Media.Comment: 19 pages, Proceedings of SPIE Workshop on Applications of Digital Image Processing (ADIP), 201