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

REMOVAL OF GAUSSIAN AND IMPULSE NOISE IN THE COLOUR IMAGE PROGRESSION WITH FUZZY FILTERS

This paper is concerned with algebraic features based filtering technique, named as the adaptive statistical quality based filtering technique (ASQFT), is presented for removal of Impulse and Gaussian noise in corrupted colour images. A combination of these two filters also helps in eliminating a mixture of these two noises. One strong filtering step that should remove all noise at once would inevitably also remove a considerable amount of detail. Therefore, the noise is filtered step by step. In each step, noisy pixels are detected by the help of fuzzy rules, which are very useful for the processing of human knowledge where linguistic variables are used. The proposed filter is able to efficiently suppress both Gaussian noise and impulse noise, as well as mixed Gaussian impulse noise. The experiments shows that proposed method outperforms novel modern filters both visually and in terms of objective quality measures such as the mean absolute error (MAE), the peaksignal- to-noise ratio (PSNR) and the normalized color difference (NCD). The expectations filter achieves a promising performance

Copasetic analysis: a framework for the blind analysis of microarray imagery

The official published version can be found at the link below.From its conception, bioinformatics has been a multidisciplinary field which blends domain expert knowledge with new and existing processing techniques, all of which are focused on a common goal. Typically, these techniques have focused on the direct analysis of raw microarray image data. Unfortunately, this fails to utilise the image's full potential and in practice, this results in the lab technician having to guide the analysis algorithms. This paper presents a dynamic framework that aims to automate the process of microarray image analysis using a variety of techniques. An overview of the entire framework process is presented, the robustness of which is challenged throughout with a selection of real examples containing varying degrees of noise. The results show the potential of the proposed framework in its ability to determine slide layout accurately and perform analysis without prior structural knowledge. The algorithm achieves approximately, a 1 to 3 dB improved peak signal-to-noise ratio compared to conventional processing techniques like those implemented in GenePix® when used by a trained operator. As far as the authors are aware, this is the first time such a comprehensive framework concept has been directly applied to the area of microarray image analysis

Microarray image processing: A novel neural network framework

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.Aleppo University, Syri

Fuzzy metrics and fuzzy logic for colour image filtering

El filtrado de imagen es una tarea fundamental para la mayoría de los sistemas de visión por computador cuando las imágenes se usan para análisis automático o, incluso, para inspección humana. De hecho, la presencia de ruido en una imagen puede ser un grave impedimento para las sucesivas tareas de procesamiento de imagen como, por ejemplo, la detección de bordes o el reconocimiento de patrones u objetos y, por lo tanto, el ruido debe ser reducido. En los últimos años el interés por utilizar imágenes en color se ha visto incrementado de forma significativa en una gran variedad de aplicaciones. Es por esto que el filtrado de imagen en color se ha convertido en un área de investigación interesante. Se ha observado ampliamente que las imágenes en color deben ser procesadas teniendo en cuenta la correlación existente entre los distintos canales de color de la imagen. En este sentido, la solución probablemente más conocida y estudiada es el enfoque vectorial. Las primeras soluciones de filtrado vectorial, como por ejemplo el filtro de mediana vectorial (VMF) o el filtro direccional vectorial (VDF), se basan en la teoría de la estadística robusta y, en consecuencia, son capaces de realizar un filtrado robusto. Desafortunadamente, estas técnicas no se adaptan a las características locales de la imagen, lo que implica que usualmente los bordes y detalles de las imágenes se emborronan y pierden calidad. A fin de solventar este problema, varios filtros vectoriales adaptativos se han propuesto recientemente. En la presente Tesis doctoral se han llevado a cabo dos tareas principales: (i) el estudio de la aplicabilidad de métricas difusas en tareas de procesamiento de imagen y (ii) el diseño de nuevos filtros para imagen en color que sacan provecho de las propiedades de las métricas difusas y la lógica difusa. Los resultados experimentales presentados en esta Tesis muestran que las métricas difusas y la lógica difusa son herramientas útiles para diseñar técnicas de filtrado,Morillas Gómez, S. (2007). Fuzzy metrics and fuzzy logic for colour image filtering [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/1879Palanci

Implementation of Impulse Noise Reduction Method to Color Images using Fuzzy Logic

Image Processing is a technique to enhance raw images received from cameras/sensors placed on satellites, space probes and aircrafts or pictures taken in normal day-to-day life for various applications. Impulse noise reduction method is one of the critical techniques to reduce the noise in color images. In this paper the impulse noise reduction method for color images by using Fuzzy Logic is implemented. Generally Grayscale algorithm is used to filter the impulse noise in corrupted color images by separate the each color component or using a vector-based approach where each pixel is considered as a single vector. In this paper the concepts of Fuzzy logic has been used in order to distinguish between noise and image characters and filter only the corrupted pixels while preserving the color and the edge sharpness. Due to this a good noise reduction performance is achieved. The main difference between this method and other classical noise reduction methods is that the color information is taken into account to develop a better impulse noise detection a noise reduction that filters only the corrupted pixels while preserving the color and the edge sharpness. The Fuzzy based impulse noise reduction method is implemented on set of selected images and the obtained results are presented

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB

<p>Abstract</p> <p>Background</p> <p>The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods.</p> <p>Results</p> <p>We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime.</p> <p>Conclusion</p> <p>Gene ARMADA provides a highly adaptable, integrative, yet flexible tool which can be used for automated quality control, analysis, annotation and visualization of microarray data, constituting a starting point for further data interpretation and integration with numerous other tools.</p