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

Noise Removal in Microarray Images Using Variational Mode Decomposition Technique

Microarray technology allows the simultaneous monitoring of thousands of genes in parallel. Based on the gene expression measurements, microarray technology have proven powerful in gene expression profiling for discovering new types of diseases and for predicting the type of a disease. Enhancement, Gridding, Segmentation and Intensity extraction are important steps in microarray image analysis. This paper presents a noise removal method in microarray images based on Variational Mode Decomposition (VMD). VMD is a signal processing method which decomposes any input signal into discrete number of sub-signals (called Variational Mode Functions) with each mode chosen to be its band width in spectral domain. First the noisy image is processed using 2-D VMD to produce 2-D VMFs. Then Discrete Wavelet Transform (DWT) thresholding technique is applied to each VMF for denoising.  The denoised microarray image is reconstructed by the summation of VMFs.  This method is named as 2-D VMD and DWT thresholding method. The proposed method is compared with DWT thresholding and BEMD and DWT thresholding methods. The qualitative and quantitative analysis shows that 2-D VMD and DWT thresholding method produces better noise removal than other two methods

An Improved Adaptive Filtering Technique to Remove High Density Salt-and-Pepper Noise using Multiple Last Processed Pixels

This paper presents an efficient algorithm which can remove high density salt-and-pepper noise from corrupted digital image This technique differentiates between corrupted and uncorrupted pixels and performs the filtering process only on the corrupted ones The proposed algorithm calculates median only among the noise-free neighborhoods in the processing window and replaces the centre corrupted pixel with that median value The adaptive behavior is enabled here by expanding the processing window based on neighbourhood noise-free pixels In case of high density noise corruption where no noise-free neighborhood is found within the maximum size of window this algorithm takes last processed pixels into the account While most of the existing filtering techniques use only one last processed pixel after reaching maximum window the proposed algorithm considers multiple last processed pixels rather than considering a single one so that more accurate decision can be taken in order to replace the corrupted pixe

Colour image denoising by eigenvector analysis of neighbourhood colour samples

[EN] Colour image smoothing is a challenging task because it is necessary to appropriately distinguish between noise and original structures, and to smooth noise conveniently. In addition, this processing must take into account the correlation among the image colour channels. In this paper, we introduce a novel colour image denoising method where each image pixel is processed according to an eigenvector analysis of a data matrix built from the pixel neighbourhood colour values. The aim of this eigenvector analysis is threefold: (i) to manage the local correlation among the colour image channels, (ii) to distinguish between flat and edge/textured regions and (iii) to determine the amount of needed smoothing. Comparisons with classical and recent methods show that the proposed approach is competitive and able to provide significative improvements.Latorre-Carmona, P.; Miñana, J.; Morillas, S. (2020). Colour image denoising by eigenvector analysis of neighbourhood colour samples. 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SCDT: FC-NNC-structured Complex Decision Technique for Gene Analysis Using Fuzzy Cluster based Nearest Neighbor Classifier

In many diseases classification an accurate gene analysis is needed, for which selection of most informative genes is very important and it require a technique of decision in complex context of ambiguity. The traditional methods include for selecting most significant gene includes some of the statistical analysis namely 2-Sample-T-test (2STT), Entropy, Signal to Noise Ratio (SNR). This paper evaluates gene selection and classification on the basis of accurate gene selection using structured complex decision technique (SCDT) and classifies it using fuzzy cluster based nearest neighborclassifier (FC-NNC). The effectiveness of the proposed SCDT and FC-NNC is evaluated for leave one out cross validation metric(LOOCV) along with sensitivity, specificity, precision and F1-score with four different classifiers namely 1) Radial Basis Function (RBF), 2) Multi-layer perception(MLP), 3) Feed Forward(FF) and 4) Support vector machine(SVM) for three different datasets of DLBCL, Leukemia and Prostate tumor. The proposed SCDT &FC-NNC exhibits superior result for being considered more accurate decision mechanism

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