English

Microarray images, which allow the analysis of hybridization expressions of genes, have been one of the most widely used high-throughput technologies with many different applications. Accurate and automatic microarray image analysis is very important since researchers trust the information provided in these experiments and construct conclusions based on the results produced by the software responsible in analyzing the hybridized arrays. Every microarray image contains thousands of spots, so how to do the spots finding in microarray images accurately and automatically is very meaningful. There are always some problems, such as rotation and distortion, in a microarray image caused by mechanical errors and/or optical errors in the system. All these problems will hinder "doi"ng analysis automatically. Early research has worked out several algorithms to deal with the rotation problem, but those algorithms can not handle microarray images with distortions. In this paper, we propose a robust spots finding method to deal with both rotation and/or distortion in microarray images. The proposed method provides automatic gridding and can handle a microarray image with different type of rotation (global or sub-array rotation) and optical distortions.

Segmentation is a low-level processing aimed at the partition of an image in disjoint regions, each one homogeneous with respect to some properties like intensity, texture, shape, etc. Such a task is needed in many high-level processing and applications in such diverse fields as remote-sensing, medical imaging, video coding, and industrial automation, just to name a few. In this work of thesis, we first deal with the problem of color based image segmentation, that is based on some form of homogeneity in the color/spectral properties of the image, and then move to the more complex task of texture based segmentation, where the aim is to recognize complex structures in the image which are typically non homogeneous in terms of spectral properties. Concerning color based segmentation, we focus on a specific class of Markov Random Field (MRF) probability models, namely the Tree-Structured Markov Random Fields (TS-MRF), recently proposed to provide a hierarchical multiscale description of images. Based on such a model, the unsupervised image segmentation is carried out by means of a sequence of nested class splits, where each class is modeled as a local binary MRF. As a first contribution, we first extend the model to generic tree structures removing the unnecessary binary constraint, and then devise a new TS-MRF unsupervised segmentation technique which improves upon the original algorithm by selecting a better tree structure and eliminating spurious classes. Such results are obtained by using the Mean-Shift procedure to estimate the number of pdf modes at each node, and to obtain a more reliable initial clustering for subsequent MRF optimization. To this end, we devise a new reliable and fast clustering algorithm based on the Mean-Shift technique, which makes use of a variable-bandwidth strategy based on the k-Nearest Neighbors (k-NN) technique, and is implemented with a speed-up strategy that cuts significantly the computational complexity. Experimental results on synthetic data and real life images from the remote sensing domain prove the potential of the proposed method. Turning to texture based segmentation, we present a novel multiscale texture model, and a related algorithm for the unsupervised segmentation of color images. Elementary textures are characterized by their spatial interactions with neighboring regions along selected directions. Such interactions are modeled in turn by means of a set of Markov chains, one for each direction, whose parameters are collected in a feature vector that synthetically describes the texture. Based on the feature vectors, the texture are then recursively merged, giving rise to larger and more complex textures, which appear at different scales of observation: accordingly, the model is named Hierarchical Multiple Markov Chain (H-MMC). The Texture Fragmentation and Reconstruction (TFR) algorithm, addresses the unsupervised segmentation problem based on the H-MMC model. The ``fragmentation'' step allows one to find the elementary textures of the model, while the ``reconstruction'' step defines the hierarchical image segmentation based on a probabilistic measure (texture score) which takes into account both region scale and inter-region interactions. The performance of the proposed method was assessed through the Prague segmentation benchmark, based on mosaics of real natural textures, and also tested on real-world natural images from the Berkeley dataset. Finally, an application of the TFR algorithm for the unsupervised segmentation of multiresolution remotely sensed images is proposed, based on the significant presence of textural content in last generation high-resolution satellite images. The obtained results further assess the potential of the proposed method for such real life applications.

We present a new method using the Bayesian approach and a Markov random field (MRF) model of integrating several low level visual modules. Using this approach, we have shown how results from an edge based stereo module can be integrated with an intensity based stereo algorithm. In another example, results from a shape from shading module are combined with intensity based stereo. We first derive the intensity based stereo algorithm using the MRF model. The integration is then performed by coupling the results from other modules to the energy functional of the MRF associated with the intensity based stereo. The maximum a prosteriori (MAP) estimate of the resulting MRF is obtained using the mean field annealing algorithm. Results from real and artificial images show a consistent improvement in the accuracy after integration.

A wavelet-based Markov random field segmentation model in segmenting microarray experiments

A deoxyribonucleic acid (DNA) microarray image requires a three-stage process to enhance and preserve the image’s important information. These are gridding, segmentation, and intensity extraction. Of these three processes, segmentation is considered the most difficult, as its function is to differentiate between features in the foreground and background. The elements in the foreground form the object or the vital information of the image, while the background features less critical information for DNA microarray image analysis. This paper presents a study that utilises the Markov random field (MRF) segmentation algorithm on a DNA microarray image. The MRF algorithm evaluates the current pixel depends on its neighbouring pixels. The experimental results show that the MRF algorithm works effectively in the segmentation process for a DNA microarray image.

DNA microarray technology has permitted the analysis of global gene expression profiles in clinical diagnosis, treatment, and environmental health research for several diseases including cancer. Microarray images analysis, processing and segmentation are decisive steps in gene expression analysis, since any error leads to improper diagnosis. These techniques increased and enhanced over the past few years. However, the segmentation of the unshaped spots within the microarray image is still a problem due to the variations of spots in shapes and sizes. Hence, we introduce a new unshaped microarray spot segmentation model, which focuses on spots detection and segmentation regardless of their size and shape using fractal dimensions transform. Real microarray images from the Stanford Microarray Images Database (SMD) and Universal Microarray Images Database (UNC) are used to evaluate the efficiency of the proposed model. The numerical and visual results show that the proposed model improves the accuracy and the efficiency of the spots segmentation process. Biological researchers can use this model in their labs and clinics, as a free priceless software instead of using expensive ones like ScanAlyze, GenePix or spot software.

Microarray image processing plays an important role among array analysis and its precision will affect the application of gene chip. However, real microarray images drawn from various experimental procedures may contain noises and other artifacts, which result in a lower image processing accuracy. Hence, in this paper, we propose a novel image denoising method by introducing the compressed sensing theory into microarray image noise reduction. To improve the matching pursuit efficiency, the correlation coefficient is adopted. Experiments on 17 simulated images and 59 real microarray images obtained from the DeRisi, SIB and BCM data sets are conducted. Qualitative and quantitative results compared with the Donoho threshold, generalized wavelet and adaptive thresholding algorithm, reveal that our proposed method performs better on reducing the noises.

Markov random field (MRF) modelling techniques have been recently proposed as a novel approach to probabilistic modelling for estimation of distribution algorithms (EDAs). An EDA using this technique was called distribution estimation using Markov random fields (DEUM). DEUM was later extended to DEUMd. DEUM and DEUMd use a univariate model of probability distribution, and have been shown to perform better than other univariate EDAs for a range of optimization problems. This paper extends DEUM to use a bivariate model and applies it to the Ising spin glass problems. We propose two variants of DEUM that use different sampling techniques. Our experimental result show a noticeable gain in performance.

The authors investigate a method of efficiently labeling images using the Markov random field (MRF). The MRF model is defined on the region adjacency graph and the labeling is then optimally determined using simulated annealing. The MRF model parameters are automatically estimated using an error backpropagation network. The proposed method is analyzed through experiments using real natural scene images. >

Markov mesh models

A microarray-image model is used that takes into account many factors, including spot morphology, signal strength, background fluorescent noise, and shape and surface degradation. The model yields synthetic images whose appearance and quality reflect that of real microarray images. The model is used to link noise factors to the fidelity of signal extraction with respect to a standard image-extraction algorithm. Of particular interest is the identification of the noise factors and their interactions that significantly degrade the ability to accurately detect the true gene-expression signal. This study uses statistical criteria in conjunction with the simulation of various noise conditions to better understand the noise influence on signal extraction for cDNA microarray images. It proposes a paradigm that is implemented in software. It specifically considers certain kinds of noise in the noise model and sets these at certain levels; however, one can choose other types of noise or use different noise levels. In sum, it develops a statistical package that can work in conjunction with the existing image simulation toolbox.

Gridding and spot segmentation are two critical steps in microarray gene expression data analysis. However, the problems of noise contamination and donut-shaped spots often make signal extraction process a laborintensive task. In this paper, we propose a three-step method for automatic gridding and spot segmentation. The method starts with a background removal and noise eliminating step, and then proceeds in two steps. The first step applies a fully unsupervised method to extract blocks and grids from the cleaned data. The second step applies a simple, progressive spot segmentation method to deal with inner holes and noise in spots. We tested its performance on real microarray images against a widely used software GenePix. Our results show that the proposed method deals effectively with poor-conditioned microarray images in both gridding and spot segmentation.

Hidden Markov fields have been extensively applied in the field of synthetic aperture radar (SAR) image processing, mainly for segmentation and change detection. In such models, the hidden process of interest $X$ is assumed to be a Markov field that is to be searched from an observable process $Y$ . The possibility of such estimation lies, however, on several assumptions that turn out to be unsuitable for many natural systems. These models have then been extended in many directions, leading to triplet Markov fields among other extensions. A link has then been established between these models and the theory of evidence, opening new possibilities of uncertainty modeling and information fusion. The aim of this letter is to further generalize the hidden evidential Markov field (EMF) to consider more general forms of noise with application to unsupervised segmentation of SAR images. For parameters estimation, we use iterative conditional estimation, whereas maximization is performed through iterative conditional mode. The performance of the proposed model is assessed against the original EMF on real SAR images.

An MRF model-based approach to the detection of rectangular shape objects in color images

One of the major factors plaguing the performance of synthetic aperture radar (SAR) imagery is the presence of signal-dependent speckle noise. Grainy in appearance, speckle noise is primarily due to the phase fluctuations of the electromagnetic return signals. Since inherent spatial-correlation characteristics of speckle in SAR images are not exploited in existing multiplicative models for speckle noise, a new approach is proposed here that provides a new mathematical framework for modeling and reduction of speckle noise. The contribution of this paper is twofold. First, a novel model for speckled SAR imagery is introduced based on Markov random fields (MRFs) in conjunction with statistical optics. Second, utilizing the model, a global energy-minimization algorithm, based on simulated annealing (SA), is introduced for speckle reduction. In particular, the joint conditional probability density function (cpdf) of the intensity of any two points in the speckled image and the associated correlation function are used to derive the cpdf of any center pixel intensity given its four neighbors. The Hammersley- Clifford theorem is then used to derive the energy function associated with the MRF. The SA, built on the Metropolis sampler, is employed for speckle reduction. Four metrics are used to assess the quality of the speckle reduction: the mean-square error, SNR, an edge-preservation parameter and the equivalent number of looks. A comparative study using both simulated speckled images as well as real SAR images indicates that the proposed approach performs favorably in comparison to existing filtering techniques such as the modified-Lee and the enhanced Frost-algorithms.