Nikolaos Giannakeas

An automated method for gridding and clustering-based segmentation of cDNA microarray images.

Microarrays are widely used to quantify gene expression levels. Microarray image analysis is one of the tools, which are necessary when dealing with vast amounts of biological data. In this work we propose a new method for the automated analysis of microarray images. The proposed method consists of two stages: gridding and segmentation. Initially, the microarray images are preprocessed using template matching, and block and spot finding takes place. Then, the non-expressed spots are detected and a grid is fit on the image using a Voronoi diagram. In the segmentation stage, K-means and Fuzzy C means (FCM) clustering are employed. The proposed method was evaluated using images from the Stanford Microarray Database (SMD). The results that are presented in the segmentation stage show the efficiency of our Fuzzy C means-based work compared to the two already developed K-means-based methods. The proposed method can handle images with artefacts and it is fully automated.

Segmentation of microarray images using pixel classification-Comparison with clustering-based methods

OBJECTIVE DNA microarray technology yields expression profiles for thousands of genes, in a single hybridization experiment. The quantification of the expression level is performed using image analysis. In this paper we introduce a supervised method for the segmentation of microarray images using classification techniques. The method is able to characterize the pixels of the image as signal, background and artefact. METHODS AND MATERIAL The proposed method includes five steps: (a) an automated gridding method which provides a cell of the image for each spot. (b) Three multichannel vector filters are employed to preprocess the raw image. (c) Features are extracted from each pixel of the image. (d) The dimension of the feature set is reduced. (e) Support vector machines are used for the classification of pixels as signal, background, artefacts. The proposed method is evaluated using both real images from the Stanford microarray database and simulated images generated by a microarray data simulator. The signal and the background pixels, which are responsible for the quantification of the expression levels, are efficiently detected. RESULTS A quality measure (qindex) and the pixel-by-pixel accuracy are used for the evaluation of the proposed method. The obtained qindex varies from 0.742 to 0.836. The obtained accuracy for the real images is about 98%, while the accuracies for the good, normal and bad quality simulated images are 96, 93 and 71%, respectively. The proposed classification method is compared to clustering-based techniques, which have been proposed for microarray image segmentation. This comparison shows that the classification-based method reports better results, improving the performance by up to 20%. CONCLUSIONS The proposed method can be used for segmentation of microarray images with high accuracy, indicating that segmentation can be improved using classification instead of clustering. The proposed method is supervised and it can only be used when training data are available.

Spot addressing for microarray images structured in hexagonal grids

In this work, an efficient method for spot addressing in images, which are generated by the scanning of hexagonal structured microarrays, is proposed. Initially, the blocks of the image are separated using the projections of the image. Next, all the blocks of the image are processed separately for the detection of each spot. The spot addressing procedure begins with the detection of the high intensity objects, which are probably the spots of the image. Next, the Growing Concentric Hexagon algorithm, which uses the properties of the hexagonal grid, is introduced for the detection of the non-hybridized spots. Finally, the Voronoi diagram is applied to the centers of the detected spots for the gridding of the image. The method is evaluated using spots generated from the scanning of the Beadchip of Illumina, which is used for the detection of Single Nucleotide Polymorphisms in the human genome, and uses hexagonal structure for the location of the spots. For the evaluation, the detected centers for each of the spot in the image are compared to the centers of the annotation, obtaining up to 98% accuracy for the spot addressing procedure.

An Automated Method for Gridding in Microarray Images

Microarray technology is a powerful tool for analyzing the expression of a large number of genes in parallel. A typical microarray image consists of a few thousands of spots which determine the level of gene expression in the sample. In this paper we propose a method which automatically addresses each spot area in the image. Initially, a preliminary segmentation of the image is produced using a template matching algorithm. Next, grid and spot finding are realized. The position of non-expressed spots is located and finally a Voronoi diagram is employed to fit the grid on the image. Our method has been evaluated in a set of five images consisting of 45960 spots, from the Stanford microarray database and the reported accuracy for spot detection was 93%

A classification-based segmentation of cDNA microarray images using Support Vector machines

Microarray technology provides a tool for the simultaneous analysis of the expression level for an amount of genes. Microarray studies have been shown that image processing techniques can significantly influence microarray data precision. In this paper we propose a supervised method for the segmentation of microarray images based on classification techniques. Support Vector machine is employed to classify each pixel of the image into signal, background or artefacts. In addition, a preprocessing step is applied in order to filter the initial image. The proposed method is applied both to real and simulated images. The pixels of the image are classified in two classes for the real images and three classes for the simulated one. For this task, an informative set of features is used from both green and red channels. The results obtained indicate high accuracy (∼99%).

A methodology for automated CPA extraction using liver biopsy image analysis and machine learning techniques

BACKGROUND AND OBJECTIVE Collagen proportional area (CPA) extraction in liver biopsy images provides the degree of fibrosis expansion in liver tissue, which is the most characteristic histological alteration in hepatitis C virus (HCV). Assessment of the fibrotic tissue is currently based on semiquantitative staging scores such as Ishak and Metavir. Since its introduction as a fibrotic tissue assessment technique, CPA calculation based on image analysis techniques has proven to be more accurate than semiquantitative scores. However, CPA has yet to reach everyday clinical practice, since the lack of standardized and robust methods for computerized image analysis for CPA assessment have proven to be a major limitation. METHODS The current work introduces a three-stage fully automated methodology for CPA extraction based on machine learning techniques. Specifically, clustering algorithms have been employed for background-tissue separation, as well as for fibrosis detection in liver tissue regions, in the first and the third stage of the methodology, respectively. Due to the existence of several types of tissue regions in the image (such as blood clots, muscle tissue, structural collagen, etc.), classification algorithms have been employed to identify liver tissue regions and exclude all other non-liver tissue regions from CPA computation. RESULTS For the evaluation of the methodology, 79 liver biopsy images have been employed, obtaining 1.31% mean absolute CPA error, with 0.923 concordance correlation coefficient. CONCLUSIONS The proposed methodology is designed to (i) avoid manual threshold-based and region selection processes, widely used in similar approaches presented in the literature, and (ii) minimize CPA calculation time.

Developing a genomic-based point-of-care diagnostic system for rheumatoid arthritis and multiple sclerosis

In this paper the methodology of designing a genomic-based point-of-care diagnostic system composed of a microfluidic Lab-On-Chip, algorithms for microarray image information extraction and knowledge modeling of clinico-genomic patient data is presented. The data are processed by genome wide association studies for two complex diseases: rheumatoid arthritis and multiple sclerosis. Respecting current technological limitations of autonomous molecular-based Lab-On-Chip systems the approach proposed in this work aims to enhance the diagnostic accuracy of the miniaturized LOC system. By providing a decision support system based on the data mining technologies, a robust portable integrated point-of-care diagnostic assay will be implemented. Initially, the gene discovery process is described followed by the detection of the most informative SNPs associated with the diseases. The clinical data and the selected associated SNPs are modeled using data mining techniques to allow the knowledge modeling framework to provide the diagnosis for new patients performing the point-of-care examination. The microfluidic LOC device supplies the diagnostic component of the platform with a set of SNPs associated with the diseases and the ruled-based decision support system combines this genomic information with the clinical data of the patient to outcome the final diagnostic result.

Multichannel Segmentation of cDNA Microarray Images using the Bayes Classifier

Microarray technology provides a powerful tool for the quantification of the expression level for a large number of genes simultaneously. Image analysis Is a crucial step for data extraction of microarray gene expression experiments. In this paper we propose a supervised method for the segmentation of microarray Images. The Bayes classifier Is employed for a pixel by pixel classification. The proposed method classifies the pixels of the Image In two classes, foreground and background pixels. For this task, an Informative set of features Is used from both green and red channels. The method Is evaluated using a set of 5184 spots (consisting of ~15000000 pixels), from the Stanford microarray database (SMD) and the reported classification accuracy Is 82 %.

Automated Detection of Liver Histopathological Findings Based on Biopsy Image Processing

Hepatic steatosis is the accumulation of fat in the hepatic cells and the liver. Triglycerides and other kinds of molecules are included in the lipids. When there is some defect in the process, hepatic steatosis arise, during which the free fatty acids are taken by the liver and exuded as lipoproteins. Alcohol is the main cause of steatosis when excessive amounts are consumed for a long period of time. In many cases, steatosis can lead to inflammation that is mentioned as steatohepatitis or non-alcoholic steatohepatitis (NASH), which can later lead to fibrosis and finally cirrhosis. For automated detection and quantification of hepatic steatosis, a novel two-stage methodology is developed in this study. Initially, the image is processed in order to become more suitable for the detection of fat regions and steatosis quantification. In the second stage, initial candidate image regions are detected, and then they are either validated or discarded based on a series of criteria. The methodology is based on liver biopsy image analysis, and has been tested using 40 liver biopsy images obtained from patients who suffer from hepatitis C. The obtained results indicate that the proposed methodology can accurately assess liver steatosis.

Intelligent patient profiling for diagnosis, staging and treatment selection in colon cancer

The selection of a personalized treatment plan for a patient with cancer can be of critical importance for his health or even survival. A Decision Support Platform that can associate the patient clinical situation with the patient DNA Single Nucleotide Polymorphisms (SNPs) can provide the oncologist with a better understanding of the personalized conditions of every single patient. In this paper we present the MATCH platform which performs data integration between medicine and molecular biology, by developing a framework where, clinical and genomic features are appropriately combined in order to handle colon cancer diseases. The core of the platform is based on clustering techniques which provide profiles of patients with similar clinical features and genetic predispositions to cancer. The patients which share the same profile should probably have similar treatment plan and follow up. Through the integration of the clinical and genetic data of a patient, real time conclusions can be drawn for his early diagnosis, staging and more effective colon cancer treatment. Intelligent components are designed and developed which identify single nucleotide polymorphisms (SNPs) from the gene sequences and combine them with the clinical situation of the patient. The produced clinico-genomic profiles are used as a decision support tool for newly sequenced patients.