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

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

Two generalizations of Kohonen clustering

The relationship between the sequential hard c-means (SHCM), learning vector quantization (LVQ), and fuzzy c-means (FCM) clustering algorithms is discussed. LVQ and SHCM suffer from several major problems. For example, they depend heavily on initialization. If the initial values of the cluster centers are outside the convex hull of the input data, such algorithms, even if they terminate, may not produce meaningful results in terms of prototypes for cluster representation. This is due in part to the fact that they update only the winning prototype for every input vector. The impact and interaction of these two families with Kohonen's self-organizing feature mapping (SOFM), which is not a clustering method, but which often leads ideas to clustering algorithms is discussed. Then two generalizations of LVQ that are explicitly designed as clustering algorithms are presented; these algorithms are referred to as generalized LVQ = GLVQ; and fuzzy LVQ = FLVQ. Learning rules are derived to optimize an objective function whose goal is to produce 'good clusters'. GLVQ/FLVQ (may) update every node in the clustering net for each input vector. Neither GLVQ nor FLVQ depends upon a choice for the update neighborhood or learning rate distribution - these are taken care of automatically. Segmentation of a gray tone image is used as a typical application of these algorithms to illustrate the performance of GLVQ/FLVQ

Artificial neural network-statistical approach for PET volume analysis and classification

Copyright © 2012 The Authors. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.The increasing number of imaging studies and the prevailing application of positron emission tomography (PET) in clinical oncology have led to a real need for efficient PET volume handling and the development of new volume analysis approaches to aid the clinicians in the clinical diagnosis, planning of treatment, and assessment of response to therapy. A novel automated system for oncological PET volume analysis is proposed in this work. The proposed intelligent system deploys two types of artificial neural networks (ANNs) for classifying PET volumes. The first methodology is a competitive neural network (CNN), whereas the second one is based on learning vector quantisation neural network (LVQNN). Furthermore, Bayesian information criterion (BIC) is used in this system to assess the optimal number of classes for each PET data set and assist the ANN blocks to achieve accurate analysis by providing the best number of classes. The system evaluation was carried out using experimental phantom studies (NEMA IEC image quality body phantom), simulated PET studies using the Zubal phantom, and clinical studies representative of nonsmall cell lung cancer and pharyngolaryngeal squamous cell carcinoma. The proposed analysis methodology of clinical oncological PET data has shown promising results and can successfully classify and quantify malignant lesions.This study was supported by the Swiss National Science Foundation under Grant SNSF 31003A-125246, Geneva Cancer League, and the Indo Swiss Joint Research Programme ISJRP 138866. This article is made available through the Brunel Open Access Publishing Fund

Segmentation and Classification Models Validation Area Mapping of Peat Lands as Initial Value of Fuzzy Kohonen Clustering Network

Ogan Komering Ilir (OKI) is located at the eastern of South Sumatra Province, 2030'-4015' latitude and 104020'-106000' longitude. Digital image of land was captured from Landsat 8 satellite path 124/row 062. Landsat 8 is new generation satellite which has two sensors, Operation Land Manager (OLI) and Thermal Infra-Red Sensor (TIRS). In pre-processing step, there are a geometric correction, radiometric correction, and cropping of the digital images which resulting coordinated geography. Classification uses maximum likelihood estimator algorithm. In segmentation process and classification, grey value spread is into evenly after applying histogram technique. The results of entropy value are7.42 which is the highest of result image classification, then the smallest entropy value in the result of correction mapping are 6.39. The three of them prove that they have enough high entropy value. Then the result of peatlands classification is given overall accuracy value = = 94.0012% and overall kappa value = 0.9230 so the result of classification can be considered to be right

Human Face Detection: Manual vs. Kohonen Self Organizing Map

In today's world it is very much important to maintain the security of information and its risks. The biometric-based techniques are very much useful in these problems. Among the several kinds of biometric-based technique, face detection is much complex and much more important. Due to the age and several other problems, a human face structure changes over time, again a human has lots of expressions. Sometimes due to the lighting condition or the variation of the angle of an input device, the pattern of a human face structure also changed. As a result, the face cannot be detected properly. In this paper, a method is proposed that can detect the human faces both automatically and manually very efficiently. In manual mode, a user can select the input faces referred by the system according to their choice. In automated mode, the system detected all possible face areas using the Kohonen Self-Organizing Feature Map technique. This method reduced the complex color image into a vector quantized image with desired colors. Then a color segmentation technique is used to detect the possible face skin areas from the vector quantized image. Then the Histogram Oriented Gradient technique used to detect the feature from the faces and K-Nearest Neighbor Classifier is used to compare both face images detected by the two modes. The automated method prosed better accuracy than the manual method

An Adaptive Color Image Segmentation

A novel Adaptive Color Image Segmentation (ACIS) System for color image segmentation is presented. The proposed ACIS system uses a neural network with architecture similar to the multilayer perceptron (MLP) network. The main difference is that neurons here uses a multisigmoid activation function. The multisigmoid function is the key for segmentation. The number of steps i.e. thresholds in the multisigmoid function are dependant on the number of clusters in the image. The threshold values for detecting the clusters and their labels are found automatically from the first order derivative of histograms of saturation and intensity in the HSV color space. Here, the main use of neural network is to detect the number of objects automatically from an image. The advantage of this method is that no a priori knowledge is required to segment the color image. ACIS label the objects with their mean colors. The algorithm is found to be reliable and works satisfactorily on different kinds of color images. Experimental results show that the performance of ACIS is robust on noisy images also