A Review of Image Analysis Techniques for Gene Spot Identification in cDNA Microarray Images Rezaul Karim Md. Khaliluzzaman Sohel Mahmud Dept. of Computer Science & Engineering Dept. of Computer Science & Engineering Dept. of Computer Science & Engineering University of Chittagong University of Information Technology & Sciences Shah Jalal University of Science & Technology Chittagong, Bangladesh Chittagong, Bangladesh Sylhet, Bangladesh E-mail: pinnacle_of_success@yahoo.com E-mail: khalil_021@yahoo.co.in E-mail: sohel.digitalhive@gmail.com Abstract -This paper reports about the latest instrumentation technique of Gene Expression using DNA Microarray. DNA Microarray Image Analysis is a new and exciting computing paradigm with biological background. It involves the concepts ranging from Molecular Biology, Statistics to Computation while including theories and practices of computer science. Study in DNA Microarray includes the Gene Expression, Genetic Data Management, Repository system and the algorithms of image analysis. The aim of this review paper is to give an overview of the basic concepts of DNA Microarray based Genomic research, methodology and to discuss the pros and cons of some algorithms for cDNA Microarray image analysis. This paper is expected to benefit researchers and academics in Genomics. Keywords - Genomics, Gridding, Hybridization, Microarray, Probe, Segmentation. I. INTRODUCTION The term “MICROARRAY” has come to refer to a series of high density DNA spots bound to some solid support. DNA microarray is a collection of microscopic DNA spots attached to a solid surface, such as glass, plastic or silicon chip forming an array for the purpose of monitoring of expression levels for thousands of genes simultaneously. Microarrays are microscope slides that contain an ordered series of samples (DNA, RNA, protein, tissue). The type of microarray depends upon the material placed onto the slide: DNA, DNA microarray; RNA, RNA microarray; protein, protein microarray; tissue, tissue microarray [2]. Since the samples are arranged in an ordered fashion data obtained from the microarray can be traced back to any of the samples. This means that genes on the microarray are addressable. The number of ordered samples on a microarray can number into the hundred of thousands. Basis is the Southern Blot technique as devised by Edwin Southern [1]. While capillary transfer of DNA to a support membrane (nylon or nitrocellulose) does a southern blot, microarrays bind DNA to a solid support, such as glass, using automated processes. This allows for much higher and more consistent spot densities to be realized, thus increasing the number of samples that can be probed at once. The immobilized DNA molecules can be probed with labeled complementary sequences of DNA. Microarrays have many uses in the research lab. The typical microarray contains several thousands of addressable genes. The most commonly used microarray is the DNA microarray. The DNA printed or spotted onto the slides can be chemically synthesized long oligonucleotides or enzymatically generated PCR products. The slides contain chemically reactive groups (typically aldehydes or primary amines) that help to stabilize the DNA onto the slide, either by covalent bonds or electrostatic interactions. An alternative technology allows the DNA to be synthesized directly onto the slide itself by a photolithographic process. This process has been commercialized and is widely available. [2] The key applications are:  The expression levels of genes in a sample, commonly termed Gene Expression Profiling - 36 -