An Automated Gridding and Segmentation Method for cDNA Microarray Image Analysis

Abstract

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 labor intensive 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