A new FPGA-based edge detection system for the gridding of DNA microarray images

A deoxyribonucleic acid (DNA) microarray is a collection of microscopic DNA spots attached to a solid surface, such as glass, plastic or silicon chip forming an array. DNA microarray technologies are an essential part of modern biomedical research. The analysis of DNA microarray images allows the identification of gene expressions in order to draw biologically meaningful conclusions for applications that ranges from the genetic profiling to the diagnosis of oncology diseases. Unfortunately, DNA microarray technology has a high variation of data quality. Therefore, in order to obtain reliable results, complex and extensive image analysis algorithms should be applied before actual DNA microarray information can be used for biomedical purpose. In this paper, we present a novel hardware acceleration architecture specifically designed to process and measure DNA microarray images. The proposed architecture uses several units working in a single instruction-multiple data fashion managed by a microprocessor core. An FPGA-based prototypal implementation of the developed architecture is presented. Experimental results on several realistic DNA microarray images show a reduction of the computation time of one order of magnitude if compared with previously developed software-based approach.