A new hardware architecture for performing the gridding of DNA microarray images

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 drawn 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 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.

[1]  Yuan-Kai Wang,et al.  DNA microarray image analysis using active contour model , 2004 .

[2]  R.S.H. Istepanian,et al.  Microarray image enhancement by denoising using stationary wavelet transform , 2003, IEEE Transactions on NanoBioscience.

[3]  Peter Bajcsy,et al.  An Overview of DNA Microarray Image Requirements for Automated Processing , 2005, 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Workshops.

[4]  Terence P. Speed,et al.  Comparison of Methods for Image Analysis on cDNA Microarray Data , 2002 .

[5]  I. Xilinx,et al.  Virtex-II Pro and Virtex-II Pro X Platform FPGAs: Complete data sheet , 2004 .

[6]  Robert B. Fisher,et al.  Hypermedia image processing reference , 1996 .

[7]  Shadrokh Samavi,et al.  A Pipeline Architecture for Processing of DNA Microarrays Images , 2004, J. VLSI Signal Process..

[8]  Yuan-Kai Wang,et al.  DNA microarray image analysis using active contour model , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[9]  Peter Bajcsy.  Gridline: automatic grid alignment DNA microarray scans , 2004, IEEE Transactions on Image Processing.

[10]  David Botstein,et al.  The Stanford Microarray Database , 2001, Nucleic Acids Res..

[11]  John F. Canny,et al.  A Computational Approach to Edge Detection , 1986, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[12]  M. Goldstein,et al.  Analysis of Gene Expression Data , 2022 .