Microarray Image Denoising Using Complex Gaussian Scale Mixtures of Complex Wavelets

Microarray images when contaminated with noise may severely affect the detection and quantification of gene expression. In this paper, we propose to use the complex Gaussian scale mixture (CGSM) model in complex wavelet domain for noise reduction in complementary DNA microarray images. Based on the joint information in the red and green channel microarray images, we model the complex wavelet coefficients of the channel images jointly using the CGSM, and subsequently perform image denoising using Bayes least square estimator in complex wavelet domain. The experimental results show that using the CGSM of complex wavelet coefficients provides better noise reduction of microarray images compared to other complex wavelet-based models.

[1]  Donald A. Adjeroh,et al.  On denoising and compression of DNA microarray images , 2006, Pattern Recognit..

[2]  Soontorn Oraintara,et al.  The Shiftable Complex Directional Pyramid—Part I: Theoretical Aspects , 2008, IEEE Transactions on Signal Processing.

[3]  G. C. Tiao,et al.  Bayesian inference in statistical analysis , 1973 .

[4]  Nick G. Kingsbury,et al.  Image Denoising Using Derotated Complex Wavelet Coefficients , 2008, IEEE Transactions on Image Processing.

[5]  Levent Sendur,et al.  Bivariate shrinkage functions for wavelet-based denoising exploiting interscale dependency , 2002, IEEE Trans. Signal Process..

[6]  H. Chauris,et al.  Uniform Discrete Curvelet Transform for Seismic Processing , 2008 .

[7]  B. Smolka,et al.  Fast Noise Reduction in CDNA Microarray Images , 2006, 23rd Biennial Symposium on Communications, 2006.

[8]  Richard Baraniuk,et al.  The Dual-tree Complex Wavelet Transform , 2007 .

[9]  A. Venetsanopoulos,et al.  A multichannel order-statistic technique for cDNA microarray image processing , 2004, IEEE Transactions on NanoBioscience.

[10]  Pantelis Georgiadis,et al.  Segmentation of Complementary DNA Microarray Images by Wavelet-Based Markov Random Field Model , 2009, IEEE Transactions on Information Technology in Biomedicine.

[11]  Martin J. Wainwright,et al.  Image denoising using scale mixtures of Gaussians in the wavelet domain , 2003, IEEE Trans. Image Process..

[12]  Zidong Wang,et al.  Microarray Image Analysis: An Algorithmic Approach , 2010 .

[13]  N. Kingsbury Complex Wavelets for Shift Invariant Analysis and Filtering of Signals , 2001 .

[14]  Shahriar Gharibzadeh,et al.  Microarray image enhancement by denoising using decimated and undecimated multiwavelet transforms , 2010, Signal Image Video Process..

[15]  Kostas Marias,et al.  Microarray Image Denoising Using a Two-Stage Multiresolution Technique , 2007, 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007).

[16]  G. Magoulas,et al.  Improved processing of microarray data using image reconstruction techniques , 2003, IEEE Transactions on NanoBioscience.

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

[18]  Pramod Kumar Meher,et al.  The Role of Combined OSR and SDF Method for Pre-Processing of Microarray Data that Accounts for Effective Denoising and Quantification , 2011, J. Signal Inf. Process..

[19]  Geoffrey J. McLachlan,et al.  Analyzing Microarray Gene Expression Data , 2004 .

[20]  I. Selesnick,et al.  Bivariate shrinkage with local variance estimation , 2002, IEEE Signal Processing Letters.

[21]  Roslin Russell,et al.  Microarray Technology in Practice , 2008 .

[22]  Fionn Murtagh,et al.  Fast communication , 2002 .

[23]  Soontorn Oraintara,et al.  Complex Gaussian Scale Mixtures of Complex Wavelet Coefficients , 2010, IEEE Transactions on Signal Processing.

[24]  Musa H. Asyali,et al.  Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling , 2005, Bioinform..

[25]  N. Kingsbury Image processing with complex wavelets , 1999, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[26]  Tamanna Howlader,et al.  Noise Reduction of cDNA Microarray Images Using Complex Wavelets , 2010, IEEE Transactions on Image Processing.

[27]  Kay A. Robbins,et al.  Exploring and Organizing Spatiotemporal Features such as Waves in High Throughput Brain Recordings by Lifting to Feature Space , 2007, 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007).

[28]  Mario Mastriani,et al.  Microarrays Denoising via Smoothing of Coefficients in Wavelet Domain , 2007, 1807.11571.

[29]  Rastislav Lukac,et al.  APPLICATION OF THE ADAPTIVE CENTER-WEIGHTED VECTOR MEDIAN FRAMEWORK FOR THE ENHANCEMENT OF CDNA MICROARRAY IMAGES , 2003 .

[30]  M. West On scale mixtures of normal distributions , 1987 .

[31]  Eero P. Simoncelli,et al.  Image quality assessment: from error visibility to structural similarity , 2004, IEEE Transactions on Image Processing.

[32]  John Quackenbush,et al.  Genesis: cluster analysis of microarray data , 2002, Bioinform..

[33]  Pekka Ruusuvuori,et al.  Evaluating the performance of microarray segmentation algorithms , 2006, Bioinform..