Abstract
cDNA micro arrays are more and more frequently used in molecular biology as they can give insight into the relation of an organism’s metabolism and its genome. The process of imaging a micro array sample can introduce a great deal of noise and bias into the data with higher variance than the original signal which may swamp the useful information. As imperfections and fabrication artifacts often impair our ability to measure accurately the quantities of interest in micro array images, image processing for analysis of these images is an important and challenging problem. How to eliminate the effect of the noise imposes a challenging problem in micro array analysis. In this paper we implemented a novel algorithm for image sifting which could remove objects with definite size from macro array images. We used regular moving grids to sift noise object and obtained clean images for segmentation. The results have been compared with SWT, DWT and wiener filter denoising.
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References
Southern, E.M.: Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503–517 (1975)
Schena, M., Shalon, D., Davis, R.W., Brown, P.O.: uantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995)
Fodor, S.P.A., Read, J.L., Pirrung, M.C., Stryer, L., Lu, A.T., Solas, D.: Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767–773 (1991)
Steinfath, M., Wruch, W., Seidel, H., Lehrach, H., Radelof, U., O’Brien, J.: Automated image analysis for array hybridization experiments. Bioinformatics 17(7), 634–641 (2001)
Bozinov, D., Rahnenfuhrer, J.: Unsupervised technique for robust target separation and analysis of DNA microarray spots. Bioinformatics 18(5), 747–756 (2002)
Wruch, W., Griffiths, H., Steinfath, M., Lehrach, H., Radelof, U., O’Brien, J.: Xdigitise: Visualization of hybridization experiments. Bioinformatics 18(5), 757–760 (2002)
Zapala, M.A., Lockhart, D.J., Pankratz, D.G., Garcia, A.J., Barlow, C., Lockhard, D.J.: Software and methods for oligonucleotide and cDNA array data analysis. Genome Biol. 3(6) (2002)
Jain, A.N., Tokuyasu, T.A., Snijders, A.M., Segraves, R., Albertson, D.G., Pinkel, D.: Fully automatic quantification of microarray image data. Genome Res. 12, 325–332 (2002)
Kerr, M.K., Martin, M., Churchill, G.A.: Analysis of variance gene expression microarray data. J.Comput. Biol. 7, 819 (2001)
Chen, Y., Dougherty, E.R., Bittner, M.L.: Ratio-based decision the quantitative analysis of cDNA microarray images. J. Biomed. Optics, 364–374 (1997)
Ermolaeva, O., Rastogi, M., Pruitt, K.D., Schuler, G.D., Bittner, M.L., Chen, R., Simon, P.M., Trent, J.M., Boguski, M.: Data management and analysis for gene expression arrays. Nature Genetics 20, 19–23 (1998)
Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R., Tsui, K.W.: On differential variability of expression ratios: Improving statistical inference about gene xpression changes from microarray data. J. Computat. Biol. 8, 37–52 (2001)
Otsu, N.: A Threshold Selection Method from Gray-Level Histograms. IEEE Transactions on Systems, Man, and Cybernetics 9(1), 62–66 (1979)
Wang, Z., Bovik, A.: A universal image quality index. IEEE Trans. Signal Processing Letter 9, 81–84 (2002)
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Jafari Moghadam, P., Moradi, M.H. (2007). Image Sifting for Micro Array Image Enhancement. In: Kropatsch, W.G., Kampel, M., Hanbury, A. (eds) Computer Analysis of Images and Patterns. CAIP 2007. Lecture Notes in Computer Science, vol 4673. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74272-2_108
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DOI: https://doi.org/10.1007/978-3-540-74272-2_108
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