Abstract
We present an algorithm for automatic spot localization for microarray images with rectangular spot and block packing. As an input, the algorithm requires only the common array design parameters: number of block rows and columns and number of spot rows and columns within each block. It proved to be robust with respect to different types of contamination and can tolerate a high percentage of the missing spots. The validity of the developed algorithm has been tested and confirmed using a large set of images of various designs from different microarray platforms. Comparison with academic and commercial packages has shown that for uncontaminated images our algorithm performs similarly, whereas for certain problematic images it outperforms the other packages.
Similar content being viewed by others
References
Angulo J., Serra J. (2003) Automatic analysis of DNA microarray images using mathematical morphology. Bioinformatics 19, 553–562
Axon Instruments, Inc.: GenePix Pro 5.0. http://www.axon. com, User’s Guide and Tutorial (2003)
Buhler, J., Ideker, T., Haynor, D.: Dapple: improved techniques for finding spots on DNA microarrays. UW CSE Technical Report UWTP 2000-08-05 (2000)
Galinsky V.L. (2003) Automatic registration of microarray images. I. Rectangular grid. Bioinformatics 19, 1824–1831
Hegde P., Qi R., Abernathy K., Gay C., Dharap S., Gaspard R., Hughes J.E., Snesrud E., Lee N., Quackenbush J. (2000) A concise guide to cDNA microarray analysis. Biotechniques 29, 548–562
Herzel H., Beule D., Kielbasa S., Korbel J., Sers C., Malik A., Eickhoff H., Lehrach H., Schuchhardt J. (2001) Extracting information from cDNA arrays. Chaos 11, 98–107
Ishkanian A.S., Malloff C.A., Watson S.K., DeLeeuw R.J., Chi B., Coe B.P., Snijders A., Albertson D.G., Pinkel D., Marra M.A., Ling V., MacAulay C., Lam W.L. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36, 299–303
Jain A.N., Tokuyasu T.A., Snijders A.M., Segraves R., Albertson D.G., Pinkel D. (2002) Fully automated quantification of microarray image data. Genome Res. 12, 325–332
Jung H.Y., Cho H.G. (2002) An automatic block and spot indexing with k-nearest neighbors graph for microarray image analysis. Bioinformatics 18, (Suppl. 2) S141–S151
Koada Technology (2004) Koadarray V.2.3.16. http://www.koada.com
Niles Scientific (2004) SpotReader V.1.1.1.4. http://www.nilesscientific.com
Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W.L., Chen C., Zhai Y., Dairkee S.H., Ljung B.M., Gray J.W., Albertson D.G. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207–211
Steinfath M., Wruck W., Seidel H., Lehrach H., Redelof U., O’Brien J. (2001) Automated image analysis for array hybrodization experiments. Bioinformatics 17, 634–641
Yang Y.H., Buckley M.J., Dudoit S., Speed T.P. (2002) Comparison of methods for image analysis on cDNA microarray data. J. Comput. Graph. Stat. 11, 108–136
Author information
Authors and Affiliations
Corresponding author
Additional information
Patent pending.
Rights and permissions
About this article
Cite this article
Novikov, E., Barillot, E. A noise-resistant algorithm for grid finding in microarray image analysis. Machine Vision and Applications 17, 337–345 (2006). https://doi.org/10.1007/s00138-006-0040-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00138-006-0040-4