Abstract
A new method is proposed for improving microarray spot segmentation for gene quantification. The method introduces a novel combination of three image processing stages, applied locally to each spot image: i/ Fuzzy C-Means unsupervised clustering, for automatic spot background noise estimation, ii/ power spectrum deconvolution filter design, employing background noise information, for spot image restoration, iii/ Gradient-Vector-Flow (GVF-Snake), for spot boundary delineation. Microarray images used in this study comprised a publicly available dataset obtained from the database of the MicroArray Genome Imaging & Clustering Tool website. The proposed method performed better than the GVF-Snake algorithm (Kullback-Liebler metric: 0.0305 bits against 0.0194 bits) and the SPOT commercial software (pairwise mean absolute error between replicates: 0.234 against 0.303). Application of efficient adaptive spot-image restoration on cDNA microarray images improves spot segmentation and subsequent gene quantification.
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Daskalakis, A. et al. (2007). Development of a Cascade Processing Method for Microarray Spot Segmentation. In: MartÃ, J., BenedÃ, J.M., Mendonça, A.M., Serrat, J. (eds) Pattern Recognition and Image Analysis. IbPRIA 2007. Lecture Notes in Computer Science, vol 4477. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72847-4_53
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DOI: https://doi.org/10.1007/978-3-540-72847-4_53
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