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Journal of Biomedical Optics

Nonlinear matching measure for the analysis of on-off type DNA microarray images
Author(s): Munho Ryu; Jong Dae Kim; Byoung Goo Min; Myung-Geol Pang; Jongwon Kim
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Paper Abstract

We propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by a template-matching method. The proposed measure is obtained by binary thresholding over the entire template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance method in terms of classifying the ability to successfully locate markers. The proposed measure was evaluated for scanned images of human papillomavirus (HPV) DNA microarrays where locating markers is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping twenty-two types of the human papillomavirus. The proposed measure is proven to give a more discriminative response, reducing the missed cases of successful marker location. The locating accuracy of the proposed method is also shown to have the same performance as that of the normalized covariance.

Paper Details

Date Published: 1 May 2004
PDF: 7 pages
J. Biomed. Opt. 9(3) doi: 10.1117/1.1691026
Published in: Journal of Biomedical Optics Volume 9, Issue 3
Show Author Affiliations
Munho Ryu, Seoul National Univ. (South Korea)
Jong Dae Kim, Hallym Univ. (South Korea)
Byoung Goo Min, Seoul National University - College of Medicine (South Korea)
Myung-Geol Pang, Chung-Ang Univ - College of Industrial Sciences (South Korea)
Jongwon Kim, BioMedLab Co., Ltd. (South Korea)

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