The Journal of Korean Institute of Communications and Information Sciences (한국통신학회논문지)

The Korean Institute of Commucations and Information Sciences (한국통신학회)
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Nonlinear matching measure for the analysis of on-off type microarray image

온-오프 형태의 DNA 마이크로어레이 영상 분석을 위한 비선형 정합도

  • 류문호 ((주)바이오메드랩) ;
  • 김종대 (한림대학교 정보전자공과대학 정보통신공학부)
  • Published : 2005.03.01
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Abstract

In this paper, 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 the template matching method. The proposed measure is obtained by binary-thresholding over the whole template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance in terms of the classification ability of the successfulness of the locating markers. The proposed measure is evaluated for the scanned images of HPV DNA microarrays where the marker locating is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping 22 types of the human papilloma virus(HPV). The proposed measure is proven to give more discriminative response reducing the miss cases of the successful marker locating.

본 논문에서는 교잡반응된 스팟을 템플릿 정합법으로 감지하는 온-오프 형태의 DNA 마이크로어레이 영상의 자동분석을 위한 새로운 비선형 정합도를 제안한다. HPV DNA 칩의 목표 스팟은 인유두종 바이러스(HPV)의 종을 알아내기 위해서 설계된다. 제안하는 척도는 전체 템플릿 영역을 이진 문턱값으로 양극화하여 스팟 영역 내의 밝은 화소의 개수를 취해서 얻는다. 이 척도를 추정된 마커 위치의 정확도 관점에서 평가하여 정규화된 상관도보다 우수함을 보인다.

Keywords

References

  1. N. Brandle, H. Bischof and H. Lapp, 'A generic and robust approach for the analysis of spot array images,' Proceedings of SPIE vol. 4266, pp. 1-12, 2001 https://doi.org/10.1117/12.427983
  2. L. M. Kegelmeyer, L. Tomsascik-Cheeseman, M. S. Burnett, P. van Hummelen and A. J. Wyrobek, 'A groundtruth approach to accurate quantitation of fluorescence microarrays,' Proceedings of SPIE vol. 4266, pp. 35-45, 2001
  3. Z. Z. Zhou, J. A. Stein and Q. Z. Ji, 'GLEAMS: A novel approach to high throughput genetic micro-array image capture and analysis,' Proceedings of SPIE vol. 4266, pp. 13-23, 2001 https://doi.org/10.1117/12.427992
  4. T. Bergermann, F. Quiaoit, J. Delrow and L. P. Zhao, 'Statistical issues in signal extraction from microarrays,' Proceedings of SPIE vol. 4266, pp. 24-33, 2001 https://doi.org/10.1117/12.427997
  5. J. D. Kim, S. K. Kim, J. S. Cho and J. Kim, 'Knowledge-based image processing for on-off type DNA microarray,' Proceedings of SPIE vol. 4623, pp. 38-46, 2002 https://doi.org/10.1117/12.469458
  6. Y. Chen, E. R. Dougherty, and M. L. Bittner, 'Ratio-based decisions and the quantitative analysis of cDNA microarray images,' Journal of Biomedical Optics 2(4), pp. 364-374, Oct. 1997 https://doi.org/10.1117/12.281504
  7. J. C. Russ, The Image Processing Handbook, CRC Press, 1999