A hierarchical refinement algorithm for fully automatic gridding in spotted DNA microarray image processing

Yu Wang, Marc Q. Ma, Kai Zhang, Frank Shih

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

Gridding, the first step in spotted DNA microarray image processing, usually requires human intervention to achieve acceptable accuracy. We present a new algorithm for automatic gridding based on hierarchical refinement to improve the efficiency, robustness and reproducibility of microarray data analysis. This algorithm employs morphological reconstruction along with global and local rotation detection, non-parametric optimal thresholding and local fine-tuning without any human intervention. Using synthetic data and real microarray images of different sizes and with different degrees of rotation of subarrays, we demonstrate that this algorithm can detect and compensate for alignment and rotation problems to obtain reliable and robust results.

Original languageEnglish (US)
Pages (from-to)1123-1135
Number of pages13
JournalInformation sciences
Volume177
Issue number4
DOIs
StatePublished - Feb 15 2007

All Science Journal Classification (ASJC) codes

  • Software
  • Control and Systems Engineering
  • Theoretical Computer Science
  • Computer Science Applications
  • Information Systems and Management
  • Artificial Intelligence

Keywords

  • Automatic gridding
  • DNA microarray image
  • Gene expression
  • Image processing

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