Gridding spot centers of smoothly distorted microarray images

Jinn Ho*, Wen Liang Hwang, Henry Horn Shing Lu, D. T. Lee

*Corresponding author for this work

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images, and we compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically.

Original languageEnglish
Pages (from-to)342-353
Number of pages12
JournalIEEE Transactions on Image Processing
Volume15
Issue number2
DOIs
StatePublished - 1 Feb 2006

Keywords

  • Microarray image
  • Spot gridding

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