Gridding spot centers of smoothly distorted microarray images

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

doi:10.1109/TIP.2005.860610

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

Institute of Statistics

Research output: Contribution to journal › Article › peer-review

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 language	English
Pages (from-to)	342-353
Number of pages	12
Journal	IEEE Transactions on Image Processing
Volume	15
Issue number	2
DOIs	https://doi.org/10.1109/TIP.2005.860610
State	Published - 1 Feb 2006

Keywords

Microarray image
Spot gridding

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10.1109/TIP.2005.860610

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AB - 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.

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Gridding spot centers of smoothly distorted microarray images

Abstract

Keywords

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