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Proceedings Paper

GLEAMS: a novel approach to high-throughput genetic microarray image capture and analysis
Author(s): Zheng Zheng Zhou; Jaime A. Stein; Qien Zhou Ji
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Paper Abstract

GLEAMS is a robust, stable and accurate image capture and quantification method for microarrays. It is capable of fully and automatically detecting and quantifying the expression spots. This can be done in a batch mode, without human intervention, achieving a high throughput of parallel data processing. Simple to use visual tools are provided to estimate parameters and to submit, monitor and control jobs execution. The un-supervised batch auto-alignment is based on a novel method requiring only knowledge of the number of rows and columns of dots in the array. Distances between dots along rows and columns are estimated from the image's auto- correlation function. This is also used to align the array and the sides of the image. Applying intensity and geometric constraints to the cross-correlation function between the image and a template sub-array, the location of the sub-arrays can be determined. Carefully implemented, the algorithm can approach human vision in its sensitivity and accuracy in finding the general positions of dots in a micro-array image. Subsequent spot quantification uses Ostu's thresholding method followed by some morphological operations, including the application of a constraining shape mask. Segmentation techniques are applied to detect and remove speckles from the targets and to ensure the veracity of the data extracted.

Paper Details

Date Published: 4 June 2001
PDF: 11 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427992
Show Author Affiliations
Zheng Zheng Zhou, NuTec Sciences, Inc. (United States)
Jaime A. Stein, NuTec Sciences, Inc. (United States)
Qien Zhou Ji, NuTec Sciences, Inc. (United States)

Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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