Title page for ETD etd-07112001-112357

Type of Document Master's Thesis
Author Jouenne, Vincent Y
URN etd-07112001-112357
Title Critical Issues in the Processing of cDNA Microarray Images
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Heath, Lenwood S. Committee Chair
Alscher, Ruth G. Committee Member
Struble, Craig A. Committee Member
  • Mann-Whitney Test
  • Image Processing
  • Segmentation
  • Gene Expression
  • Data Extraction
  • Seeded Region Growing Algorithm
  • Automatic Gridding
Date of Defense 2001-06-28
Availability unrestricted

Microarray technology enables simultaneous gene expression level

monitoring for thousands of genes. While this technology has now

been recognized as a powerful and cost-effective tool for

large-scale analysis, the many systematic sources of experimental

variations introduce inherent errors in the extracted data. Data

is gathered by processing scanned images of microarray slides.

Therefore robust image processing is particularly important and

has a large impact on downstream analysis. The processing of the

scanned images can be subdivided in three phases: gridding,

segmentation and data extraction. To measure the gene expression

levels, the processing of cDNA microarray images must overcome a

large set of issues in these three phases that motivates this


This study presents automatic gridding methods and compares their

performances. Two segmentation techniques already used, the Seeded

Region Growing Algorithm and the Mann-Whitney Test, are examined.

We present limitations of these techniques. Finally, we studied

the data extraction method used in MicroArray Suite (MS), a

microarray analysis software, via synthetic images and explain its


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