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Products - Books & Software - DNA Array Image Analysis Compilation Focusing on Microarray Scanning and Data Analysis

DNA Array Image Analysis Nuts & Bolts
Edited by
Gerda Kamberova, Ph.D. and Shishir Shah, Ph.D.
Publisher: Xela Schenk
Cover Design and Production Layout: Alex Nartea
200 Pages
ISBN 0-9664027-5-8

Chapter 1
Microarray and Image Analysis: Introduction
Gerda Kamberova, Shishir Shah

Chapter 2
Introduction to Image Analysis
Gerda Kamberova

Chapter 3
Advantages of Laser Confocal Microarray Scanning
Mark McGovern, Reda Fayek

Chapter 4
Considerations for a Quality Microarray Scanner
Scott J. Vacha, Jeffrey McMillan, Andreas Dorsel (Agilent Technologies, Inc.)

Chapter 5
Key Considerations for Accurate Microarray Scanning
and Image Analysis.
Shawn Handran, Siobahn Pickett, Damian Verdnik (Axon Instruments, Inc.)

Chapter 6
Microarray Image Processing and Quality Control
Anton Petrov, Shishir Shah, Sorin Draghici, Soheil Shams

Chapter 7
Microarray Data Normalization
Michael F. Ochs, Ghislain Bidaut

Chapter 8
Quantitative Comparison of Image Analysis Software
Diane Moody, Bassem Fadlia, Abhay Singh, Swapnal Shah, Lauren McIntyreDNA-Arrayit-Image-Analysis-Nuts-Bolt

Chapter 9
DNA Array Information Workflow and Data Management
Manuel Duval

Chapter 10
BAC Microarrays
S. Shah, J.P. Gregg, M. Mohammed, W. Yu, S. Damani, R. Locker


Chapter 1: Microarrays and Image Analysis: Introduction
The chapter provides brief introduction to microarray technology and the challenges of image analysis in this field. It outlines the objectives of the book. Chapter 1 is intended as a reading material for students and researchers with different scientific backgrounds who are just entering the exciting field of microarray research and applications.

Chapter 2: Introduction to Image Analysis
The chapter introduces basic image analysis terminology and techniques. The digital image, its various representations, and properties are presented. The process of image formation, noise, and noise sources are reviewed. The author discusses important image processing operations. Estimation of image parameters in the presence of noise is addressed. The chapter contains an appendix including mathematical definitions from Fourier analysis and probability theory.

Chapter 3: Advantages of Laser Confocal Microarray Scanning
This chapter provides a general understanding of different approaches used to design commercial microarray scanners. Particular attention is given to laser confocal microarray scanners. Important issues in the authors’ discussion are resolution, sensitivity, the use of multiple dyes, and other requirements in the design of commercial microarray scanners.

Chapter 4: Considerations for a Quality Microarray Scanner
This chapter continues the discussion on microarray scanners. Although intended as a general introduction, several features of Agilent’s SureScan™ Technology are introduced. The authors discuss issues of instrument noise, sensitivity and resolution.

Chapter 5: Key Considerations for Accurate Microarray Scanning and Image Analysis
This chapter reviews how to obtain the most reliable performance from the microarray scanner. The authors from Axon, Inc. discuss several image analysis methods used in microarray experiments, including numerical pre-processing methods that can be considered prior to cluster analysis of large sets of microarray data.

Chapter 6: Microarray Image Processing and Quality Control
Chapter 6 describes the issues of spot finding, microarray image segmentation, and quality control issues in microarray image analysis. The authors discuss automated batch analysis of microarray images.

Chapter 7: Microarray Data Normalization
This chapter discusses the issue of data normalization for spotted microarrays. The authors dwell on background correction, and data normalization, including a summary of each of the methods which have been widely used. A sample procedure for data normalization is then given along with a brief discussion of types of noise which normalization cannot handle.

Chapter 8: Quantitative Comparison of Image Analysis Software
In this chapter, the authors from Purdue University describe a systematic evaluation of three microarray data acquisition software packages. In order to provide a benchmark to which investigators may compare the reliability of data acquisition in their own experiments, they have evaluated these software packages using a variety of different types of arrays (macro and microarrays; glass and nylon; cDNA and bacterial). The reliability, accuracy, and throughput of data generated from each type of microarray and each software package are discussed.

Chapter 9: DNA Array Information Workflow and Data Management
This chapter outlines the flow of data in a microarray experiment. It discusses some aspects of microarray database management and data mining.

Chapter 10: BAC Microarrays
This chapter discusses an emerging application for microarray technology, which utilizes bacterial artificial chromosomes (BACs). The authors focus on the experimental design, image analysis and data normalization.

Gerda Kamberova, Ph.D. is an Assistant Professor in Computer Science at Hofstra University, New York. She teaches computer vision, computer graphics, and artificial intelligence. Her Ph.D in Computer Science is from the University of Pennsylvania, Philadelphia. Dr. Kamberova has published research papers in computer vision, robotics, and applied statistics. Her current research interests are in shape representation and recovery and 3D data compression.

Gerda L. Kamberova, Ph.D., 103 Hofstra University, Department of Computer Science, Hempstead, NY 11549 U.S.A. E-mail:

Shishir Shah, Ph.D. is an Associate Professor at Wayne State University (Detroit, MI). Dr. Shah is an author of numerous publications on image analysis and data mining. His current interests are developing new applications for BAC arrays, enhanced microarray image processing and data analysis.

Shishir Shah, Ph.D., 2302 Oak Links Avenue, Houston, TX 77059 U.S.A.

This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Efforts have been made to publish reliable data and information, but the author and the publisher can not assume responsibility for the validity of all materials or for the consequences of their use. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any information storage or retrieval system, without prior permission in writing from the publisher. All rights reserved. Authorization to photocopy items for internal use or personal use, or the personal or internal use of specific clients, may be granted by DNA Press LLC, provided that $0.50 per page photocopied is paid directly to Copyright Clearance Center, 27 Congress Street, Salem, MA 01970 USA. The fee code for users of the Transactional Reporting Service is ISBN 0-9664027-5- 8/02/$0.00+$.50. The fee is subject to change without notice. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. The consent of DNA Press LLC does not extend to copying general distribution, for promotion, for creating new works, or for resale. Specific permission must be obtained in writing from DNA Press

LLC for such copying.

Direct all inquiries to DNA Press LLC. For information and mailing address see
©2002 by DNA Press LLC
No claim to original U.S. Government works
International Standard Book Number ISBN 0-9664027-5-8
Printed in the United States of America 2 3 4 5 6 7 8 9 0
First printing 2002
Printed on acid-free paper.

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DNA Array Image Analysis: Nuts and Bolts

A brief introduction to microarray technology and the challenges of image analysis in this field.



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