Microscope Image Processing.pdf

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Microscope Image Processing

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Microscope Image Processing Qiang Wu Fatima A. Merchant Kenneth R. Castleman AMSTERDAM • BOSTON HEIDELBERG LONDON NEW YORK OXFORD PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO Academic Press is an imprint of Elsevier

Academic Press is an imprint of Elsevier 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald’s Road, London WC1X 8RR, UK This book is printed on acid-free paper. Copyright ß 2008, Elsevier Inc. All rights reserved. Exception: The appendix, Glossary of Microscope Image Processing Terms, is copyright ß 1996 Pearson Education (from Digital Image Processing, First Edition by Kenneth R. Castleman and reprinted by permission of Pearson Education, Inc.). No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (þ 44) 1865 843830, fax: (þ 44) 1865 853333, E-mail: permissions@elsevier.com. You may also complete your request on-line via the Elsevier homepage (http://elsevier.com), by selecting ‘‘Support & Contact’’ then ‘‘Copyright and Permission’’ and then ‘‘Obtaining Permissions.’’ Library of Congress Cataloging-in-Publication Data Application submitted. British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. ISBN: 978-0-12-372578-3 For information on all Academic Press publications visit our Web site at www.books.elsevier.com Printed in the United States of America 08 09 10 11 12 8 7 6 5 4 3 2 1

Foreword Preface Acknowledgments 1 Introduction Kenneth R. Castleman and Ian T. Young 1.1 The Microscope and Image Processing 1.2 Scope of This Book 1.3 Our Approach 1.3.1 The Four Types of Images 1.3.1.1 Optical Image 1.3.1.2 Continuous Image 1.3.1.3 Digital Image 1.3.1.4 Displayed Image 1.3.2 The Result 1.3.2.1 Analytic Functions 1.3.3 The Sampling Theorem 1.4 The Challenge 1.5 Nomenclature 1.6 Summary of Important Points 2 Fundamentals of Microscopy Kenneth R. Castleman and Ian T. Young 2.1 Origins of the Microscope 2.2 Optical Imaging 2.2.1 Image Formation by a Lens 2.2.1.1 Imaging a Point Source 2.2.1.2 Focal Length 2.2.1.3 Numerical Aperture 2.2.1.4 Lens Shape 2.3 Diffraction-Limited Optical Systems 2.3.1 Linear System Analysis Contents xxi xxiii xxv 1 1 1 3 3 4 4 4 5 5 6 7 8 8 8 11 11 12 12 13 13 14 15 15 16 v

Contents 2.4 Incoherent Illumination 2.4.1 The Point Spread Function 2.4.2 The Optical Transfer Function 2.5 Coherent Illumination 2.5.1 The Coherent Point Spread Function 2.5.2 The Coherent Optical Transfer Function 2.6 Resolution 2.6.1 Abbe Distance 2.6.2 Rayleigh Distance 2.6.3 Size Calculations 2.7 Aberration 2.8 Calibration 2.8.1 Spatial Calibration 2.8.2 Photometric Calibration 2.9 Summary of Important Points 3 Image Digitization Kenneth R. Castleman 3.1 3.2 Resolution 3.3 Sampling Introduction 3.3.1 Interpolation 3.3.2 Aliasing 3.4 Noise 3.5 Shading 3.6 Photometry 3.7 Geometric Distortion 3.8 Complete System Design 3.8.1 Cumulative Resolution 3.8.2 Design Rules of Thumb 3.8.2.1 Pixel Spacing 3.8.2.2 Resolution 3.8.2.3 Noise 3.8.2.4 Photometry 3.8.2.5 Distortion 3.9 Summary of Important Points Image Display Kenneth R. Castleman 4.1 4.2 Display Characteristics Introduction 4.2.1 Displayed Image Size 4 vi 16 16 17 18 18 19 20 21 21 21 22 22 23 23 24 27 27 28 29 30 32 33 34 34 35 35 35 36 36 36 36 36 37 37 39 39 40 40

4.2.2 Aspect Ratio 4.2.3 Photometric Resolution 4.2.4 Grayscale Linearity 4.2.5 Low-Frequency Response 4.2.5.1 Pixel Polarity 4.2.5.2 Pixel Interaction 4.2.6 High-Frequency Response 4.2.7 The Spot-Spacing Compromise 4.2.8 Noise Considerations 4.3 Volatile Displays 4.4 Sampling for Display Purposes 4.4.1 Oversampling 4.4.2 Resampling 4.5 Display Calibration 4.6 Summary of Important Points 5 Geometric Transformations Kenneth R. Castleman 5.1 5.2 5.3 Gray-Level Interpolation Introduction Implementation 5.3.1 Nearest-Neighbor Interpolation 5.3.2 Bilinear Interpolation 5.3.3 Bicubic Interpolation 5.3.4 Higher-Order Interpolation 5.4 Spatial Transformation 5.4.1 Control-Grid Mapping 5.5 Applications 5.5.1 Distortion Removal 5.5.2 Image Registration 5.5.3 Stitching 5.6 Summary of Important Points 6 Image Enhancement Yu-Ping Wang, Qiang Wu, and Kenneth R. Castleman 6.1 6.2 Spatial Domain Methods Introduction 6.2.1 Contrast Stretching 6.2.2 Clipping and Thresholding 6.2.3 Image Subtraction and Averaging 6.2.4 Histogram Equalization 6.2.5 Histogram Speciﬁcation Contents 40 41 42 42 42 43 43 43 43 44 45 46 46 47 47 51 51 52 52 53 53 54 54 55 55 56 56 56 56 57 59 59 60 60 61 61 62 62 vii

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