bernd jahne - practical handbook on image processing for scientific and technical applications

Practical Handbook on IMAGE PROCESSING for SCIENTIFIC and TECHNICAL APPLICATIONS SECOND EDITION © 2004 by CRC Press LLC CRC PRESS Boca Raton London New York Washington, D.C. Practical Handbook on IMAGE PROCESSING for SCIENTIFIC and TECHNICAL APPLICATIONS Bernd Jähne University of Heidelberg SECOND EDITION © 2004 by CRC Press LLC 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. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. 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Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identiÞcation and explanation, without intent to infringe. © 2004 by CRC Press LLC No claim to original U.S. Government works International Standard Book Number 0-8493-1900-5 Library of Congress Card Number 2004043570 Printed in the United States of America 1 2 3 4 5 6 7 8 9 0 Printed on acid-free paper Library of Congress Cataloging-in-Publication Data Jèahne, Bernd, 1953- Practical handbook on image processing for scientiÞc and technical applications / Berne Jèahne.— 2nd ed. p. cm. Includes bibliographical references and index. ISBN 0-8493-1900-5 (alk. paper) 1. Image processing—Digital techniques—Handbooks, manuals, etc. I. Title. TA1637.J347 2004 621.36¢7—dc22 2004043570 © 2004 by CRC Press LLC Visit the CRC Press Web site at www.crcpress.com Preface What This Handbook Is About Digital image processing is a fascinating subject in several aspects. Human beings perceive most of the information about their environment through their visual sense. While for a long time images could only be captured by photography, we are now at the edge of another technological revolution that allows image data to be captured, manipulated, and evaluated electronically with computers. With breathtaking pace, computers are becoming more powerful and at the same time less expensive. Thus, the hardware required for digital image processing is readily available. In this way, image processing is becoming a common tool to analyze multidi- mensional scientific data in all areas of natural science. For more and more scientists, digital image processing will be the key to studying complex scientific problems they could not have dreamed of tackling only a few years ago. A door is opening for new interdisciplinary cooperation merging computer science with corresponding research areas. Thus, there is a need for many students, engineers, and researchers in natural and technical disciplines to learn more about digital image processing. Since original image processing literature is spread over many disciplines, it is hard to gather this information. Furthermore, it is important to realize that image process- ing has matured in many areas from ad hoc, empirical approaches to a sound science based on well-established principles in mathematics and physical sciences. This handbook tries to close this gap by providing the reader with a sound basic knowledge of image processing, an up-to-date overview of advanced concepts, and a critically evaluated collection of the best algorithms, demonstrating with real-world applications. Furthermore, the handbook is augmented with usually hard-to-find prac- tical tips that will help to avoid common errors and save valuable research time. The wealth of well-organized knowledge collected in this handbook will inspire the reader to discover the power of image processing and to apply it adequately and successfully to his or her research area. However, the reader will not be overwhelmed by a mere collection of all available methods and techniques. Only a carefully and critically eval- uated selection of techniques that have been proven to solve real-world problems is presented. Many concepts and mathematical tools, which find widespread application in nat- ural sciences, are also applied to digital image processing. Such analogies are pointed out because they provide an easy access to many complex problems in digital image processing for readers with a general background in natural sciences. The author — himself educated in physics and computer science — merges basic research in digital image processing with key applications in various disciplines. This handbook covers all aspects of image processing from image formation to im- age analysis. Volumetric images and image sequences are treated as a natural extension of image processing techniques from two to higher dimensions. III © 2004 by CRC Press LLC IV Prerequisites It is assumed that the reader is familiar with elementary matrix algebra as well as the Fourier transform. Wherever possible, mathematical topics are described intuitively, making use of the fact that image processing is an ideal subject to illustrate even complex mathematical relations. transform to the extent required to understand this handbook. This appendix serves also as a convenient reference to these mathematical topics. How to Use This Handbook This handbook is organized by the tasks required to acquire images and to analyze them. Thus, the reader is guided in an intuitive way and step by step through the chain of tasks. The structure of most chapters is as follows: 1. A summary page highlighting the major topics discussed in the chapter. 2. Description of the tasks from the perspective of the application, specifying and detailing what functions the specific image processing task performs. 3. Outline of concepts and theoretical background to the extent that is required to fully understand the task. 4. Collection of carefully evaluated procedures including illustration of the theoretical performance with test images, annotated algorithms, and demonstration with real- world applications. 5. Ready-to-use reference data, practical tips, references to advanced topics, emerg- ing new developments, and additional reference material. This reference material is parted into small units, consecutively numbered within one chapter with boxed numbers, e. g., 3.1 . The reference item is referred to by this number in the follow- ing style: 3.1 and 3.3. individual chapters are written as much as possible in an internally consistent way. The glossary is unique in the sense that it covers not only image processing in a narrow sense but all important associated topics: optics, photonics, some important general terms in computer science, photogrammetry, mathematical terms of relevance, and terms from important applications of image processing. The glossary contains a brief definition of terms used in image processing with cross-references to find further infor- mation in the main text of the handbook. Thus, you can take the glossary as a starting point for a search on a specific item. All terms contained in the indices are emphasized by typesetting in italic style. Acknowledgments Many of the examples shown in this handbook are taken from my research at Scripps Institution of Oceanography (University of California, San Diego) and at the Institute for Environmental Physics and the Interdisciplinary Center for Scientific Computing (University of Heidelberg). I gratefully acknowledge financial support for this research from the US National Science Foundation (OCE91-15944-02, OCE92-17002, and OCE94- 09182), the US Office of Naval Research (N00014-93-J-0093, N00014-94-1-0050), and the German Science Foundation, especially through the interdisciplinary research unit © 2004 by CRC Press LLC Exceptions from this organization are only the two introductory Chapters 1 and 2. The Another key to the usage of the handbook is the detailed indices and the glossary. Appendix B outlines linear algebra and the Fourier V FOR240 “Image Sequence Analysis to Study Dynamical Processes”. I cordially thank I would also express my sincere thanks to the staff of CRC Press for their constant interest in this handbook and their professional advice. I am most grateful for the invaluable help of my friends at AEON Verlag & Studio in proofreading, maintaining the databases, and in designing most of the drawings. I am also grateful to the many individuals, organizations, and companies that pro- vided valuable material for this handbook: • Many of my colleagues — too many to be named individually here — who worked together with me during the past seven years within the research unit “Image Se- quence Analysis to Study Dynamical Processes” at Heidelberg University • Dr. M. Bock, DKFZ Heidelberg • Dr. J. Klinke, PORD, Scripps Institution of Oceanography, University of California, San Diego • Prof. H G. Maas, Institute of Photogrammetry and Remote Sensing, University of Dresden • Prof. J. Ohser, FH Darmstadt • Dr. T. Scheuermann, Fraunhofer Institute for Chemical Technology, Pfinztal, Ger- many • Prof. Trümper, Max-Planck-Institute for Extraterrestric Physics, Munich • ELTEC Elektronik GmbH, Mainz, Germany • Dr. Klee, Hoechst AG, Frankfurt, Germany • Optische Werke G. Rodenstock, Precision Optics Division, D-80469 Munich • Prof. J. Weickert, University of Saarbrücken, Germany • Zeiss Jena GmbH, Jena, Germany • Dr. G. Zinser, Heidelberg Engineering, Heidelberg, Germany camera test program. I am grateful to the manufacturers and distributors who provided cameras at no cost: Adimec, Allied Vision, Basler Vision Technologies, IDS, PCO, Pulnix, and Stemmer Imaging (Dalsa, Jai). Most examples contained in this handbook have been processed using heurisko®, a versatile and powerful image processing package. heurisko® has been developed by AEON 1 in cooperation with the author. In a rapid progressing field such as digital image processing, a major work like this handbook is never finished or completed. Therefore, any comments on further improvements or additions to the handbook are very welcome. I am also grateful for hints on errors, omissions, or typing errors, which despite all the care taken may have slipped my attention. Heidelberg, Germany, January 2004 Bernd Jähne 1 © 2004 by CRC Press LLC my colleague F. Hamprecht. He contributed the last chapter about classification (Chap- ter 17) to this handbook. The detailed description on imaging sensors in Chapter 5 is based on an extensive AEON Verlag & Studio, Hanau, Germany, http://www.heurisko.de Contents 1 Introduction 1 1.1 Highlights 1 1.2 From Drawings to Electronic Images 2 1.3 Geometric Measurements: Gauging and Counting 3 1.3.1 Size Distribution of Pigment Particles 4 1.3.2 Gas Bubble Size Distributions 4 1.3.3 In Situ Microscopy of Cells in Bioreactors 6 1.4 Radiometric Measurements: Revealing the Invisible 8 1.4.1 Fluorescence Measurements of Concentration Fields 8 1.4.2 Thermography for Botany 11 1.4.3 Imaging of Short Ocean Wind Waves 12 1.4.4 SAR Imaging for Planetology and Earth Sciences 15 1.4.5 X-Ray Astronomy with ROSAT 19 1.4.6 Spectroscopic Imaging for Atmospheric Sciences 19 1.5 Depth Measurements: Exploring 3-D Space 21 1.5.1 Optical Surface Profiling 21 1.5.2 3-D Retina Imaging 24 1.5.3 Distribution of Chromosomes in Cell Nuclei 25 1.5.4 X-Ray and Magnetic Resonance 3-D Imaging 25 1.6 Velocity Measurements: Exploring Dynamic Processes 27 1.6.1 Particle Tracking Velocimetry 27 1.6.2 3-D Flow Tomography 28 1.6.3 Motor Proteins 30 2 Tasks and Tools 33 2.1 Highlights 33 2.2 Basic Concepts 34 2.2.1 Goals for Applications of Image Processing 34 2.2.2 Measuring versus Recognizing 36 2.2.3 Signals and Uncertainty 38 2.2.4 Representation and Algorithms 39 2.2.5 Models 41 2.2.6 Hierarchy of Image Processing Tasks 42 2.3 Tools 45 2.3.1 Overview 45 2.3.2 Camera and Frame Grabber 45 2.3.3 Computer 46 2.3.4 Software and Algorithms 50 VII © 2004 by CRC Press LLC VIII Contents I From Objects to Images 3 Quantitative Visualization 55 3.1 Highlights 55 3.2 Task 56 3.3 Concepts 58 3.3.1 Electromagnetic Waves 58 3.3.2 Particle Radiation 63 3.3.3 Acoustic Waves 64 3.3.4 Radiometric Terms 64 3.3.5 Photometric Terms 67 3.3.6 Surface-Related Interactions of Radiation with Matter 70 3.3.7 Volume-Related Interactions of Radiation with Matter 76 3.4 Procedures 82 3.4.1 Introduction 82 3.4.2 Types of Illumination 82 3.4.3 Illumination Techniques for Geometric Measurements 84 3.4.4 Illumination Techniques for Depth Measurements 86 3.4.5 Illumination Techniques for Surface Slope Measurements . . 88 3.4.6 Color and Multi-Spectral Imaging 96 3.4.7 Human Color Vision 100 3.4.8 Thermal Imaging 103 3.4.9 Imaging of Chemical Species and Material Properties 106 3.5 Advanced Reference Material 108 3.5.1 Classification of Radiation 108 3.5.2 Radiation Sources 110 3.5.3 Human Vision 113 3.5.4 Selected Optical Properties 114 3.5.5 Further References 116 4 Image Formation 119 4.1 Highlights 119 4.2 Task 120 4.3 Concepts 122 4.3.1 Coordinate Systems 122 4.3.2 Geometrical Optics 125 4.3.3 Wave Optics 137 4.3.4 Radiometry of Imaging 140 4.3.5 Linear System Theory 143 4.4 Procedures 147 4.4.1 Geometry of Imaging 147 4.4.2 Stereo Imaging 154 4.4.3 Confocal Laser Scanning Microscopy 159 4.4.4 Tomography 161 4.5 Advanced Reference Material 163 4.5.1 Data of Optical Systems for CCD Imaging 163 4.5.2 Optical Design 166 4.5.3 Further References 166 © 2004 by CRC Press LLC Contents IX 5 Imaging Sensors 169 5.1 Highlights 169 5.2 Task 169 5.3 Concepts 170 5.3.1 Overview 170 5.3.2 Detector Performance 171 5.3.3 Quantum Detectors 176 5.3.4 Thermal Detectors 176 5.3.5 Imaging Detectors 177 5.3.6 Television Video Standards 180 5.3.7 CCD Sensor Architectures 181 5.4 Procedures 185 5.4.1 Measuring Performance Parameters of Imaging Sensors 185 5.4.2 Sensor and Camera Selection 189 5.4.3 Spectral Sensitivity 191 5.4.4 Artifacts and Operation Errors 192 5.5 Advanced Reference Material 197 5.5.1 Basic Properties of Imaging Sensors 197 5.5.2 Standard Video Signals; Timing and Signal Forms 199 5.5.3 Color Video Signals 201 5.5.4 Cameras and Connectors 204 5.5.5 Further References 205 6 Digitalization and Quantization 207 6.1 Highlights 207 6.2 Task 207 6.3 Concepts 208 6.3.1 Digital Images 208 6.3.2 The Sampling Theorem 213 6.3.3 Sampling Theorem in xt Space 217 6.3.4 Reconstruction from Sampling 218 6.3.5 Sampling and Subpixel Accurate Gauging 220 6.3.6 Quantization 221 6.4 Procedures 226 6.4.1 The Transfer Function of an Image Acquisition System 226 6.4.2 Quality Control of Quantization 228 6.5 Advanced Reference Material 230 6.5.1 Evolution of Image Acquisition Hardware 230 6.5.2 Analog Video Input 232 6.5.3 Digital Video Input 234 6.5.4 Real-Time Image Processing 236 6.5.5 Further References 238 II Handling and Enhancing Images 7 Pixels 241 7.1 Highlights 241 7.2 Task 242 7.3 Concepts 243 7.3.1 Random Variables and Probability Density Functions 243 7.3.2 Functions of Random Variables 246 7.3.3 Multiple Random Variables and Error Propagation 247 © 2004 by CRC Press LLC X Contents 7.3.4 Homogenous Point Operations 251 7.3.5 Inhomogeneous Point Operations 252 7.3.6 Point Operations with Multichannel Images 253 7.4 Procedures 255 7.4.1 Gray Value Evaluation and Interactive Manipulation 255 7.4.2 Correction of Inhomogeneous Illumination 259 7.4.3 Radiometric Calibration 262 7.4.4 Noise Variance Equalization 263 7.4.5 Histogram Equalization 264 7.4.6 Noise Reduction by Image Averaging 265 7.4.7 Windowing 266 7.5 Advanced Reference Material 267 8 Geometry 269 8.1 Highlights 269 8.2 Task 270 8.3 Concepts 271 8.3.1 Geometric Transformations 271 8.3.2 Interpolation 274 8.4 Procedures 285 8.4.1 Scaling 286 8.4.2 Translation 288 8.4.3 Rotation 288 8.4.4 Affine and Perspective Transforms 290 8.5 Advanced Reference Material 291 9 Restoration and Reconstruction 293 9.1 Highlights 293 9.2 Task 294 9.3 Concepts 294 9.3.1 Types of Image Distortions 294 9.3.2 Defocusing and Lens Aberrations 296 9.3.3 Velocity Smearing 297 9.3.4 Inverse Filtering 297 9.3.5 Model-based Restoration 299 9.3.6 Radon Transform and Fourier Slice Theorem 300 9.4 Procedures 302 9.4.1 Reconstruction of Depth Maps from Focus Series 302 9.4.2 3-D Reconstruction by Inverse Filtering 304 9.4.3 Filtered Backprojection 308 9.5 Advanced Reference Material 311 III From Images to Features 10 Neighborhoods 315 10.1 Highlights 315 10.2 Task 316 10.3 Concepts 317 10.3.1 Masks 317 10.3.2 Operators 319 10.3.3 Convolution 319 10.3.4 Point Spread Function 321 © 2004 by CRC Press LLC [...]... transmitted and received, blue component; middle: C-band, horizontally transmitted and vertically received, green component; right: L-band, horizontally transmitted and vertically received, red component A heavy rain storm with large droplets scatters the short wavelength in the X-band range and thus appears as a black cloud in the expanded image The same area shows up only faintly in the C-band image and. .. 1.4.6) Three-dimensional measurements from volumetric images (Section 1.5) • surface topography measurements of press forms and the human retina (Sections 1.5.1 and 1.5.2) • 3-D microscopy of cell nuclei (Section 1.5.3) • X-ray and magnetic resonance 3-D imaging (Section 1.5.4) Velocity measurements from image sequences (Section 1.6) • particle tracking velocimetry for 2-D flow measurements (Section 1.6.1)... Introduction 1.1 Highlights Electronic imaging and digital image processing constitute — after the invention of photography — the second revolution in the use of images in science and engineering (Section 1.2) Because of its inherently interdisciplinary nature, image processing has become a major integrating factor stimulating communication throughout engineering and natural sciences For technical and scientific... clusters and non-separable particles on size distribution 1.3.2 Gas Bubble Size Distributions Bubbles are submerged into the ocean by breaking waves and play an important role in various small-scale air-sea interaction processes They form an additional surface for the exchange of climate-relevant trace gases between the atmosphere and the ocean, are a main source for marine aerosols and acoustic noise, and. .. increasing specialization of science This section introduces typical scientific and technical applications of image processing The idea is to make the reader aware of the enormous possibilities of modern visualization techniques and digital image processing We will show how new insight is gained into scientific or technical problems by using advanced visualization techniques and digital image processing techniques... symbionts Therefore the oxygen production within the skeleton was measured in relation to various illumination intensities One result is © 2004 by CRC Press LLC 1 Introduction 10 b a c d Figure 1.10: Optical measurement of oxygen in corals: a Sample place for the coral, the lagoon of Heron Island, Capricorn Islands, Great Barrier Reef, Australia b Set-up with the coral in the glass container placed on. .. applications, images have been mostly used in science for qualitative observations and documentation of experimental results Now we are experiencing the second revolution of scientific imaging Images can be converted to electronic form, i e., digital images, that are analyzed quantitatively using computers to perform exact measurements and to visualize complex new phenomena This second revolution is more... Konrad W Röntgen, X-ray images have found widespread application in medicine, science, and technology As it is easy to have a point X-ray source, optics are not required to take an absorption image of an object from X-ray examination To take an image of an X-ray source, however, X-ray optics are required This is a very difficult task as the index of refraction for all materials is very low in the X-ray... crosswind alongwind alongwind 5 m/s b NH95-May 3, 199 5-5 .0m/s D9 1-7 7cm-100m-5.0m/s 0.002 0.002 0.001 0.0005 90 0.0002 45 0.0001 B(k) 0.0005 90 0.0002 45 1000 k [r 2000 ad/m ] θ 500 -4 5 5000 -9 0 0 200 500 k [r 1000 ad/m 2000 ] [ °] [ °] 0.0001 0 200 θ B(k) 0.001 -4 5 -9 0 Figure 1.13: a Sample images taken from the wave-riding buoy at a wind speed of about 5 m/s The left image shows the slope in horizontal... Left: X-band, Middle: C-band, Right: Lband) have been composed into a color image Pristine rain forest appears in pink colors while clear areas for agricultural usage are greenish and bluish A heavy rain storm appears in red and yellow colors since it scatters the shorter wavelength micro waves Image taken with the imaging radar-C/X-band aperture radar (SIRC/X-SAR) on April 10, 1994 on board the space . Practical Handbook on IMAGE PROCESSING for SCIENTIFIC and TECHNICAL APPLICATIONS SECOND EDITION © 2004 by CRC Press LLC CRC PRESS Boca Raton London New York Washington, D.C. Practical Handbook. Data Jèahne, Bernd, 195 3- Practical handbook on image processing for scientiÞc and technical applications / Berne Jèahne.— 2nd ed. p. cm. Includes bibliographical references and index. ISBN 0-8 49 3-1 90 0-5 . D.C. Practical Handbook on IMAGE PROCESSING for SCIENTIFIC and TECHNICAL APPLICATIONS Bernd Jähne University of Heidelberg SECOND EDITION © 2004 by CRC Press LLC This book contains information obtained from