Wu / Merchant / Castleman Microscope Image Processing

1. Auflage 2010
ISBN: 978-0-08-055854-7
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 576 Seiten, Web PDF

Digital image processing, an integral part of microscopy, is increasingly important to the fields of medicine and scientific research. This book provides a unique one-stop reference on the theory, technique, and applications of this technology.
Written by leading experts in the field, this book presents a unique practical perspective of state-of-the-art microscope image processing and the development of specialized algorithms. It contains in-depth analysis of methods coupled with the results of specific real-world experiments. Microscope Image Processing covers image digitization and display, object measurement and classification, autofocusing, and structured illumination.
Key Features:
• Detailed descriptions of many leading-edge methods and algorithms
• In-depth analysis of the method and experimental results, taken from real-life examples
• Emphasis on computational and algorithmic aspects of microscope image processing
•Advanced material on geometric, morphological, and wavelet image processing, fluorescence, three-dimensional and time-lapse microscopy, microscope image enhancement, MultiSpectral imaging, and image data management
This book is of interest to all scientists, engineers, clinicians, post-graduate fellows, and graduate students working in the fields of biology, medicine, chemistry, pharmacology, and other related fields. Anyone who uses microscopes in their work and needs to understand the methodologies and capabilities of the latest digital image processing techniques will find this book invaluable.
* Presents a unique practical perspective of state-of-the-art microcope image processing and the development of specialized algorithms.
* Each chapter includes in-depth analysis of methods coupled with the results of specific real-world experiments.
* Co-edited by Kenneth R. Castleman, world-renowned pioneer in digital image processing and author of two seminal textbooks on the subject.

Autoren/Hrsg.

Wu, Qiang

Merchant, Fatima

Castleman, Kenneth

Inhaltsverzeichnis

1;Front Cover;1
2;Microscope Image Processing;4
3;Copyright Page;5
4;Contents;6
5;Foreword;22
5.1;Reference;23
6;Preface;24
7;Acknowledgments;26
8;Chapter 1: Introduction;30
8.1;1.1 The Microscope and Image Processing;30
8.2;1.2 Scope of This Book;30
8.3;1.3 Our Approach;32
8.3.1;1.3.1 The Four Types of Images;32
8.3.1.1;1.3.1.1 Optical Image;33
8.3.1.2;1.3.1.2 Continuous Image;33
8.3.1.3;1.3.1.3 Digital Image;33
8.3.1.4;1.3.1.4 Displayed Image;34
8.3.2;1.3.2 The Result;34
8.3.2.1;1.3.2.1 Analytic Functions;35
8.3.3;1.3.3 The Sampling Theorem;36
8.4;1.4 The Challenge;37
8.5;1.5 Nomenclature;37
8.6;1.6 Summary of Important Points;37
8.7;References;38
9;Chapter 2: Fundamentals of Microscopy;40
9.1;2.1 Origins of the Microscope;40
9.2;2.2 Optical Imaging;41
9.2.1;2.2.1 Image Formation by a Lens;41
9.2.1.1;2.2.1.1 Imaging a Point Source;42
9.2.1.2;2.2.1.2 Focal Length;42
9.2.1.3;2.2.1.3 Numerical Aperture;43
9.2.1.4;2.2.1.4 Lens Shape;44
9.3;2.3 Diffraction-Limited Optical Systems;44
9.3.1;2.3.1 Linear System Analysis;45
9.4;2.4 Incoherent Illumination;45
9.4.1;2.4.1 The Point Spread Function;45
9.4.2;2.4.2 The Optical Transfer Function;46
9.5;2.5 Coherent Illumination;47
9.5.1;2.5.1 The Coherent Point Spread Function;47
9.5.2;2.5.2 The Coherent Optical Transfer Function;48
9.6;2.6 Resolution;49
9.6.1;2.6.1 Abbe Distance;50
9.6.2;2.6.2 Rayleigh Distance;50
9.6.3;2.6.3 Size Calculations;50
9.7;2.7 Aberration;51
9.8;2.8 Calibration;51
9.8.1;2.8.1 Spatial Calibration;52
9.8.2;2.8.2 Photometric Calibration;52
9.9;2.9 Summary of Important Points;53
9.10;References;54
10;Chapter 3: Image Digitization;56
10.1;3.1 Introduction;56
10.2;3.2 Resolution;57
10.3;3.3 Sampling;58
10.3.1;3.3.1 Interpolation;59
10.3.2;3.3.2 Aliasing;61
10.4;3.4 Noise;62
10.5;3.5 Shading;63
10.6;3.6 Photometry;63
10.7;3.7 Geometric Distortion;64
10.8;3.8 Complete System Design;64
10.8.1;3.8.1 Cumulative Resolution;64
10.8.2;3.8.2 Design Rules of Thumb;65
10.8.2.1;3.8.2.1 Pixel Spacing;65
10.8.2.2;3.8.2.2 Resolution;65
10.8.2.3;3.8.2.3 Noise;65
10.8.2.4;3.8.2.4 Photometry;65
10.8.2.5;3.8.2.5 Distortion;66
10.9;3.9 Summary of Important Points;66
10.10;References;66
11;Chapter 4: Image Display;68
11.1;4.1 Introduction;68
11.2;4.2 Display Characteristics;69
11.2.1;4.2.1 Displayed Image Size;69
11.2.2;4.2.2 Aspect Ratio;69
11.2.3;4.2.3 Photometric Resolution;70
11.2.4;4.2.4 Grayscale Linearity;71
11.2.5;4.2.5 Low-Frequency Response;71
11.2.5.1;4.2.5.1 Pixel Polarity;71
11.2.5.2;4.2.5.2 Pixel Interaction;72
11.2.6;4.2.6 High-Frequency Response;72
11.2.7;4.2.7 The Spot-Spacing Compromise;72
11.2.8;4.2.8 Noise Considerations;72
11.3;4.3 Volatile Displays;73
11.4;4.4 Sampling for Display Purposes;74
11.4.1;4.4.1 Oversampling;75
11.4.2;4.4.2 Resampling;75
11.5;4.5 Display Calibration;76
11.6;4.6 Summary of Important Points;76
11.7;References;77
12;Chapter 5: Geometric Transformations;80
12.1;5.1 Introduction;80
12.2;5.2 Implementation;81
12.3;5.3 Gray-Level Interpolation;81
12.3.1;5.3.1 Nearest-Neighbor Interpolation;82
12.3.2;5.3.2 Bilinear Interpolation;82
12.3.3;5.3.3 Bicubic Interpolation;83
12.3.4;5.3.4 Higher-Order Interpolation;83
12.4;5.4 Spatial Transformation;84
12.4.1;5.4.1 Control-Grid Mapping;84
12.5;5.5 Applications;85
12.5.1;5.5.1 Distortion Removal;85
12.5.2;5.5.2 Image Registration;85
12.5.3;5.5.3 Stitching;85
12.6;5.6 Summary of Important Points;86
12.7;References;86
13;Chapter 6: Image Enhancement;88
13.1;6.1 Introduction;88
13.2;6.2 Spatial Domain Methods;89
13.2.1;6.2.1 Contrast Stretching;89
13.2.2;6.2.2 Clipping and Thresholding;90
13.2.3;6.2.3 Image Subtraction and Averaging;90
13.2.4;6.2.4 Histogram Equalization;91
13.2.5;6.2.5 Histogram Specification;91
13.2.6;6.2.6 Spatial Filtering;92
13.2.7;6.2.7 Directional and Steerable Filtering;94
13.2.8;6.2.8 Median Filtering;96
13.3;6.3 Fourier Transform Methods;97
13.3.1;6.3.1 Wiener Filtering and Wiener Deconvolution;97
13.3.2;6.3.2 Deconvolution Using a Least-Squares Approach;99
13.3.3;6.3.3 Low-Pass Filtering in the Fourier Domain;100
13.3.4;6.3.4 High-Pass Filtering in the Fourier Domain;100
13.4;6.4 Wavelet Transform Methods;101
13.4.1;6.4.1 Wavelet Thresholding;101
13.4.2;6.4.2 Differential Wavelet Transform and Multiscale Pointwise Product;102
13.5;6.5 Color Image Enhancement;103
13.5.1;6.5.1 Pseudo-Color Transformations;104
13.5.2;6.5.2 Color Image Smoothing;104
13.5.3;6.5.3 Color Image Sharpening;104
13.6;6.6 Summary of Important Points;105
13.7;References;106
14;Chapter 7: Wavelet Image Processing;108
14.1;7.1 Introduction;108
14.1.1;7.1.1 Linear Transformations;109
14.1.2;7.1.2 Short-Time Fourier Transform and Wavelet Transform;110
14.2;7.2 Wavelet Transforms;112
14.2.1;7.2.1 Continuous Wavelet Transform;112
14.2.2;7.2.2 Wavelet Series Expansion;113
14.2.3;7.2.3 Haar Wavelet Functions;114
14.3;7.3 Multiresolution Analysis;114
14.3.1;7.3.1 Multiresolution and Scaling Function;115
14.3.2;7.3.2 Scaling Functions and Wavelets;116
14.4;7.4 Discrete Wavelet Transform;117
14.4.1;7.4.1 Decomposition;117
14.4.2;7.4.2 Reconstruction;120
14.4.3;7.4.3 Filter Banks;121
14.4.3.1;7.4.3.1 Two-Channel Subband Coding;121
14.4.3.2;7.4.3.2 Orthogonal Filter Design;122
14.4.4;7.4.4 Compact Support;124
14.4.5;7.4.5 Biorthogonal Wavelet Transforms;125
14.4.5.1;7.4.5.1 Biorthogonal Filter Banks;126
14.4.5.2;7.4.5.2 Examples of Biorthogonal Wavelets;128
14.4.6;7.4.6 Lifting Schemes;129
14.4.6.1;7.4.6.1 Biorthogonal Wavelet Design;129
14.4.6.2;7.4.6.2 Wavelet Transform Using Lifting;130
14.5;7.5 Two-Dimensional Discrete Wavelet Transform;131
14.5.1;7.5.1 Two-Dimensional Wavelet Bases;131
14.5.2;7.5.2 Forward Transform;132
14.5.3;7.5.3 Inverse Transform;134
14.5.4;7.5.4 Two-Dimensional Biorthogonal Wavelets;134
14.5.5;7.5.5 Overcomplete Transforms;135
14.6;7.6 Examples;136
14.6.1;7.6.1 Image Compression;136
14.6.2;7.6.2 Image Enhancement;136
14.6.3;7.6.3 Extended Depth-of-Field by Wavelet Image Fusion;137
14.7;7.7 Summary of Important Points;137
14.8;References;139
15;Chapter 8: Morphological Image Processing;142
15.1;8.1 Introduction;142
15.2;8.2 Binary Morphology;144
15.2.1;8.2.1 Binary Erosion and Dilation;144
15.2.2;8.2.2 Binary Opening and Closing;145
15.2.3;8.2.3 Binary Morphological Reconstruction from Markers;147
15.2.3.1;8.2.3.1 Connectivity;147
15.2.3.2;8.2.3.2 Markers;148
15.2.3.3;8.2.3.3 The Edge-Off Operation;149
15.2.4;8.2.4 Reconstruction from Opening;149
15.2.5;8.2.5 Area Opening and Closing;151
15.2.6;8.2.6 Skeletonization;152
15.3;8.3 Grayscale Operations;156
15.3.1;8.3.1 Threshold Decomposition;157
15.3.2;8.3.2 Erosion and Dilation;158
15.3.2.1;8.3.2.1 Gradient;160
15.3.3;8.3.3 Opening and Closing;160
15.3.3.1;8.3.3.1 Top-Hat Filtering;160
15.3.3.2;8.3.3.2 Alternating Sequential Filters;162
15.3.4;8.3.4 Component Filters and Grayscale Morphological Reconstruction;163
15.3.4.1;8.3.4.1 Morphological Reconstruction;164
15.3.4.2;8.3.4.2 Alternating Sequential Component Filters;164
15.3.4.3;8.3.4.3 Grayscale Area Opening and Closing;164
15.3.4.4;8.3.4.4 Edge-Off Operator;165
15.3.4.5;8.3.4.5 h-Maxima and h-Minima Operations;166
15.3.4.6;8.3.4.6 Regional Maxima and Minima;166
15.3.4.7;8.3.4.7 Regional Extrema as Markers;167
15.4;8.4 Watershed Segmentation;167
15.4.1;8.4.1 Classical Watershed Transform;168
15.4.2;8.4.2 Filtering the Minima;169
15.4.3;8.4.3 Texture Detection;172
15.4.4;8.4.4 Watershed from Markers;174
15.4.5;8.4.5 Segmentation of Overlapped Convex Cells;175
15.4.6;8.4.6 Inner and Outer Markers;177
15.4.7;8.4.7 Hierarchical Watershed;180
15.4.8;8.4.8 Watershed Transform Algorithms;181
15.5;8.5 Summary of Important Points;183
15.6;References;185
16;Chapter 9: Image Segmentation;188
16.1;9.1 Introduction;188
16.1.1;9.1.1 Pixel Connectivity;189
16.2;9.2 Region-Based Segmentation;189
16.2.1;9.2.1 Thresholding;189
16.2.1.1;9.2.1.1 Global Thresholding;190
16.2.1.2;9.2.1.2 Adaptive Thresholding;191
16.2.1.3;9.2.1.3 Threshold Selection;192
16.2.1.4;9.2.1.4 Thresholding Circular Spots;194
16.2.1.5;9.2.1.5 Thresholding Noncircular and Noisy Spots;196
16.2.2;9.2.2 Morphological Processing;198
16.2.2.1;9.2.2.1 Hole Filling;200
16.2.2.2;9.2.2.2 Border-Object Removal;200
16.2.2.3;9.2.2.3 Separation of Touching Objects;201
16.2.2.4;9.2.2.4 The Watershed Algorithm;201
16.2.3;9.2.3 Region Growing;202
16.2.4;9.2.4 Region Splitting;204
16.3;9.3 Boundary-Based Segmentation;205
16.3.1;9.3.1 Boundaries and Edges;205
16.3.2;9.3.2 Boundary Tracking Based on Maximum Gradient Magnitude;206
16.3.3;9.3.3 Boundary Finding Based on Gradient Image Thresholding;207
16.3.4;9.3.4 Boundary Finding Based on Laplacian Image Thresholding;208
16.3.5;9.3.5 Boundary Finding Based on Edge Detection and Linking;209
16.3.5.1;9.3.5.1 Edge Detection;209
16.3.5.2;9.3.5.2 Edge Linking and Boundary Refinement;212
16.3.6;9.3.6 Encoding Segmented Images;217
16.3.6.1;9.3.6.1 Object Label Map;218
16.3.6.2;9.3.6.2 Boundary Chain Code;218
16.4;9.4 Summary of Important Points;219
16.5;References;221
17;Chapter 10: Object Measurement;224
17.1;10.1 Introduction;224
17.2;10.2 Measures for Binary Objects;225
17.2.1;10.2.1 Size Measures;225
17.2.1.1;10.2.1.1 Area;225
17.2.1.2;10.2.1.2 Perimeter;225
17.2.1.3;10.2.1.3 Area and Perimeter of a Polygon;226
17.2.2;10.2.2 Pose Measures;228
17.2.2.1;10.2.2.1 Centroid;228
17.2.2.2;10.2.2.2 Orientation;229
17.2.3;10.2.3 Shape Measures;229
17.2.3.1;10.2.3.1 Thinness Ratio;230
17.2.3.2;10.2.3.2 Rectangularity;230
17.2.3.3;10.2.3.3 Circularity;230
17.2.3.4;10.2.3.4 Euler Number;232
17.2.3.5;10.2.3.5 Moments;232
17.2.3.6;10.2.3.6 Elongation;234
17.2.4;10.2.4 Shape Descriptors;235
17.2.4.1;10.2.4.1 Differential Chain Code;235
17.2.4.2;10.2.4.2 Fourier Descriptors;235
17.2.4.3;10.2.4.3 Medial Axis Transform;236
17.2.4.4;10.2.4.4 Graph Representations;237
17.3;10.3 Distance Measures;238
17.3.1;10.3.1 Euclidean Distance;238
17.3.2;10.3.2 City-Block Distance;238
17.3.3;10.3.3 Chessboard Distance;239
17.4;10.4 Gray-Level Object Measures;239
17.4.1;10.4.1 Intensity Measures;239
17.4.1.1;10.4.1.1 Integrated Optical Intensity;239
17.4.1.2;10.4.1.2 Average Optical Intensity;239
17.4.1.3;10.4.1.3 Contrast;240
17.4.2;10.4.2 Histogram Measures;240
17.4.2.1;10.4.2.1 Mean Gray Level;240
17.4.2.2;10.4.2.2 Standard Deviation of Gray Levels;240
17.4.2.3;10.4.2.3 Skew;241
17.4.2.4;10.4.2.4 Entropy;241
17.4.2.5;10.4.2.5 Energy;241
17.4.3;10.4.3 Texture Measures;241
17.4.3.1;10.4.3.1 Statistical Texture Measures;242
17.4.3.2;10.4.3.2 Power Spectrum Features;243
17.5;10.5 Object Measurement Considerations;244
17.6;10.6 Summary of Important Points;244
17.7;References;246
18;Chapter 11: Object Classification;250
18.1;11.1 Introduction;250
18.2;11.2 The Classification Process;250
18.2.1;11.2.1 Bayes’ Rule;251
18.3;11.3 The Single-Feature, Two-Class Case;251
18.3.1;11.3.1 A Priori Probabilities;252
18.3.2;11.3.2 Conditional Probabilities;252
18.3.3;11.3.3 Bayes’ Theorem;253
18.4;11.4 The Three-Feature, Three-Class Case;254
18.4.1;11.4.1 Bayes Classifier;255
18.4.1.1;11.4.1.1 Prior Probabilities;255
18.4.1.2;11.4.1.2 Classifier Training;256
18.4.1.3;11.4.1.3 The Mean Vector;256
18.4.1.4;11.4.1.4 Covariance;257
18.4.1.5;11.4.1.5 Variance and Standard Deviation;257
18.4.1.6;11.4.1.6 Correlation;257
18.4.1.7;11.4.1.7 The Probability Density Function;258
18.4.1.8;11.4.1.8 Classification;258
18.4.1.9;11.4.1.9 Log Likelihoods;258
18.4.1.10;11.4.1.10 Mahalanobis Distance Classifier;259
18.4.1.11;11.4.1.11 Uncorrelated Features;259
18.4.2;11.4.2 A Numerical Example;260
18.5;11.5 Classifier Performance;261
18.5.1;11.5.1 The Confusion Matrix;262
18.6;11.6 Bayes Risk;263
18.6.1;11.6.1 Minimum-Risk Classifier;263
18.7;11.7 Relationships Among Bayes Classifiers;264
18.8;11.8 The Choice of a Classifier;264
18.8.1;11.8.1 Subclassing;265
18.8.2;11.8.2 Feature Normalization;265
18.9;11.9 Nonparametric Classifiers;267
18.9.1;11.9.1 Nearest-Neighbor Classifiers;268
18.10;11.10 Feature Selection;269
18.10.1;11.10.1 Feature Reduction;269
18.10.1.1;11.10.1.1 Principal Component Analysis;270
18.10.1.2;11.10.1.2 Linear Discriminant Analysis;271
18.11;11.11 Neural Networks;272
18.12;11.12 Summary of Important Points;273
18.13;References;274
19;Chapter 12: Fluorescence Imaging;276
19.1;12.1 Introduction;276
19.2;12.2 Basics of Fluorescence Imaging;277
19.2.1;12.2.1 Image Formation in Fluorescence Imaging;278
19.3;12.3 Optics in Fluorescence Imaging;279
19.4;12.4 Limitations in Fluorescence Imaging;280
19.4.1;12.4.1 Instrumentation-Based Aberrations;280
19.4.1.1;12.4.1.1 Photon Shot Noise;280
19.4.1.2;12.4.1.2 Dark Current;281
19.4.1.3;12.4.1.3 Auxiliary Noise Sources;281
19.4.1.4;12.4.1.4 Quantization Noise;282
19.4.1.5;12.4.1.5 Other Noise Sources;282
19.4.2;12.4.2 Sample-Based Aberrations;282
19.4.2.1;12.4.2.1 Photobleaching;282
19.4.2.2;12.4.2.2 Autofluorescence;283
19.4.2.3;12.4.2.3 Absorption and Scattering;284
19.4.3;12.4.3 Sample and Instrumentation Handling–Based Aberrations;284
19.5;12.5 Image Corrections in Fluorescence Microscopy;285
19.5.1;12.5.1 Background Shading Correction;285
19.5.2;12.5.2 Correction Using the Recorded Image;286
19.5.3;12.5.3 Correction Using Calibration Images;287
19.5.3.1;12.5.3.1 Two-Image Calibration;287
19.5.3.2;12.5.3.2 Background Subtraction;287
19.5.4;12.5.4 Correction Using Surface Fitting;288
19.5.5;12.5.5 Histogram-Based Background Correction;290
19.5.6;12.5.6 Other Approaches for Background Correction;290
19.5.7;12.5.7 Autofluorescence Correction;290
19.5.8;12.5.8 Spectral Overlap Correction;291
19.5.9;12.5.9 Photobleaching Correction;291
19.5.10;12.5.10 Correction of Fluorescence Attenuation in Depth;294
19.6;12.6 Quantifying Fluorescence;295
19.6.1;12.6.1 Fluorescence Intensity Versus Fluorophore Concentration;295
19.7;12.7 Fluorescence Imaging Techniques;296
19.7.1;12.7.1 Immunofluorescence;296
19.7.2;12.7.2 Fluorescence in situ Hybridization (FISH);299
19.7.3;12.7.3 Quantitative Colocalization Analysis;300
19.7.4;12.7.4 Fluorescence Ratio Imaging (RI);304
19.7.5;12.7.5 Fluorescence Resonance Energy Transfer (FRET);306
19.7.6;12.7.6 Fluorescence Lifetime Imaging (FLIM);313
19.7.7;12.7.7 Fluorescence Recovery After Photobleaching (FRAP);315
19.7.8;12.7.8 Total Internal Reflectance Fluorescence Microscopy (TIRFM);317
19.7.9;12.7.9 Fluorescence Correlation Spectroscopy (FCS);318
19.8;12.8 Summary of Important Points;319
19.9;References;320
20;Chapter 13: Multispectral Imaging;328
20.1;13.1 Introduction;328
20.2;13.2 Principles of Multispectral Imaging;329
20.2.1;13.2.1 Spectroscopy;330
20.2.2;13.2.2 Imaging;331
20.2.3;13.2.3 Multispectral Microscopy;333
20.2.4;13.2.4 Spectral Image Acquisition Methods;333
20.2.4.1;13.2.4.1 Wavelength-Scan Methods;333
20.2.4.2;13.2.4.2 Spatial-Scan Methods;334
20.2.4.3;13.2.4.3 Time-Scan Methods;335
20.3;13.3 Multispectral Image Processing;335
20.3.1;13.3.1 Calibration for Multispectral Image Acquisition;336
20.3.2;13.3.2 Spectral Unmixing;341
20.3.2.1;13.3.2.1 Fluorescence Unmixing;344
20.3.2.2;13.3.2.2 Brightfield Unmixing;346
20.3.2.3;13.3.2.3 Unsupervised Unmixing;347
20.3.3;13.3.3 Spectral Image Segmentation;350
20.3.3.1;13.3.3.1 Combining Segmentation with Classification;351
20.3.3.2;13.3.3.2 M-FISH Pixel Classification;351
20.4;13.4 Summary of Important Points;352
20.5;References;353
21;Chapter 14: Three-Dimensional Imaging;358
21.1;14.1 Introduction;358
21.2;14.2 Image Acquisition;358
21.2.1;14.2.1 Wide-Field Three-Dimensional Microscopy;359
21.2.2;14.2.2 Confocal Microscopy;359
21.2.3;14.2.3 Multiphoton Microscopy;360
21.2.4;14.2.4 Other Three-Dimensional Microscopy Techniques;362
21.3;14.3 Three-Dimensional Image Data;363
21.3.1;14.3.1 Three-Dimensional Image Representation;363
21.3.1.1;14.3.1.1 Three-Dimensional Image Notation;363
21.4;14.4 Image Restoration and Deblurring;364
21.4.1;14.4.1 The Point Spread Function;364
21.4.1.1;14.4.1.1 Theoretical Model of the Point Spread Function;366
21.4.2;14.4.2 Models for Microscope Image Formation;367
21.4.2.1;14.4.2.1 Poisson Noise;367
21.4.2.2;14.4.2.2 Gaussian Noise;367
21.4.3;14.4.3 Algorithms for Deblurring and Restoration;368
21.4.3.1;14.4.3.1 No-Neighbor Methods;368
21.4.3.2;14.4.3.2 Nearest-Neighbor Method;369
21.4.3.3;14.4.3.3 Linear Methods;371
21.4.3.4;14.4.3.4 Nonlinear Methods;375
21.4.3.5;14.4.3.5 Maximum-Likelihood Restoration;378
21.4.3.6;14.4.3.6 Blind Deconvolution;382
21.4.3.7;14.4.3.7 Interpretation of Deconvolved Images;383
21.4.3.8;14.4.3.8 Commercial Deconvolution Packages;383
21.5;14.5 Image Fusion;384
21.6;14.6 Three-Dimensional Image Processing;385
21.7;14.7 Geometric Transformations;385
21.8;14.8 Pointwise Operations;386
21.9;14.9 Histogram Operations;386
21.10;14.10 Filtering;388
21.10.1;14.10.1 Linear Filters;388
21.10.1.1;14.10.1.1 Finite Impulse Response (FIR) Filter;388
21.10.2;14.10.2 Nonlinear Filters;389
21.10.2.1;14.10.2.1 Median Filter;389
21.10.2.2;14.10.2.2 Weighted Median Filter;389
21.10.2.3;14.10.2.3 Minimum and Maximum Filters;390
21.10.2.4;14.10.2.4 alpha-Trimmed Mean Filters;390
21.10.3;14.10.3 Edge-Detection Filters;390
21.11;14.11 Morphological Operators;391
21.11.1;14.11.1 Binary Morphology;392
21.11.2;14.11.2 Grayscale Morphology;393
21.12;14.12 Segmentation;394
21.12.1;14.12.1 Point-Based Segmentation;395
21.12.2;14.12.2 Edge-Based Segmentation;396
21.12.3;14.12.3 Region-Based Segmentation;398
21.12.3.1;14.12.3.1 Connectivity;398
21.12.3.2;14.12.3.2 Region Growing;399
21.12.3.3;14.12.3.3 Region Splitting and Region Merging;399
21.12.4;14.12.4 Deformable Models;400
21.12.5;14.12.5 Three-Dimensional Segmentation Methods in the Literature;401
21.13;14.13 Comparing Three-Dimensional Images;404
21.14;14.14 Registration;404
21.15;14.15 Object Measurements in Three Dimensions;405
21.15.1;14.15.1 Euler Number;405
21.15.2;14.15.2 Bounding Box;406
21.15.3;14.15.3 Center of Mass;406
21.15.4;14.15.4 Surface Area Estimation;407
21.15.5;14.15.5 Length Estimation;408
21.15.6;14.15.6 Curvature Estimation;409
21.15.6.1;14.15.6.1 Surface Triangulation Method;410
21.15.6.2;14.15.6.2 Cross-Patch Method;410
21.15.7;14.15.7 Volume Estimation;410
21.15.8;14.15.8 Texture;411
21.16;14.16 Three-Dimensional Image Display;411
21.16.1;14.16.1 Montage;411
21.16.2;14.16.2 Projected Images;413
21.16.2.1;14.16.2.1 Voxel Projection;413
21.16.2.2;14.16.2.2 Ray Casting;413
21.16.3;14.16.3 Surface and Volume Rendering;414
21.16.3.1;14.16.3.1 Surface Rendering;414
21.16.3.2;14.16.3.2 Volume Rendering;415
21.16.4;14.16.4 Stereo Pairs;416
21.16.5;14.16.5 Color Anaglyphs;417
21.16.6;14.16.6 Animations;417
21.17;14.17 Summary of Important Points;418
21.18;References;421
22;Chapter 15: Time-Lapse Imaging;430
22.1;15.1 Introduction;430
22.2;15.2 Image Acquisition;432
22.2.1;15.2.1 Microscope Setup;433
22.2.2;15.2.2 Spatial Dimensionality;434
22.2.3;15.2.3 Temporal Resolution;439
22.3;15.3 Image Preprocessing;440
22.3.1;15.3.1 Image Denoising;440
22.3.2;15.3.2 Image Deconvolution;441
22.3.3;15.3.3 Image Registration;442
22.4;15.4 Image Analysis;443
22.4.1;15.4.1 Cell Tracking;444
22.4.1.1;15.4.1.1 Cell Segmentation;444
22.4.1.2;15.4.1.2 Cell Association;446
22.4.2;15.4.2 Particle Tracking;446
22.4.2.1;15.4.2.1 Particle Detection;447
22.4.2.2;15.4.2.2 Particle Association;448
22.5;15.5 Trajectory Analysis;449
22.5.1;15.5.1 Geometry Measurements;450
22.5.2;15.5.2 Diffusivity Measurements;450
22.5.3;15.5.3 Velocity Measurements;452
22.6;15.6 Sample Algorithms;452
22.6.1;15.6.1 Cell Tracking;453
22.6.2;15.6.2 Particle Tracking;456
22.7;15.7 Summary of Important Points;461
22.8;References;463
23;Chapter 16: Autofocusing;470
23.1;16.1 Introduction;470
23.1.1;16.1.1 Autofocus Methods;470
23.1.2;16.1.2 Passive Autofocusing;471
23.2;16.2 Principles of Microscope Autofocusing;471
23.2.1;16.2.1 Fluorescence and Brightfield Autofocusing;472
23.2.2;16.2.2 Autofocus Functions;473
23.2.3;16.2.3 Autofocus Function Sampling and Approximation;474
23.2.3.1;16.2.3.1 Gaussian Fitting;476
23.2.3.2;16.2.3.2 Parabola Fitting;476
23.2.4;16.2.4 Finding the In-Focus Imaging Position;477
23.3;16.3 Multiresolution Autofocusing;477
23.3.1;16.3.1 Multiresolution Image Representations;478
23.3.2;16.3.2 Wavelet-Based Multiresolution Autofocus Functions;480
23.3.3;16.3.3 Multiresolution Search for In-Focus Position;480
23.4;16.4 Autofocusing for Scanning Microscopy;481
23.5;16.5 Extended Depth-of-Field Microscope Imaging;483
23.5.1;16.5.1 Digital Image Fusion;484
23.5.2;16.5.2 Pixel-Based Image Fusion;485
23.5.3;16.5.3 Neighborhood-Based Image Fusion;486
23.5.4;16.5.4 Multiresolution Image Fusion;487
23.5.5;16.5.5 Noise and Artifact Control in Image Fusion;488
23.5.5.1;16.5.5.1 Multiscale Pointwise Product;489
23.5.5.2;16.5.5.2 Consistency Checking;490
23.5.5.3;16.5.5.3 Reassignment;491
23.6;16.6 Examples;491
23.7;16.7 Summary of Important Points;491
23.8;References;494
24;Chapter 17: Structured Illumination Imaging;498
24.1;17.1 Introduction;498
24.1.1;17.1.1 Conventional Light Microscope;498
24.1.2;17.1.2 Sectioning the Specimen;499
24.1.3;17.1.3 Structured Illumination;500
24.2;17.2 Linear SIM Instrumentation;501
24.2.1;17.2.1 Spatial Light Modulator;502
24.3;17.3 The Process of Structured Illumination Imaging;502
24.3.1;17.3.1 Extended-Depth-of-Field Image;504
24.3.2;17.3.2 SIM for Optical Sectioning;504
24.3.3;17.3.3 Sectioning Strength;506
24.4;17.4 Limitations of Optical Sectioning with SIM;508
24.4.1;17.4.1 Artifact Reduction via Image Processing;509
24.4.1.1;17.4.1.1 Intensity Normalization;509
24.4.1.2;17.4.1.2 Grid Position Error;511
24.4.1.3;17.4.1.3 Statistical Waveform Compensation;513
24.4.1.4;17.4.1.4 Parameter Optimization;514
24.5;17.5 Color Structured Illumination;515
24.5.1;17.5.1 Processing Technique;516
24.5.2;17.5.2 Chromatic Aberration;517
24.5.3;17.5.3 SIM Example;519
24.6;17.6 Lateral Superresolution;520
24.6.1;17.6.1 Bypassing the Optical Transfer Function;520
24.6.2;17.6.2 Mathematical Foundation;521
24.6.2.1;17.6.2.1 Shifting Frequency Space;521
24.6.2.2;17.6.2.2 Extracting the Enhanced Image;522
24.6.3;17.6.3 Lateral Resolution Enhancement Simulation;524
24.7;17.7 Summary of Important Points;525
24.8;References;525
25;Chapter 18: Image Data and Workflow Management;528
25.1;18.1 Introduction;528
25.1.1;18.1.1 Open Microscopy Environment;529
25.1.2;18.1.2 Image Management in Other Fields;529
25.1.3;18.1.3 Requirements for Microscopy Image Management Systems;529
25.2;18.2 Architecture of Microscopy Image/Data/Workflow Systems;530
25.2.1;18.2.1 Client–Server Architecture;530
25.2.2;18.2.2 Image and Data Servers;531
25.2.3;18.2.3 Users, Ownership, Permissions;532
25.3;18.3 Microscopy Image Management;533
25.3.1;18.3.1 XYZCT Five-Dimensional Imaging Model;533
25.3.2;18.3.2 Image Viewers;533
25.3.3;18.3.3 Image Hierarchies;535
25.3.3.1;18.3.3.1 Predefined Containers;535
25.3.3.2;18.3.3.2 User-Defined Containers;536
25.3.4;18.3.4 Browsing and Search;537
25.3.5;18.3.5 Microscopy Image File Formats and OME-XML;538
25.3.5.1;18.3.5.1 OME-XML Image Acquisition Ontology;540
25.4;18.4 Data Management;541
25.4.1;18.4.1 Biomedical Ontologies;542
25.4.2;18.4.2 Building Ontologies with OME SemanticTypes;543
25.4.3;18.4.3 Data Management Software with Plug-in Ontologies;545
25.4.4;18.4.4 Storing Data with Ontological Structure;546
25.4.4.1;18.4.4.1 Image Acquisition Meta-Data;546
25.4.4.2;18.4.4.2 Mass Annotations;546
25.4.4.3;18.4.4.3 Spreadsheet Annotations;547
25.5;18.5 Workflow Management;548
25.5.1;18.5.1 Data Provenance;548
25.5.1.1;18.5.1.1 OME AnalysisModules;549
25.5.1.2;18.5.1.2 Editing and Deleting Data;549
25.5.2;18.5.2 Modeling Quantitative Image Analysis;550
25.5.2.1;18.5.2.1 Coupling Algorithms to Informatics Platforms;551
25.5.2.2;18.5.2.2 Composing Workflows;553
25.5.2.3;18.5.2.3 Enacting Workflows;553
25.6;18.6 Summary of Important Points;556
25.7;References;558
26;Glossary of Microscope Image Processing Terms;560
26.1;References;568
27;Index;570
28;Color Plate Section;578