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Image processing and analysis : a practical approach / edited by Richard Baldock and Jim Graham. — Oxford : Oxford University Press, c2000.—(73.772/I31i) |
Contents
Contents
1. Microscope image acquisition 1
Stephanie L. Ellenberger and Ian T. Young
1. Introduction 1
Microscope systems 1
Case study 2
2. Basic optics 3
Nature of light 3
Illumination 7
Optical system 9
3. Microscope image acquisition system 12
Microscope types and components 12
Camera types and performance 19
Images 28
4. Application 29
Objective 29
Materials and methods 30
Performance 34
References 35
2. Biological image processing and enhancement 37
G. W. Horgan， C. A. Reid， and C. A. Glasbey
1. Introduction 37
2. Contrast manipulation 39
Functional transformation 40
Histogram-based transformations 41
Pseudocolour 42
Thresholding 43
Zooming 46
3. Filtering 46
Linear filters 46
Non-linear filters 50
4. Mathematical morphology 53
Basic ideas 54
Greylevel morphology 56
Complex operations 58
Top-hat transform and background subtraction 58
5. Texture measures 60
Statistical approaches 61
Structural approaches 64
Modelling approaches 64
Texture transforms 65
Acknowledgements 66
References 66
3. Image analysis: quantitative interpretation of chromosome images 69
Kenneth R. Castleman
1. Introduction 69
The karotyping problem 70
Historical perspective 70
Current practice 70
Automatic karyotyping 70
2. Image segmentation 72
Thresholding 73
The watershed algorithm 76
Gradient image thresholding 76
Laplacian edge detection 77
Edge detection and linking 78
Region growing 84
3. Boundary refinement 85
Active contours 85
Binary image processing 87
Morphological image processing 88
Boundary curvature analysis 91
Touch and overlap resolution 92
4. Chromosome measurement 93
Morphological features 94
Banding pattern features 94
5. Chromosome classification 96
The Bayes classifier 96
6. Karotype generation 99
Chromosome straightening 99
Chromosome enhancement 99
Chromosome assignment 101
7. Other cytogenetics applications 102
Multiplex-FISH 103
Metaphase finding 104
8. Image processing software 105
Academic packages 105
Commercial packages 105
References 106
4. Pattern recognition: classification of chromosomes 111
Jim Graham
1. Introduction 111
2. The chromosome classification problem 112
3. Classification methods 114
Defining classification in terms of probabilities 114
Using Bayes' formula 115
Non-parametric methods 121
4. Features and feature selection 124
Selecting features 126
Combining features 128
Clustering 129
5. Neural networks 131
Introduction 131
Supervised training 132
Unsupervised training 135
6. Classifying chromosomes 137
Features 137
Data sets 138
Classifiers 139
7. Classifier validation 141
The need for validation 141
Cross-validation， the jackknife and the bootstrap 141
The confusion matrix 142
Validating issues for neural networks 143
Training-set size and validation 143
Validation issues for the two-class problem 144
8. Available material 148
Software 148
Further reading 149
Acknowledgements 150
References 150
5. Three-dimensional (3D) reconstruction from serial sections 153
Fons J. Verbeek
1. Introduction 153
3D reconstruction in microscopy 153
Why serial sectioning is necessary 154
2. Methodological aspects 156
Modes of action 158
Organizing the reconstruction data 159
Methods and devices for the input of the data 161
Spatial resolution 166
Alignment and deformation correction 166
3. Mathematical aspects 173
Estimation of transformations 173
Spatial transformation of image values 174
Image correspondences 175
Point-pattern matching methods 175
Shape-based assessment methods 178
Registration and congruencing using image moment 180
Affine transform component estimation 181
Evaluation using similarity measures 184
Intensity-based methods 185
4. Systems for routine application of 3D reconstruction 186
Reconstruction under rigid transformation 187
Reconstruction including deformation correction 187
References 194
6. 3D analysis: registration of biomedical images 197
Daniel Rueckert and David J. Hawkes
1. Introduction 197
Intra-subject registration 198
Inter-subject registration 198
Serial registration 198
Image to physical space registration 198
Overview 199
2. Registration transformation 200
Rigid transformation 200
Affine transformation 200
Projective transformation 201
Elastic or fluid transformation 201
3. Registration basis 202
Point-based registration 202
Contour- and surface-based registration 204
Voxel-based registration 207
4. Optimization 211
5. Applications 212
2D registration 212
3D-3D rigid registration 212
3D-3D non-rigid registration 214
Validation 215
6. Summary 217
Acknowledgements 218
References 219
7. Model-based methods in analysis of biomedical images 223
Tim Cootes
1. Introduction 223
2. Background 223
3. Application 225
4. Theoretical background 227
Building models 227
Image interpretation with models 232
Active shape models 234
5. Discussion 240
6. Implementation 242
Appendices 242
Aligning the training set 242
Principal component analysis 244
Applying a PCA when there are fewer samples than dimensions 245
Aligning two shapes 246
Acknowledgements 246
References 246
8. Projective stereology in biological microscopy 249
Andrew D. Carothers
1. Introduction 249
2. Points and distances 250
3. Lines 253
4. Surface areas 254
5. Volumes 255
6. Applications 256
Determining the order of three DNA loci 256
Location of chromosomal domains in cell nuclei 257
Size of chromosomal domains in cell nuclei 259
7. Discussion 259
Acknowledgements 260
References 260
9. Image warping and spatial data mapping 261
Richard A. Baldock and Bill Hill
1. Introduction 261
Notation and numerical methods 262
2 Image comparison 264
Binary image overlay 264
Colour comparator 267
Blink comparator 268
3. Image re-sampling 269
Nearest neighbour interpolation 270
Bilinear interpolation 270
Computational efficiency 270
4. Defining correspondence 273
5. Global transforms 274
Affine 275
Polynomial 278
Conformal 279
Thin-plate spline 282
Multiquadric 284
Gaussian 284
6. Local transforms 285
Simple mesh transformation 285
Elastic plate warping 286
7. Mapping gene-expression data 286
8. Summary 286
References 288
List of Suppliers 289
Index 294
