Microscope Image Processing
Wu, Qiang; Merchant, Fatima; Castleman, Kenneth
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Table of contents
- Contentsv
- Forewordxxi
- Referencexxii
- Prefacexxiii
- Acknowledgmentsxxv
- Chapter 1: Introduction1
- 1.1 The Microscope and Image Processing1
- 1.2 Scope of This Book1
- 1.3 Our Approach3
- 1.3.1 The Four Types of Images3
- 1.3.1.1 Optical Image4
- 1.3.1.2 Continuous Image4
- 1.3.1.3 Digital Image4
- 1.3.1.4 Displayed Image5
- 1.3.2 The Result5
- 1.3.2.1 Analytic Functions6
- 1.3.3 The Sampling Theorem7
- 1.4 The Challenge8
- 1.5 Nomenclature8
- 1.6 Summary of Important Points8
- References9
- Chapter 2: Fundamentals of Microscopy11
- 2.1 Origins of the Microscope11
- 2.2 Optical Imaging12
- 2.2.1 Image Formation by a Lens12
- 2.2.1.1 Imaging a Point Source13
- 2.2.1.2 Focal Length13
- 2.2.1.3 Numerical Aperture14
- 2.2.1.4 Lens Shape15
- 2.3 Diffraction-Limited Optical Systems15
- 2.3.1 Linear System Analysis16
- 2.4 Incoherent Illumination16
- 2.4.1 The Point Spread Function16
- 2.4.2 The Optical Transfer Function17
- 2.5 Coherent Illumination18
- 2.5.1 The Coherent Point Spread Function18
- 2.5.2 The Coherent Optical Transfer Function19
- 2.6 Resolution20
- 2.6.1 Abbe Distance21
- 2.6.2 Rayleigh Distance21
- 2.6.3 Size Calculations21
- 2.7 Aberration22
- 2.8 Calibration22
- 2.8.1 Spatial Calibration23
- 2.8.2 Photometric Calibration23
- 2.9 Summary of Important Points24
- References25
- Chapter 3: Image Digitization27
- 3.1 Introduction27
- 3.2 Resolution28
- 3.3 Sampling29
- 3.3.1 Interpolation30
- 3.3.2 Aliasing32
- 3.4 Noise33
- 3.5 Shading34
- 3.6 Photometry34
- 3.7 Geometric Distortion35
- 3.8 Complete System Design35
- 3.8.1 Cumulative Resolution35
- 3.8.2 Design Rules of Thumb36
- 3.8.2.1 Pixel Spacing36
- 3.8.2.2 Resolution36
- 3.8.2.3 Noise36
- 3.8.2.4 Photometry36
- 3.8.2.5 Distortion37
- 3.9 Summary of Important Points37
- References37
- Chapter 4: Image Display39
- 4.1 Introduction39
- 4.2 Display Characteristics40
- 4.2.1 Displayed Image Size40
- 4.2.2 Aspect Ratio40
- 4.2.3 Photometric Resolution41
- 4.2.4 Grayscale Linearity42
- 4.2.5 Low-Frequency Response42
- 4.2.5.1 Pixel Polarity42
- 4.2.5.2 Pixel Interaction43
- 4.2.6 High-Frequency Response43
- 4.2.7 The Spot-Spacing Compromise43
- 4.2.8 Noise Considerations43
- 4.3 Volatile Displays44
- 4.4 Sampling for Display Purposes45
- 4.4.1 Oversampling46
- 4.4.2 Resampling46
- 4.5 Display Calibration47
- 4.6 Summary of Important Points47
- References48
- Chapter 5: Geometric Transformations51
- 5.1 Introduction51
- 5.2 Implementation52
- 5.3 Gray-Level Interpolation52
- 5.3.1 Nearest-Neighbor Interpolation53
- 5.3.2 Bilinear Interpolation53
- 5.3.3 Bicubic Interpolation54
- 5.3.4 Higher-Order Interpolation54
- 5.4 Spatial Transformation55
- 5.4.1 Control-Grid Mapping55
- 5.5 Applications56
- 5.5.1 Distortion Removal56
- 5.5.2 Image Registration56
- 5.5.3 Stitching56
- 5.6 Summary of Important Points57
- References57
- Chapter 6: Image Enhancement59
- 6.1 Introduction59
- 6.2 Spatial Domain Methods60
- 6.2.1 Contrast Stretching60
- 6.2.2 Clipping and Thresholding61
- 6.2.3 Image Subtraction and Averaging61
- 6.2.4 Histogram Equalization62
- 6.2.5 Histogram Specification62
- 6.2.6 Spatial Filtering63
- 6.2.7 Directional and Steerable Filtering65
- 6.2.8 Median Filtering67
- 6.3 Fourier Transform Methods68
- 6.3.1 Wiener Filtering and Wiener Deconvolution68
- 6.3.2 Deconvolution Using a Least-Squares Approach70
- 6.3.3 Low-Pass Filtering in the Fourier Domain71
- 6.3.4 High-Pass Filtering in the Fourier Domain71
- 6.4 Wavelet Transform Methods72
- 6.4.1 Wavelet Thresholding72
- 6.4.2 Differential Wavelet Transform and Multiscale Pointwise Product73
- 6.5 Color Image Enhancement74
- 6.5.1 Pseudo-Color Transformations75
- 6.5.2 Color Image Smoothing75
- 6.5.3 Color Image Sharpening75
- 6.6 Summary of Important Points76
- References77
- Chapter 7: Wavelet Image Processing79
- 7.1 Introduction79
- 7.1.1 Linear Transformations80
- 7.1.2 Short-Time Fourier Transform and Wavelet Transform81
- 7.2 Wavelet Transforms83
- 7.2.1 Continuous Wavelet Transform83
- 7.2.2 Wavelet Series Expansion84
- 7.2.3 Haar Wavelet Functions85
- 7.3 Multiresolution Analysis85
- 7.3.1 Multiresolution and Scaling Function86
- 7.3.2 Scaling Functions and Wavelets87
- 7.4 Discrete Wavelet Transform88
- 7.4.1 Decomposition88
- 7.4.2 Reconstruction91
- 7.4.3 Filter Banks92
- 7.4.3.1 Two-Channel Subband Coding92
- 7.4.3.2 Orthogonal Filter Design93
- 7.4.4 Compact Support95
- 7.4.5 Biorthogonal Wavelet Transforms96
- 7.4.5.1 Biorthogonal Filter Banks97
- 7.4.5.2 Examples of Biorthogonal Wavelets99
- 7.4.6 Lifting Schemes100
- 7.4.6.1 Biorthogonal Wavelet Design100
- 7.4.6.2 Wavelet Transform Using Lifting101
- 7.5 Two-Dimensional Discrete Wavelet Transform102
- 7.5.1 Two-Dimensional Wavelet Bases102
- 7.5.2 Forward Transform103
- 7.5.3 Inverse Transform105
- 7.5.4 Two-Dimensional Biorthogonal Wavelets105
- 7.5.5 Overcomplete Transforms106
- 7.6 Examples107
- 7.6.1 Image Compression107
- 7.6.2 Image Enhancement107
- 7.6.3 Extended Depth-of-Field by Wavelet Image Fusion108
- 7.7 Summary of Important Points108
- References110
- Chapter 8: Morphological Image Processing113
- 8.1 Introduction113
- 8.2 Binary Morphology115
- 8.2.1 Binary Erosion and Dilation115
- 8.2.2 Binary Opening and Closing116
- 8.2.3 Binary Morphological Reconstruction from Markers118
- 8.2.3.1 Connectivity118
- 8.2.3.2 Markers119
- 8.2.3.3 The Edge-Off Operation120
- 8.2.4 Reconstruction from Opening120
- 8.2.5 Area Opening and Closing122
- 8.2.6 Skeletonization123
- 8.3 Grayscale Operations127
- 8.3.1 Threshold Decomposition128
- 8.3.2 Erosion and Dilation129
- 8.3.2.1 Gradient131
- 8.3.3 Opening and Closing131
- 8.3.3.1 Top-Hat Filtering131
- 8.3.3.2 Alternating Sequential Filters133
- 8.3.4 Component Filters and Grayscale Morphological Reconstruction134
- 8.3.4.1 Morphological Reconstruction135
- 8.3.4.2 Alternating Sequential Component Filters135
- 8.3.4.3 Grayscale Area Opening and Closing135
- 8.3.4.4 Edge-Off Operator136
- 8.3.4.5 h-Maxima and h-Minima Operations137
- 8.3.4.6 Regional Maxima and Minima137
- 8.3.4.7 Regional Extrema as Markers138
- 8.4 Watershed Segmentation138
- 8.4.1 Classical Watershed Transform139
- 8.4.2 Filtering the Minima140
- 8.4.3 Texture Detection143
- 8.4.4 Watershed from Markers145
- 8.4.5 Segmentation of Overlapped Convex Cells146
- 8.4.6 Inner and Outer Markers148
- 8.4.7 Hierarchical Watershed151
- 8.4.8 Watershed Transform Algorithms152
- 8.5 Summary of Important Points154
- References156
- Chapter 9: Image Segmentation159
- 9.1 Introduction159
- 9.1.1 Pixel Connectivity160
- 9.2 Region-Based Segmentation160
- 9.2.1 Thresholding160
- 9.2.1.1 Global Thresholding161
- 9.2.1.2 Adaptive Thresholding162
- 9.2.1.3 Threshold Selection163
- 9.2.1.4 Thresholding Circular Spots165
- 9.2.1.5 Thresholding Noncircular and Noisy Spots167
- 9.2.2 Morphological Processing169
- 9.2.2.1 Hole Filling171
- 9.2.2.2 Border-Object Removal171
- 9.2.2.3 Separation of Touching Objects172
- 9.2.2.4 The Watershed Algorithm172
- 9.2.3 Region Growing173
- 9.2.4 Region Splitting175
- 9.3 Boundary-Based Segmentation176
- 9.3.1 Boundaries and Edges176
- 9.3.2 Boundary Tracking Based on Maximum Gradient Magnitude177
- 9.3.3 Boundary Finding Based on Gradient Image Thresholding178
- 9.3.4 Boundary Finding Based on Laplacian Image Thresholding179
- 9.3.5 Boundary Finding Based on Edge Detection and Linking180
- 9.3.5.1 Edge Detection180
- 9.3.5.2 Edge Linking and Boundary Refinement183
- 9.3.6 Encoding Segmented Images188
- 9.3.6.1 Object Label Map189
- 9.3.6.2 Boundary Chain Code189
- 9.4 Summary of Important Points190
- References192
- Chapter 10: Object Measurement195
- 10.1 Introduction195
- 10.2 Measures for Binary Objects196
- 10.2.1 Size Measures196
- 10.2.1.1 Area196
- 10.2.1.2 Perimeter196
- 10.2.1.3 Area and Perimeter of a Polygon197
- 10.2.2 Pose Measures199
- 10.2.2.1 Centroid199
- 10.2.2.2 Orientation200
- 10.2.3 Shape Measures200
- 10.2.3.1 Thinness Ratio201
- 10.2.3.2 Rectangularity201
- 10.2.3.3 Circularity201
- 10.2.3.4 Euler Number203
- 10.2.3.5 Moments203
- 10.2.3.6 Elongation205
- 10.2.4 Shape Descriptors206
- 10.2.4.1 Differential Chain Code206
- 10.2.4.2 Fourier Descriptors206
- 10.2.4.3 Medial Axis Transform207
- 10.2.4.4 Graph Representations208
- 10.3 Distance Measures209
- 10.3.1 Euclidean Distance209
- 10.3.2 City-Block Distance209
- 10.3.3 Chessboard Distance210
- 10.4 Gray-Level Object Measures210
- 10.4.1 Intensity Measures210
- 10.4.1.1 Integrated Optical Intensity210
- 10.4.1.2 Average Optical Intensity210
- 10.4.1.3 Contrast211
- 10.4.2 Histogram Measures211
- 10.4.2.1 Mean Gray Level211
- 10.4.2.2 Standard Deviation of Gray Levels211
- 10.4.2.3 Skew212
- 10.4.2.4 Entropy212
- 10.4.2.5 Energy212
- 10.4.3 Texture Measures212
- 10.4.3.1 Statistical Texture Measures213
- 10.4.3.2 Power Spectrum Features214
- 10.5 Object Measurement Considerations215
- 10.6 Summary of Important Points215
- References217
- Chapter 11: Object Classification221
- 11.1 Introduction221
- 11.2 The Classification Process221
- 11.2.1 Bayes’ Rule222
- 11.3 The Single-Feature, Two-Class Case222
- 11.3.1 A Priori Probabilities223
- 11.3.2 Conditional Probabilities223
- 11.3.3 Bayes’ Theorem224
- 11.4 The Three-Feature, Three-Class Case225
- 11.4.1 Bayes Classifier226
- 11.4.1.1 Prior Probabilities226
- 11.4.1.2 Classifier Training227
- 11.4.1.3 The Mean Vector227
- 11.4.1.4 Covariance228
- 11.4.1.5 Variance and Standard Deviation228
- 11.4.1.6 Correlation228
- 11.4.1.7 The Probability Density Function229
- 11.4.1.8 Classification229
- 11.4.1.9 Log Likelihoods229
- 11.4.1.10 Mahalanobis Distance Classifier230
- 11.4.1.11 Uncorrelated Features230
- 11.4.2 A Numerical Example231
- 11.5 Classifier Performance232
- 11.5.1 The Confusion Matrix233
- 11.6 Bayes Risk234
- 11.6.1 Minimum-Risk Classifier234
- 11.7 Relationships Among Bayes Classifiers235
- 11.8 The Choice of a Classifier235
- 11.8.1 Subclassing236
- 11.8.2 Feature Normalization236
- 11.9 Nonparametric Classifiers238
- 11.9.1 Nearest-Neighbor Classifiers239
- 11.10 Feature Selection240
- 11.10.1 Feature Reduction240
- 11.10.1.1 Principal Component Analysis241
- 11.10.1.2 Linear Discriminant Analysis242
- 11.11 Neural Networks243
- 11.12 Summary of Important Points244
- References245
- Chapter 12: Fluorescence Imaging247
- 12.1 Introduction247
- 12.2 Basics of Fluorescence Imaging248
- 12.2.1 Image Formation in Fluorescence Imaging249
- 12.3 Optics in Fluorescence Imaging250
- 12.4 Limitations in Fluorescence Imaging251
- 12.4.1 Instrumentation-Based Aberrations251
- 12.4.1.1 Photon Shot Noise251
- 12.4.1.2 Dark Current252
- 12.4.1.3 Auxiliary Noise Sources252
- 12.4.1.4 Quantization Noise253
- 12.4.1.5 Other Noise Sources253
- 12.4.2 Sample-Based Aberrations253
- 12.4.2.1 Photobleaching253
- 12.4.2.2 Autofluorescence254
- 12.4.2.3 Absorption and Scattering255
- 12.4.3 Sample and Instrumentation Handling–Based Aberrations255
- 12.5 Image Corrections in Fluorescence Microscopy256
- 12.5.1 Background Shading Correction256
- 12.5.2 Correction Using the Recorded Image257
- 12.5.3 Correction Using Calibration Images258
- 12.5.3.1 Two-Image Calibration258
- 12.5.3.2 Background Subtraction258
- 12.5.4 Correction Using Surface Fitting259
- 12.5.5 Histogram-Based Background Correction261
- 12.5.6 Other Approaches for Background Correction261
- 12.5.7 Autofluorescence Correction261
- 12.5.8 Spectral Overlap Correction262
- 12.5.9 Photobleaching Correction262
- 12.5.10 Correction of Fluorescence Attenuation in Depth265
- 12.6 Quantifying Fluorescence266
- 12.6.1 Fluorescence Intensity Versus Fluorophore Concentration266
- 12.7 Fluorescence Imaging Techniques267
- 12.7.1 Immunofluorescence267
- 12.7.2 Fluorescence in situ Hybridization (FISH)270
- 12.7.3 Quantitative Colocalization Analysis271
- 12.7.4 Fluorescence Ratio Imaging (RI)275
- 12.7.5 Fluorescence Resonance Energy Transfer (FRET)277
- 12.7.6 Fluorescence Lifetime Imaging (FLIM)284
- 12.7.7 Fluorescence Recovery After Photobleaching (FRAP)286
- 12.7.8 Total Internal Reflectance Fluorescence Microscopy (TIRFM)288
- 12.7.9 Fluorescence Correlation Spectroscopy (FCS)289
- 12.8 Summary of Important Points290
- References291
- Chapter 13: Multispectral Imaging299
- 13.1 Introduction299
- 13.2 Principles of Multispectral Imaging300
- 13.2.1 Spectroscopy301
- 13.2.2 Imaging302
- 13.2.3 Multispectral Microscopy304
- 13.2.4 Spectral Image Acquisition Methods304
- 13.2.4.1 Wavelength-Scan Methods304
- 13.2.4.2 Spatial-Scan Methods305
- 13.2.4.3 Time-Scan Methods306
- 13.3 Multispectral Image Processing306
- 13.3.1 Calibration for Multispectral Image Acquisition307
- 13.3.2 Spectral Unmixing312
- 13.3.2.1 Fluorescence Unmixing315
- 13.3.2.2 Brightfield Unmixing317
- 13.3.2.3 Unsupervised Unmixing318
- 13.3.3 Spectral Image Segmentation321
- 13.3.3.1 Combining Segmentation with Classification322
- 13.3.3.2 M-FISH Pixel Classification322
- 13.4 Summary of Important Points323
- References324
- Chapter 14: Three-Dimensional Imaging329
- 14.1 Introduction329
- 14.2 Image Acquisition329
- 14.2.1 Wide-Field Three-Dimensional Microscopy330
- 14.2.2 Confocal Microscopy330
- 14.2.3 Multiphoton Microscopy331
- 14.2.4 Other Three-Dimensional Microscopy Techniques333
- 14.3 Three-Dimensional Image Data334
- 14.3.1 Three-Dimensional Image Representation334
- 14.3.1.1 Three-Dimensional Image Notation334
- 14.4 Image Restoration and Deblurring335
- 14.4.1 The Point Spread Function335
- 14.4.1.1 Theoretical Model of the Point Spread Function337
- 14.4.2 Models for Microscope Image Formation338
- 14.4.2.1 Poisson Noise338
- 14.4.2.2 Gaussian Noise338
- 14.4.3 Algorithms for Deblurring and Restoration339
- 14.4.3.1 No-Neighbor Methods339
- 14.4.3.2 Nearest-Neighbor Method340
- 14.4.3.3 Linear Methods342
- 14.4.3.4 Nonlinear Methods346
- 14.4.3.5 Maximum-Likelihood Restoration349
- 14.4.3.6 Blind Deconvolution353
- 14.4.3.7 Interpretation of Deconvolved Images354
- 14.4.3.8 Commercial Deconvolution Packages354
- 14.5 Image Fusion355
- 14.6 Three-Dimensional Image Processing356
- 14.7 Geometric Transformations356
- 14.8 Pointwise Operations357
- 14.9 Histogram Operations357
- 14.10 Filtering359
- 14.10.1 Linear Filters359
- 14.10.1.1 Finite Impulse Response (FIR) Filter359
- 14.10.2 Nonlinear Filters360
- 14.10.2.1 Median Filter360
- 14.10.2.2 Weighted Median Filter360
- 14.10.2.3 Minimum and Maximum Filters361
- 14.10.2.4 alpha-Trimmed Mean Filters361
- 14.10.3 Edge-Detection Filters361
- 14.11 Morphological Operators362
- 14.11.1 Binary Morphology363
- 14.11.2 Grayscale Morphology364
- 14.12 Segmentation365
- 14.12.1 Point-Based Segmentation366
- 14.12.2 Edge-Based Segmentation367
- 14.12.3 Region-Based Segmentation369
- 14.12.3.1 Connectivity369
- 14.12.3.2 Region Growing370
- 14.12.3.3 Region Splitting and Region Merging370
- 14.12.4 Deformable Models371
- 14.12.5 Three-Dimensional Segmentation Methods in the Literature372
- 14.13 Comparing Three-Dimensional Images375
- 14.14 Registration375
- 14.15 Object Measurements in Three Dimensions376
- 14.15.1 Euler Number376
- 14.15.2 Bounding Box377
- 14.15.3 Center of Mass377
- 14.15.4 Surface Area Estimation378
- 14.15.5 Length Estimation379
- 14.15.6 Curvature Estimation380
- 14.15.6.1 Surface Triangulation Method381
- 14.15.6.2 Cross-Patch Method381
- 14.15.7 Volume Estimation381
- 14.15.8 Texture382
- 14.16 Three-Dimensional Image Display382
- 14.16.1 Montage382
- 14.16.2 Projected Images384
- 14.16.2.1 Voxel Projection384
- 14.16.2.2 Ray Casting384
- 14.16.3 Surface and Volume Rendering385
- 14.16.3.1 Surface Rendering385
- 14.16.3.2 Volume Rendering386
- 14.16.4 Stereo Pairs387
- 14.16.5 Color Anaglyphs388
- 14.16.6 Animations388
- 14.17 Summary of Important Points389
- References392
- Chapter 15: Time-Lapse Imaging401
- 15.1 Introduction401
- 15.2 Image Acquisition403
- 15.2.1 Microscope Setup404
- 15.2.2 Spatial Dimensionality405
- 15.2.3 Temporal Resolution410
- 15.3 Image Preprocessing411
- 15.3.1 Image Denoising411
- 15.3.2 Image Deconvolution412
- 15.3.3 Image Registration413
- 15.4 Image Analysis414
- 15.4.1 Cell Tracking415
- 15.4.1.1 Cell Segmentation415
- 15.4.1.2 Cell Association417
- 15.4.2 Particle Tracking417
- 15.4.2.1 Particle Detection418
- 15.4.2.2 Particle Association419
- 15.5 Trajectory Analysis420
- 15.5.1 Geometry Measurements421
- 15.5.2 Diffusivity Measurements421
- 15.5.3 Velocity Measurements423
- 15.6 Sample Algorithms423
- 15.6.1 Cell Tracking424
- 15.6.2 Particle Tracking427
- 15.7 Summary of Important Points432
- References434
- Chapter 16: Autofocusing441
- 16.1 Introduction441
- 16.1.1 Autofocus Methods441
- 16.1.2 Passive Autofocusing442
- 16.2 Principles of Microscope Autofocusing442
- 16.2.1 Fluorescence and Brightfield Autofocusing443
- 16.2.2 Autofocus Functions444
- 16.2.3 Autofocus Function Sampling and Approximation445
- 16.2.3.1 Gaussian Fitting447
- 16.2.3.2 Parabola Fitting447
- 16.2.4 Finding the In-Focus Imaging Position448
- 16.3 Multiresolution Autofocusing448
- 16.3.1 Multiresolution Image Representations449
- 16.3.2 Wavelet-Based Multiresolution Autofocus Functions451
- 16.3.3 Multiresolution Search for In-Focus Position451
- 16.4 Autofocusing for Scanning Microscopy452
- 16.5 Extended Depth-of-Field Microscope Imaging454
- 16.5.1 Digital Image Fusion455
- 16.5.2 Pixel-Based Image Fusion456
- 16.5.3 Neighborhood-Based Image Fusion457
- 16.5.4 Multiresolution Image Fusion458
- 16.5.5 Noise and Artifact Control in Image Fusion459
- 16.5.5.1 Multiscale Pointwise Product460
- 16.5.5.2 Consistency Checking461
- 16.5.5.3 Reassignment462
- 16.6 Examples462
- 16.7 Summary of Important Points462
- References465
- Chapter 17: Structured Illumination Imaging469
- 17.1 Introduction469
- 17.1.1 Conventional Light Microscope469
- 17.1.2 Sectioning the Specimen470
- 17.1.3 Structured Illumination471
- 17.2 Linear SIM Instrumentation472
- 17.2.1 Spatial Light Modulator473
- 17.3 The Process of Structured Illumination Imaging473
- 17.3.1 Extended-Depth-of-Field Image475
- 17.3.2 SIM for Optical Sectioning475
- 17.3.3 Sectioning Strength477
- 17.4 Limitations of Optical Sectioning with SIM479
- 17.4.1 Artifact Reduction via Image Processing480
- 17.4.1.1 Intensity Normalization480
- 17.4.1.2 Grid Position Error482
- 17.4.1.3 Statistical Waveform Compensation484
- 17.4.1.4 Parameter Optimization485
- 17.5 Color Structured Illumination486
- 17.5.1 Processing Technique487
- 17.5.2 Chromatic Aberration488
- 17.5.3 SIM Example490
- 17.6 Lateral Superresolution491
- 17.6.1 Bypassing the Optical Transfer Function491
- 17.6.2 Mathematical Foundation492
- 17.6.2.1 Shifting Frequency Space492
- 17.6.2.2 Extracting the Enhanced Image493
- 17.6.3 Lateral Resolution Enhancement Simulation495
- 17.7 Summary of Important Points496
- References496
- Chapter 18: Image Data and Workflow Management499
- 18.1 Introduction499
- 18.1.1 Open Microscopy Environment500
- 18.1.2 Image Management in Other Fields500
- 18.1.3 Requirements for Microscopy Image Management Systems500
- 18.2 Architecture of Microscopy Image/Data/Workflow Systems501
- 18.2.1 Client–Server Architecture501
- 18.2.2 Image and Data Servers502
- 18.2.3 Users, Ownership, Permissions503
- 18.3 Microscopy Image Management504
- 18.3.1 XYZCT Five-Dimensional Imaging Model504
- 18.3.2 Image Viewers504
- 18.3.3 Image Hierarchies506
- 18.3.3.1 Predefined Containers506
- 18.3.3.2 User-Defined Containers507
- 18.3.4 Browsing and Search508
- 18.3.5 Microscopy Image File Formats and OME-XML509
- 18.3.5.1 OME-XML Image Acquisition Ontology511
- 18.4 Data Management512
- 18.4.1 Biomedical Ontologies513
- 18.4.2 Building Ontologies with OME SemanticTypes514
- 18.4.3 Data Management Software with Plug-in Ontologies516
- 18.4.4 Storing Data with Ontological Structure517
- 18.4.4.1 Image Acquisition Meta-Data517
- 18.4.4.2 Mass Annotations517
- 18.4.4.3 Spreadsheet Annotations518
- 18.5 Workflow Management519
- 18.5.1 Data Provenance519
- 18.5.1.1 OME AnalysisModules520
- 18.5.1.2 Editing and Deleting Data520
- 18.5.2 Modeling Quantitative Image Analysis521
- 18.5.2.1 Coupling Algorithms to Informatics Platforms522
- 18.5.2.2 Composing Workflows524
- 18.5.2.3 Enacting Workflows524
- 18.6 Summary of Important Points527
- References529
- Glossary of Microscope Image Processing Terms531
- References539
- Index541
- Color Plate Section549
Book details
- Vendor Elsevier S & T
- SKU 9780123725783
- ISBN-13 9780080558547
- Author Wu, Qiang; Merchant, Fatima; Castleman, Kenneth
- Category Science
- Subject Microscopes & Microscopy
Do you have questions about this book?
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.
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.
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