Biomedical Imaging: Principles and Applications Book

Preface xv

Contributors xvii

1 Evaluation of Spectroscopic Images 1
Patrick W.T. Krooshof, Geert J. Postma, Willem J. Melssen, and Lutgarde M.C. Buydens

1.1 Introduction, 1

1.2 Data Analysis, 2

1.2.1 Similarity Measures, 3

1.2.2 Unsupervised Pattern Recognition, 4

1.2.2.1 Partitional Clustering, 4

1.2.2.2 Hierarchical Clustering, 6

1.2.2.3 Density-Based Clustering, 7

1.2.3 Supervised Pattern Recognition, 9

1.2.3.1 Probability of Class Membership, 9

1.3 Applications, 11

1.3.1 Brain Tumor Diagnosis, 11

1.3.2 MRS Data Processing, 12

1.3.2.1 Removing MRS Artifacts, 12

1.3.2.2 MRS Data Quantitation, 13

1.3.3 MRI Data Processing, 14

1.3.3.1 Image Registration, 15

1.3.4 Combining MRI and MRS Data, 16

1.3.4.1 Reference Data Set, 16

1.3.5 Probability of Class Memberships, 17

1.3.6 Class Membership of Individual Voxels, 18

1.3.7 Classification of Individual Voxels, 20

1.3.8 Clustering into Segments, 22

1.3.9 Classification of Segments, 23

1.3.10 Future Directions, 24

References, 25

2 Evaluation of Tomographic Data 30
Jörg van den Hoff

2.1 Introduction, 30

2.2 Image Reconstruction, 33

2.3 Image Data Representation: Pixel Size and Image Resolution, 34

2.4 Consequences of Limited Spatial Resolution, 39

2.5 Tomographic Data Evaluation: Tasks, 46

2.5.1 Software Tools, 46

2.5.2 Data Access, 47

2.5.3 Image Processing, 47

2.5.3.1 Slice Averaging, 48

2.5.3.2 Image Smoothing, 48

2.5.3.3 Coregistration and Resampling, 51

2.5.4 Visualization, 52

2.5.4.1 Maximum Intensity Projection (MIP), 52

2.5.4.2 Volume Rendering and Segmentation, 54

2.5.5 Dynamic Tomographic Data, 56

2.5.5.1 Parametric Imaging, 57

2.5.5.2 Compartment Modeling of Tomographic Data, 57

2.6 Summary, 61

References, 61

3 X-Ray Imaging 63
Volker Hietschold

3.1 Basics, 63

3.1.1 History, 63

3.1.2 Basic Physics, 64

3.2 Instrumentation, 66

3.2.1 Components, 66

3.2.1.1 Beam Generation, 66

3.2.1.2 Reduction of Scattered Radiation, 67

3.2.1.3 Image Detection, 69

3.3 Clinical Applications, 76

3.3.1 Diagnostic Devices, 76

3.3.1.1 Projection Radiography, 76

3.3.1.2 Mammography, 78

3.3.1.3 Fluoroscopy, 81

3.3.1.4 Angiography, 82

3.3.1.5 Portable Devices, 84

3.3.2 High Voltage and Image Quality, 85

3.3.3 Tomography/Tomosynthesis, 87

3.3.4 Dual Energy Imaging, 87

3.3.5 Computer Applications, 88

3.3.6 Interventional Radiology, 92

3.4 Radiation Exposure to Patients and Employees, 92

References, 95

4 Computed Tomography 97
Stefan Ulzheimer and Thomas Flohr

4.1 Basics, 97

4.1.1 History, 97

4.1.2 Basic Physics and Image Reconstruction, 100

4.2 Instrumentation, 102

4.2.1 Gantry, 102

4.2.2 X-ray Tube and Generator, 103

4.2.3 MDCT Detector Design and Slice Collimation, 103

4.2.4 Data Rates and Data Transmission, 107

4.2.5 Dual Source CT, 107

4.3 Measurement Techniques, 109

4.3.1 MDCT Sequential (Axial) Scanning, 109

4.3.2 MDCT Spiral (Helical) Scanning, 109

4.3.2.1 Pitch, 110

4.3.2.2 Collimated and Effective Slice Width, 110

4.3.2.3 Multislice Linear Interpolation and z-Filtering, 111

4.3.2.4 Three-Dimensional Backprojection and Adaptive Multiple Plane Reconstruction (AMPR), 114

4.3.2.5 Double z-Sampling, 114

4.3.3 ECG-Triggered and ECG-Gated Cardiovascular CT, 115

4.3.3.1 Principles of ECG-Triggering and ECG-Gating, 115

4.3.3.2 ECG-Gated Single-Segment and Multisegment Reconstruction, 118

4.4 Applications, 119

4.4.1 Clinical Applications of Computed Tomography, 119

4.4.2 Radiation Dose in Typical Clinical Applications and Methods for Dose Reduction, 122

4.5 Outlook, 125

References, 127

5 Magnetic Resonance Technology 131
Boguslaw Tomanek and Jonathan C. Sharp

5.1 Introduction, 131

5.2 Magnetic Nuclei Spin in a Magnetic Field, 133

5.2.1 A Pulsed rf Field Resonates with Magnetized Nuclei, 135

5.2.2 The MR Signal, 137

5.2.3 Spin Interactions Have Characteristic Relaxation Times, 138

5.3 Image Creation, 139

5.3.1 Slice Selection, 139

5.3.2 The Signal Comes Back—The Spin Echo, 142

5.3.3 Gradient Echo, 143

5.4 Image Reconstruction, 145

5.4.1 Sequence Parameters, 146

5.5 Image Resolution, 148

5.6 Noise in the Image—SNR, 149

5.7 Image Weighting and Pulse Sequence Parameters TE and TR, 150

5.7.1 T2-Weighted Imaging, 150

5.7.2 T ∗ 2 -Weighted Imaging, 151

5.7.3 Proton-Density-Weighted Imaging, 152

5.7.4 T1-Weighted Imaging, 152

5.8 A Menagerie of Pulse Sequences, 152

5.8.1 EPI, 154

5.8.2 FSE, 154

5.8.3 Inversion-Recovery, 155

5.8.4 DWI, 156

5.8.5 MRA, 158

5.8.6 Perfusion, 159

5.9 Enhanced Diagnostic Capabilities of MRI—Contrast Agents, 159

5.10 Molecular MRI, 159

5.11 Reading the Mind—Functional MRI, 160

5.12 Magnetic Resonance Spectroscopy, 161

5.12.1 Single Voxel Spectroscopy, 163

5.12.2 Spectroscopic Imaging, 163

5.13 MR Hardware, 164

5.13.1 Magnets, 164

5.13.2 Shimming, 167

5.13.3 Rf Shielding, 168

5.13.4 Gradient System, 168

5.13.5 MR Electronics—The Console, 169

5.13.6 Rf Coils, 170

5.14 MRI Safety, 171

5.14.1 Magnet Safety, 171

5.14.2 Gradient Safety, 173

5.15 Imaging Artefacts in MRI, 173

5.15.1 High Field Effects, 174

5.16 Advanced MR Technology and Its Possible Future, 175

References, 175

6 Toward A 3D View of Cellular Architecture: Correlative Light Microscopy and Electron Tomography 180
Jack A. Valentijn, Linda F. van Driel, Karen A. Jansen, Karine M. Valentijn, and Abraham J. Koster

6.1 Introduction, 180

6.2 Historical Perspective, 181

6.3 Stains for CLEM, 182

6.4 Probes for CLEM, 183

6.4.1 Probes to Detect Exogenous Proteins, 183

6.4.1.1 Green Fluorescent Protein, 183

6.4.1.2 Tetracysteine Tags, 186

6.4.1.3 Theme Variations: Split GFP and GFP-4C, 187

6.4.2 Probes to Detect Endogenous Proteins, 188

6.4.2.1 Antifluorochrome Antibodies, 189

6.4.2.2 Combined Fluorescent and Gold Probes, 189

6.4.2.3 Quantum Dots, 190

6.4.2.4 Dendrimers, 191

6.4.3 Probes to Detect Nonproteinaceous Molecules, 192

6.5 CLEM Applications, 193

6.5.1 Diagnostic Electron Microscopy, 193

6.5.2 Ultrastructural Neuroanatomy, 194

6.5.3 Live-Cell Imaging, 196

6.5.4 Electron Tomography, 197

6.5.5 Cryoelectron Microscopy, 198

6.5.6 Immuno Electron Microscopy, 201

6.6 Future Perspective, 202

References, 205

7 Tracer Imaging 215
Rainer Hinz

7.1 Introduction, 215

7.2 Instrumentation, 216

7.2.1 Radioisotope Production, 216

7.2.2 Radiochemistry and Radiopharmacy, 219

7.2.3 Imaging Devices, 220

7.2.4 Peripheral Detectors and Bioanalysis, 225

7.3 Measurement Techniques, 228

7.3.1 Tomographic Image Reconstruction, 228

7.3.2 Quantification Methods, 229

7.3.2.1 The Flow Model, 230

7.3.2.2 The Irreversible Model for Deoxyglucose, 230

7.3.2.3 The Neuroreceptor Binding Model, 233

7.4 Applications, 234

7.4.1 Neuroscience, 234

7.4.1.1 Cerebral Blood Flow, 234

7.4.1.2 Neurotransmitter Systems, 235

7.4.1.3 Metabolic and Other Processes, 238

7.4.2 Cardiology, 240

7.4.3 Oncology, 240

7.4.3.1 Angiogenesis, 240

7.4.3.2 Proliferation, 241

7.4.3.3 Hypoxia, 241

7.4.3.4 Apoptosis, 242

7.4.3.5 Receptor Imaging, 242

7.4.3.6 Imaging Gene Therapy, 243

7.4.4 Molecular Imaging for Research in Drug Development, 243

7.4.5 Small Animal Imaging, 244

References, 244

8 Fluorescence Imaging 248
Nikolaos C. Deliolanis, Christian P. Schultz, and Vasilis Ntziachristos

8.1 Introduction, 248

8.2 Contrast Mechanisms, 249

8.2.1 Endogenous Contrast, 249

8.2.2 Exogenous Contrast, 251

8.3 Direct Methods: Fluorescent Probes, 251

8.4 Indirect Methods: Fluorescent Proteins, 252

8.5 Microscopy, 253

8.5.1 Optical Microscopy, 253

8.5.2 Fluorescence Microscopy, 254

8.6 Macroscopic Imaging/Tomography, 260

8.7 Planar Imaging, 260

8.8 Tomography, 262

8.8.1 Diffuse Optical Tomography, 266

8.8.2 Fluorescence Tomography, 266

8.9 Conclusion, 267

References, 268

9 Infrared and Raman Spectroscopic Imaging 275
Gerald Steiner

9.1 Introduction, 275

9.2 Instrumentation, 278

9.2.1 Infrared Imaging, 278

9.2.2 Near-Infrared Imaging, 281

9.3 Raman Imaging, 282

9.4 Sampling Techniques, 283

9.5 Data Analysis and Image Evaluation, 285

9.5.1 Data Preprocessing, 287

9.5.2 Feature Selection, 287

9.5.3 Spectral Classification, 288

9.5.4 Image Processing Including Pattern Recognition, 292

9.6 Applications, 292

9.6.1 Single Cells, 292

9.6.2 Tissue Sections, 292

9.6.2.1 Brain Tissue, 294

9.6.2.2 Skin Tissue, 295

9.6.2.3 Breast Tissue, 298

9.6.2.4 Bone Tissue, 299

9.6.3 Diagnosis of Hemodynamics, 300

References, 301

10 Coherent Anti-Stokes Raman Scattering Microscopy 304
Annika Enejder, Christoph Heinrich, Christian Brackmann, Stefan Bernet, and Monika Ritsch-Marte

10.1 Basics, 304

10.1.1 Introduction, 304

10.2 Theory, 306

10.3 CARS Microscopy in Practice, 309

10.4 Instrumentation, 310

10.5 Laser Sources, 311

10.6 Data Acquisition, 314

10.7 Measurement Techniques, 316

10.7.1 Excitation Geometry, 316

10.7.2 Detection Geometry, 318

10.7.3 Time-Resolved Detection, 319

10.7.4 Phase-Sensitive Detection, 319

10.7.5 Amplitude-Modulated Detection, 320

10.8 Applications, 320

10.8.1 Imaging of Biological Membranes, 321

10.8.2 Studies of Functional Nutrients, 321

10.8.3 Lipid Dynamics and Metabolism in Living Cells and Organisms, 322

10.8.4 Cell Hydrodynamics, 324

10.8.5 Tumor Cells, 325

10.8.6 Tissue Imaging, 325

10.8.7 Imaging of Proteins and DNA, 326

10.9 Conclusions, 326

References, 327

11 Biomedical Sonography 331
Georg Schmitz

11.1 Basic Principles, 331

11.1.1 Introduction, 331

11.1.2 Ultrasonic Wave Propagation in Biological Tissues, 332

11.1.3 Diffraction and Radiation of Sound, 333

11.1.4 Acoustic Scattering, 337

11.1.5 Acoustic Losses, 338

11.1.6 Doppler Effect, 339

11.1.7 Nonlinear Wave Propagation, 339

11.1.8 Biological Effects of Ultrasound, 340

11.1.8.1 Thermal Effects, 340

11.1.8.2 Cavitation Effects, 340

11.2 Instrumentation of Real-Time Ultrasound Imaging, 341

11.2.1 Pulse-Echo Imaging Principle, 341

11.2.2 Ultrasonic Transducers, 342

11.2.3 Beamforming, 344

11.2.3.1 Beamforming Electronics, 344

11.2.3.2 Array Beamforming, 345

11.3 Measurement Techniques of Real-Time Ultrasound Imaging, 347

11.3.1 Doppler Measurement Techniques, 347

11.3.1.1 Continuous Wave Doppler, 347

11.3.1.2 Pulsed Wave Doppler, 349

11.3.1.3 Color Doppler Imaging and Power Doppler Imaging, 351

11.3.2 Ultrasound Contrast Agents and Nonlinear Imaging, 353

11.3.2.1 Ultrasound Contrast Media, 353

11.3.2.2 Harmonic Imaging Techniques, 356

11.3.2.3 Perfusion Imaging Techniques, 357

11.3.2.4 Targeted Imaging, 358

11.4 Application Examples of Biomedical Sonography, 359

11.4.1 B-Mode, M-Mode, and 3D Imaging, 359

11.4.2 Flow and Perfusion Imaging, 362

References, 365

12 Acoustic Microscopy for Biomedical Applications 368
Jürgen Bereiter-Hahn

12.1 Sound Waves and Basics of Acoustic Microscopy, 368

12.1.1 Propagation of Sound Waves, 369

12.1.2 Main Applications of Acoustic Microscopy, 371

12.1.3 Parameters to Be Determined and General Introduction into Microscopy with Ultrasound, 371

12.2 Types of Acoustic Microscopy, 372

12.2.1 Scanning Laser Acoustic Microscope (LSAM), 373

12.2.2 Pulse-Echo Mode: Reflection-Based Acoustic Microscopy, 373

12.2.2.1 Reflected Amplitude Measurements, 379

12.2.2.2 V(z) Imaging, 380

12.2.2.3 V(f) Imaging, 382

12.2.2.4 Interference-Fringe-Based Image Analysis, 383

12.2.2.5 Determination of Phase and the Complex Amplitude, 386

12.2.2.6 Combining V (f) with Reflected Amplitude and Phase Imaging, 386

12.2.2.7 Time-Resolved SAM and Full Signal Analysis, 388

12.3 Biomedical Applications of Acoustic Microscopy, 391

12.3.1 Influence of Fixation on Acoustic Parameters of Cells and Tissues, 391

12.3.2 Acoustic Microscopy of Cells in Culture, 392

12.3.3 Technical Requirements, 393

12.3.3.1 Mechanical Stability, 393

12.3.3.2 Frequency, 393

12.3.3.3 Coupling Fluid, 393

12.3.3.4 Time of Image Acquisition, 394

12.3.4 What Is Revealed by SAM: Interpretation of SAM Images, 394

12.3.4.1 Sound Velocity, Elasticity, and the Cytoskeleton, 395

12.3.4.2 Attenuation, 400

12.3.4.3 Viewing Subcellular Structures, 401

12.3.5 Conclusions, 401

12.4 Examples of Tissue Investigations using SAM, 403

12.4.1 Hard Tissues, 404

12.4.2 Cardiovascular Tissues, 405

12.4.3 Other Soft Tissues, 406

References, 406

Index 415