Biomedical Imaging

This book presents and describes imaging technologies that can be used to study chemical processes and structural interactions in dynamic systems, principally in biomedical systems. The imaging technologies, largely biomedical imaging technologies such as MRT, Fluorescence mapping, raman mapping, nanoESCA, and CARS microscopy, have been selected according to their application range and to the chemical information content of their data. These technologies allow for the analysis and evaluation of delicate biological samples, which must not be disturbed during the profess. Ultimately, this may mean fewer animal lab tests and clinical trials.

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