Index. Born approximation, 128 Bremsstrahlung, 41, 42, 53 angular distribution, 42 energy distribution, 42

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1 Index Aberrations aberration-free holography, 123 chromatic, in confocal imaging, 195 off-axis, 2, 211 optical correction methods, 122 reduction of, 2 Acetylcholine receptors, 30 Acoustic impedance, 200 and refractive index, 207 Acoustic interferometry, 226 Acoustic lens, 212 antireflection coating, 213 geometrical aberration in, 213 Acoustic microscope, 205 applied to demineralization, 224 applied to living cells, 221 compared with optical microscope, 219 nonlinear effects in, 223 scanning, 214 ultrasound in, 206 Actin, 25, 31, 32 tubular, 21 Airy pattern, 73 Amorphous ice, 259 Antibody probes, 88 Atomic force microscope, 234 Atomic scattering factors, 60 Barrier height, 242 Bessel functions, 24 Brookhaven National Laboratory, 76, 78, 122, 127, 131 Born approximation, 128 Bremsstrahlung, 41, 42, 53 angular distribution, 42 energy distribution, 42 Carcinoma colon, 137 kidney, 159 rectum, 153 Channelling radiation, 41 Coherence angular, 47 and brilliance, 75 partial, 67 in phase contrast microscope, 59, 67 and plasma sources, 75 source requirements with zone plates, 73 spatial, 50, 73 temporal, 73 in ultrasonic waves, 209 in x-ray holography, Collagen, 11, 259 Colloidal gold, 263 Components cellular, 31 cytoskeletal, 31 Confocal light microscopy, 264 Confocal microscopes edge enhancement in, 201 epifluorescent mode, 187 fluorescence, 202 laser,

2 268 INDEX Confocal microscopes (cont.) mirror systems in, 191 multiple aperture array, 188 polarization in, 188 scanning, 2, 185 single beam, 191 Confocal microscopes, tandem, 185 Confocal optical microscopy, 4 Contact microscopy, 70 Contact x-ray microscopy, 53, 54 laser-produced plasmas in, 53, 54 use of line-emission sources in, 43 of stained materials, 88, 109 z-pinch source in, 54 Contrast, 1, 59 in acoustic microscopy, 5, 218 agents, in NMR microscopy, 140, 166 amplitude, 21, 59, 64 calculation of, 69 in contact microscopy, 92 and defocus, 21, 33 in electron microscopy, 9-10 enhancement, 63 image, 62, 64 inherent, 12 in light microscopy, II mechanism, in x-ray microscopy, 69 natural, 2-3, 161 in NMR microscopy, 4, nucleic acid in water, 65 phase, 4, 10,21,59,64 protein in water, 64 and radiation dose, 63 reversed, 33 in scanning tunnelling microscopy, 244 and signal-to-noise ratio, 74 of stained muscle specimens, 78 surface, in confocal microscopy, 195 transfer function, 21 in x-ray microscopy, 78 Contrast transfer function, 21-23, 33, 257 Cross-correlation, 27 Cryoelectron microscopy, 2, 3 Crystals, 3, 10 Fourier transform of, 16 planar, 24 protein, 30 Cytoskeleton, 257 Damage, see also Radiation damage cellular, 217 Damage (cont.) in scanning tunnelling microscopy, 239, 241 thermal, 103 in electron microscopy, 241 Daresbury Laboratory, United Kingdom, 76, 80 Defects, image, 25 Defocus, 21, 27 Dehydration, 27 Demyelinated axons, 80 Demyelinating diseases, 140 Depth of field: see Depth of focus Depth of focus acoustic microscopy, 223 confocal microscopy, 194, 196 electron microscope, 17, 18, 19 Detection and image processing, 35 of mercury atom, 32 and radiation dosage, 63 of structural changes, 35 Detective quantum efficiency (DQE), 63 Detectors: see X-ray detectors Differential interference contrast, 94 Diffraction pattern, 13 absence of, in vitreous ice, 28 helical, 24 from planar crystals, 24 Diffraction in contact microscopy, 107 electron, 1, 13, 22 limits to imaging, 260 NMR,171 optical, 16 tomography, wave amplitude, 60 x-ray, 11-12, 26Off. in x-ray holography, 119 in x-ray microscopy, 70 Disorder arrays, 27 lattice, 26 type I, 26 type II, 26 DNA, 29, 129, 240 Dynamic systems, 27 Electrocardiogram, 155 Electromagnetic wave absorption coefficient, 60

3 INDEX 269 Electromagnetic wave (cont.) amplitude, 60 amplitude distribution, 60, 61 amplitude transmission, 60 refractive index, 60 Electron energy loss spectroscopy, 261 Electron microscope, high voltage, 2 Electron paramagnetic resonance (EPR), 157 Electron penetration depth, 2 Electron probe microanalysis, 260 Electron spin resonance (ESR), 133 Electron-impact x-ray sources, 41-43, continuous emission, line emission, 43 Endoplasmic reticulum, 261 Eukaryotic cells, 259 Eukaryotic flagella, 32 Ewald sphere, 128 Excluded cone, 25 Fast Fourier Transform (FFT), 124 Fibroblasts human, 99 mouse 3T3, 98 Filaments, actin, 31 Films conducting, 247 Langmuir-Blodgett, 247 semiinsulating, 250 Filtering, 9, 13 in tropomyosin paracrystals, 14 using the cosine function, 13 Fluorescent screens, 108 Fourier imaging methods, in NMR microscopy, 176 Fourier synthesis, 13 Fourier transform, 13 contrast transfer function, 21-23, 33 Fourier-Bessel, 25 random function, 14 two-dimensional, 137 synthesis, 13 Freezing, 10 rapid,28 suspensions, 29 Frequency, rotational, 23 Fresnel approximation, 124 Fresnel diffraction, 107 Fresnel Transform, 124 Fresnel zone plate, 71 applications, 72 Fresnel zone plate (cont.) as a circular diffraction grating, 71 coherent illumination of, 72 construction, 72 diffraction limited operation of, 74, 77 high resolution, 76, 83 Full-field imaging x-ray microscopy, 53, 54 Gap junctions, 30 Glow discharge, 28 Golgi stain, 88 Goniometer stage, 105 Granularity, 12 Helical objects, 23 Helices, 10, 13 Holography Gabor in-line, 120 twin image problem in, 122 X-ray, 119 Ice amorphous, 259 crystalline, 3, 28 vitreous, 28 Il\umination coherent, 67, 72 partially coherent, 67 Image interpretation, I Image quality, 1 Incoherent sources, temporal, 47 Inelastic Electron Thnnelling Spectroscopy, 238 Inertial fusion targets, 95 Information theory, 128 Interference pattern, from helical objects, 23 Isomorphous replacement, 263 KATP synthase, 30 King's College/Daresbury scanning x-ray microscope, 50 Langmuir-Blodgett films, 247 Lattice point, 16 Lattice object, 16 peaks, 17 reciprocal, 16 Layer lines, 24, 25 Least squares analysis, 21

4 270 INDEX Macromolecular organization, 256 Macromolecules, electron micrographs of, 9 Magnetic fields Dadok arrangements, 174, 178 in NMR microscopy, 174 Membrane proteins, 10 Membranes, 259 Metastases bone, 137 liver, 137 Microfocus x-ray source, Microradiography, 88 contact, 93ff shadow projection, 88, Microtomography, 114 Microtubules, 31 Miller indices, 16 Model, three dimensional, 25 Modulation transfer function, 74; see also Transfer function Monte Carlo calculation, 110 Multilayer grating, 52 Multiple sclerosis, 140 Mulvey lens, 54 Muscle, 11-\2,32,78, 173,259,262 heart, 158 mouse, 221, 228 rabbit, Myosin heads, 32 National Physical Laboratory, United Kingdom, 54 Neurons, 88, 109 NMR imaging angiography, 157 clinical evaluation projects in, 149 contrast factors, 146 flow velocity in, 146, 155 paramagnetic contrast agents in, 140 partial volume effect in, 152 phase imaging, 157 NMR imaging radiation from protons in, 134 sequential, 140 NMR microscopy of chicken embryo, 171 Fourier imaging in, 173 of plant systems, 171 resolution in, 168, 171, 177 of single cells, 166, 171 Nuclear magnetic resonance (NMR), 133 Nuclear magnetic resonance imaging, 4 Numerical aperture, 124 Organelles, 259 Patterns, moire, 9 Peak, detection, 26 Phase plate, 61 Phase-contrast, 10 use in contact microscopy, 94, 98 Plasma x-ray sources, electron beam-plasma interactions, 53, 54 gas-puff z-pinch, 53, 54 laser-generated plasmas, plasma focus, 53, 54 Point spread function, from Fresnel zone plate, 73, 74 Porosity, 30 Power spectrum, rotational, 23 Preparation, sample, 28 Projection Slice Theorem, Prokaryotic cells, 259 Protein bacterial S-Iayers, 29 catalase, 29 crystals, 30 ribosomes, 29 two-dimensional, 29 Proton-electron double resonance imaging (PEDRI), 161 signal enhancement in, 161 free radical imaging, 161, 162 Radiation damage, 34, 259; see also Damage, Radiation dose by X rays, 3, 28, 69 by electrons, 34, 259, 262 in photoresist material, 99 prevention by vitreous ice formation, 28 Radiation dose, 34, 63; see also Radiation damage protein in water, 64 in NMR microscopy, 145 nucleic acid in water, 65 and signal-to-noise ratio, 70 in x-ray holography, 127 Real time biopsy, 218 Reconstruction, three dimensional, 25 Refractive index, real and imaginary parts, 60 Relaxation times biological factors in, 149 field echo in, 155 of human tissue, 151 spin-lattice, 134, 146

5 INDEX 271 Resolution, I, 2 in acoustic microscopy, 206, 207, 216 depth, 2, 121, 131 and detection, 257 diffraction limited, 74, 211, 212 in dynamic processes, 262 in electron microscopes, 10 elemental, 260, 263 in holographic imaging, 124 limits using photochemical detectors, 92, 120 longitudinal, 127 in NMR microscopy, 145, 171 in scanning tunnelling microscopy, 233 in scanning x-ray microscopy, 71 transverse, 121, 124 of zone plates, 76 Rytov approximation, 129 Scanning electron microscopy, 98 Scanning laser acoustic microscope, 209 Scanning tunnelling microscopy, 5 barrier height, 242 electron transmission probability, 246 macromolecules in, 240 principles, 232 resonance tunnelling in, 250 surface layers in, 240 theory of electron tunnelling in, 235 tip preparation, 239 work function in, 236 Scanning x-ray microscopy, 53 Scattering potential, 130 Serial sections, 104 polyethylene glycol, use of, 109 Signal enhancement, in NMR imaging, 155 Signal-to-noise ratio (SIN), 13, 63 enhancement, 16 and filtering, in NMR imaging, 175 in NMR microscopy, 166 and radiation damage, 34, 63 Silica deposition, 94 Spatial frequencies, 33 Specimen cell, environmental, 2 Specimen preparation, 2 Spin warp, 137, 155 Staining, 10 in acoustic microscopy, 218 Golgi (silver), 88 heavy metal, 2, 12, 27, 109 Staining (cont.) negative, 21, 29, 30, in NMR imaging, 172 silver, 88, 109 trichrome, 218 Stereo image pairs, 104 Stereo imaging using confocal microscopy, 197 parallax in, 20 I Storage rings, see also Synchrotron radiation ALS, Berkeley, 52 beamlines, 48 beam lifetime, 44, 46 Bessy, Berlin, 50, 52 Bessy II, Berlin, 52 Canadian Synchrotron Radiation Facility (CSRF), Wisconsin, 88 emittance, 48 ESRF, Grenoble, 52 monochromators, NSLS, Brookhaven, 48 plane grating monochromator, 50, 51 pulsed beams, 47 spherical grating monochromator, 51 SRS, Daresbury, 46 toroidal grating and monochromator, 48 undulators, 47-48, 49 wigglers, 47 zone plate monochromator, 52 Structural levels bacterial, 12 collagen, 11 eukaryotic cells, 10 globular proteins, II interference patterns from, 17 muscle, II muscle filaments, 12 organelles, 10 prokaryotic cells, 10 virus particles, 12 Structural models, three-dimensional, 9, 13 Structural models, 25 Structures aperiodic, 14 periodic, 14 Surface imaging, using confocal microscopy, 195 Symmetry, rotational, 22 Synchrotron radiation, 44-53, 88-89; see also Storage rings angular distribution, 44

6 272 INDEX Synchrotron radiation (cont.) angular divergence, 44 characteristic frequency, 45, 46 characteristic wavelength, 45, 46, 47 radiated power, 44 spectral brightness, 49 spectral distribution, 45, 46, 47 universal function, 45 Three-dimensional imaging, 4 using confocal microscopy, 259 of crystalline objects, 13 Thon rings, 21 Tilt angle, 105 Tomography computer-assisted tomography (CAT), 134 computerized axial (CAT), 127, 128 diffraction, 127 isotope, 136 projection slice theorem, 128 Transfer function, of resist, 127; see also Modulation transfer function Transition radiation, 41 Transmission grating, 52 Tropomyosin, 32 Ultrasonic waves compared with electromagnetic waves, 206 longitudinal, 206 Undulators, 47-48, 49, 121 Ventriculography, 157 Virus particles, 259 detection of, 11 Virus adenovirus, 29 frozen suspensions of, 29 helical, 29 icosahedral, 29 influenza, 29 Semliki forest, 29 Virus (cont.) three dimensional reconstruction of, 29 tobacco mosaic, 23, 29 Water window, 2, 43 Wigglers, 47 Wolter x-ray microscope, 54 Work function, 234, 236, 237, 242, 247 X-ray detectors CCD cameras, 111 image intensifiers, III microchannel plates, 111 photochemical, 92 photoresist, 92, 10 1 PMMA,103 Xerographic plate, 92 X-ray diffraction: see Diffraction X-ray microanalysis, 95 X-ray microscopy, 2, 3-4, 53-54, 69ff. contact, 4 scanning, 76 of unstained materials, 77, 78, 80 X-ray optics, 71 diffraction, 71 diffraction grating, 51 filters, 103 monochromator, 76, 79, 103 X -ray sources laser plasma, 75 plasma, 75 rotating anode, 75 synchrotron, 75 undulator, 76 z-pinch, 99 X-ray sources, choice of, 57 requirements for x-ray microscopy, 73 Zone plates, see Fresnel zone plates Zymogen granules, 80