Modulation Transfer Function, 69
Molecular function in situ, 85
More data, 85
MosaicPlanner, 159
Movie mode, 275
MRA, 277
Multiple scattering events, 7
Multiplex-immunolabeling, 51
Multi-reference procedures, 246
Multi-ring annular detector, 53
Myelinated axons, 162
N
Nanofabrication, 24
Nanometer-resolution, 41
Native context, 273
Near-atomic resolution, 278
Near-native, 62
Noise, 302
Noise-compensatedleave-one-out, 229
Noise ratio (SNR), 262
Non-linear Anistropic Diffusion (NAD), 226
Non-linear diffusion, 291, 292
Non-local means filter, 225
Normalizing images, 220
Nuclear pore complex, 250
Number of iterations, 218
Nyquist frequency, 17, 65, 74
O
Of intact vitrified cells, 53
Optimal specimen, 87
Optimize vitrification, 87
Optimizing the signal-to-noise ratio, 72
Overfitting, 244, 275
P
Pairwise matrix, 255
Parameters, 72
Particle coordinates, 253
Particle list, 254
Particle localization, 238
Peak selection, 241
Phage attack on an E coli cell, 49
Phase contrast, 19, 70
Phase plates, 21, 70, 266
Photobleaching, 25
Pixel size, 74
Plastic sections, 39
Pleomorphic specimens, 6
Point spread function, 268, 302
Polyribosomes, 249
Post-process, 88
Poststaining, 178
Power spectrum, 222
Practical thickness limit, 38
Precision, 275
Pre-reconstructionNon-Linear Anisotropic
Diffusion (Pre-NAD), 296, 297
Pre-reconstructionNon-Linear Isotropic
Diffusion (Pre-NID), 297, 298
Preset magnifications, 71
Probe size, 45
Projection difference, 216
Projection onto convex sets, 227
Protein translocon, 245, 247
R
Radiation damage, 38
Radiation sensitivity, 11
Radiation tolerance of the specimen, 73
Radon transform, 16
Ratio of MFP for elastic to inelastic scattering,
38
Rayleigh, 261
Real space, 4, 288, 289, 291, 298
Real-space constraints, 311
Reconstruct, 88
Reconstruction, 15
Reduced representation templates, 308
Region-based approaches, 304
Relation between the inelastic and elastic
scattering cross-section, 38
Relative orientations, The, 77
Reliable production of grids, 86
Resolution, 17, 79, 227, 238, 261
Resolution anisotropy, 273
Resolution in STEM, 41
Resolution of a STEM image, 40
Retrovirus capsids, 251
Ribosomes, 240, 245, 247
Role of the microscope optics in STEM, 34
S
Sample geometry, 23
Scale space, 290
Scan generators, 53
Scanning electron microscope, 155
Scanning Transmission Electron Microscope
(STEM), 2, 33
Secretion systems, 251
Segmentation, 18, 79, 301, 303
Selection of peaks, 252
Semi-convergence angles, 40
Serial block face, 265
Serial block-face imaging, 3
Serial block-face scanning electron
microscopy, 12
322
Index
Molecular function in situ, 85
More data, 85
MosaicPlanner, 159
Movie mode, 275
MRA, 277
Multiple scattering events, 7
Multiplex-immunolabeling, 51
Multi-reference procedures, 246
Multi-ring annular detector, 53
Myelinated axons, 162
N
Nanofabrication, 24
Nanometer-resolution, 41
Native context, 273
Near-atomic resolution, 278
Near-native, 62
Noise, 302
Noise-compensatedleave-one-out, 229
Noise ratio (SNR), 262
Non-linear Anistropic Diffusion (NAD), 226
Non-linear diffusion, 291, 292
Non-local means filter, 225
Normalizing images, 220
Nuclear pore complex, 250
Number of iterations, 218
Nyquist frequency, 17, 65, 74
O
Of intact vitrified cells, 53
Optimal specimen, 87
Optimize vitrification, 87
Optimizing the signal-to-noise ratio, 72
Overfitting, 244, 275
P
Pairwise matrix, 255
Parameters, 72
Particle coordinates, 253
Particle list, 254
Particle localization, 238
Peak selection, 241
Phage attack on an E coli cell, 49
Phase contrast, 19, 70
Phase plates, 21, 70, 266
Photobleaching, 25
Pixel size, 74
Plastic sections, 39
Pleomorphic specimens, 6
Point spread function, 268, 302
Polyribosomes, 249
Post-process, 88
Poststaining, 178
Power spectrum, 222
Practical thickness limit, 38
Precision, 275
Pre-reconstructionNon-Linear Anisotropic
Diffusion (Pre-NAD), 296, 297
Pre-reconstructionNon-Linear Isotropic
Diffusion (Pre-NID), 297, 298
Preset magnifications, 71
Probe size, 45
Projection difference, 216
Projection onto convex sets, 227
Protein translocon, 245, 247
R
Radiation damage, 38
Radiation sensitivity, 11
Radiation tolerance of the specimen, 73
Radon transform, 16
Ratio of MFP for elastic to inelastic scattering,
38
Rayleigh, 261
Real space, 4, 288, 289, 291, 298
Real-space constraints, 311
Reconstruct, 88
Reconstruction, 15
Reduced representation templates, 308
Region-based approaches, 304
Relation between the inelastic and elastic
scattering cross-section, 38
Relative orientations, The, 77
Reliable production of grids, 86
Resolution, 17, 79, 227, 238, 261
Resolution anisotropy, 273
Resolution in STEM, 41
Resolution of a STEM image, 40
Retrovirus capsids, 251
Ribosomes, 240, 245, 247
Role of the microscope optics in STEM, 34
S
Sample geometry, 23
Scale space, 290
Scan generators, 53
Scanning electron microscope, 155
Scanning Transmission Electron Microscope
(STEM), 2, 33
Secretion systems, 251
Segmentation, 18, 79, 301, 303
Selection of peaks, 252
Semi-convergence angles, 40
Serial block face, 265
Serial block-face imaging, 3
Serial block-face scanning electron
microscopy, 12
322
Index