Counting mode, 70
Cross-correlation, 15, 77
Cross correlation volume, 239
Crowdsourcing, 311
Crowther criterion, 17, 75, 228, 268
Cryocartridge, 68
Cryo-correlative microscopy, 25
Cryo-electron tomography, 3
Cryo-preservation, 263
Cryo-preserved, 46, 61
Cryo-preserved specimens, 39
Cryo-sectioning, 67
Cryo-STEM, 46
Cryo-STEM images, 50
Cryo-STEM tomography (CSTET), 46
Cryo-TEM, 46
CryoTEM Tomography (CET), 47
CSTET on eukaryotic cells, 48
CSTET reconstructions, 49
CTF correction, 74, 78
Cumulative electron dose, 9, 73
D
Deep learning, 312
Defocus, 74, 221, 265
Denoising, 18, 80, 211, 223
Detective Quantum Efficiency, 69
Devitrification temperature, 8
DF detector, 42
Differential inelastic cross-sections, 37
Differential scattering cross-section, 36, 37, 39
Diffusion tensor, 291, 292
Diffusive flux, 291, 292
Direct electron detectors, 21
Discrete Algebraic Reconstruction Technique
(DART), 218, 269
Divergence, 45
Dose fractionation, 24, 47
Dose fractionation theorem, 10
Dose symmetric scheme, 76
Dose tolerance of vitrified specimens, 46
Double tilt, 226
3-D structure, 64
Dual-axis acquisition, 11
Dual-axis tilt series, 75
Dual-axis tomography, 47, 267
Dynamic focusing, 35, 45
E
Edged-based methods, 303
Edge Enhancing Diffusion (EED), 292, 293
Edge quality, 273
EDS analysis, 50
Eigenvector analysis, 304
Eigenvectors, 255
Elastic scattering, 35
Electron diffraction, 13
Electron Energy-Loss Spectrometer (EELS), 42
Electron exposure, 64
Electron-sample interactions, 35
Electron-specimen interaction, 36
Electron tomography, 1
Electrostatic Coulomb forces, 35
Elemental analysis, 42, 47
Elemental analysis of eukaryotic cells, 48
Elemental mapping using EDS or EELS, 44
Elongation, 228
Endoplasmic reticulum, 49
Energy filter, 70
Energy-minimization, 303
Envelope function, 263
Equally sloped tomography, 272
Error in defocus determination, 271
Expectation maximization, 243
Exposure filtering, 78
Extended acquisition scheme, 271
Extract peaks, 252
F
Falciparum, P., 296–298
False positives, 240
Fast Rotational Matching, 244
Feature-tracking, 14
FIB-SEM, 265
Fiducial locations, 77
Fiducial markers, 14, 51, 220
Field emission guns, 69
Filaments, 308
Filopodia, 294, 295
Filters, 79
First projection image, 76
Flagellar motor, 251
Flexible control of semi-convergence angle and
probe size, 51
Focal gradient, 223
Focused ion beam, 8, 67
Focus gradient, 24
Fourier ring correlations, 229
Fourier Shell Correlation (FSC), 80, 288
Fourier space, 4, 283, 285, 288, 298
Fourier transforms, 65, 285
Free software options, 71
Freeze-substitution, 7, 152, 156
Frequency space reconstruction, 209, 213
Frequency truncation, 286, 287
Frozen-hydrated, 4
Fully automated, 86
Fuzzy set theory, 304
320
Index
Cross-correlation, 15, 77
Cross correlation volume, 239
Crowdsourcing, 311
Crowther criterion, 17, 75, 228, 268
Cryocartridge, 68
Cryo-correlative microscopy, 25
Cryo-electron tomography, 3
Cryo-preservation, 263
Cryo-preserved, 46, 61
Cryo-preserved specimens, 39
Cryo-sectioning, 67
Cryo-STEM, 46
Cryo-STEM images, 50
Cryo-STEM tomography (CSTET), 46
Cryo-TEM, 46
CryoTEM Tomography (CET), 47
CSTET on eukaryotic cells, 48
CSTET reconstructions, 49
CTF correction, 74, 78
Cumulative electron dose, 9, 73
D
Deep learning, 312
Defocus, 74, 221, 265
Denoising, 18, 80, 211, 223
Detective Quantum Efficiency, 69
Devitrification temperature, 8
DF detector, 42
Differential inelastic cross-sections, 37
Differential scattering cross-section, 36, 37, 39
Diffusion tensor, 291, 292
Diffusive flux, 291, 292
Direct electron detectors, 21
Discrete Algebraic Reconstruction Technique
(DART), 218, 269
Divergence, 45
Dose fractionation, 24, 47
Dose fractionation theorem, 10
Dose symmetric scheme, 76
Dose tolerance of vitrified specimens, 46
Double tilt, 226
3-D structure, 64
Dual-axis acquisition, 11
Dual-axis tilt series, 75
Dual-axis tomography, 47, 267
Dynamic focusing, 35, 45
E
Edged-based methods, 303
Edge Enhancing Diffusion (EED), 292, 293
Edge quality, 273
EDS analysis, 50
Eigenvector analysis, 304
Eigenvectors, 255
Elastic scattering, 35
Electron diffraction, 13
Electron Energy-Loss Spectrometer (EELS), 42
Electron exposure, 64
Electron-sample interactions, 35
Electron-specimen interaction, 36
Electron tomography, 1
Electrostatic Coulomb forces, 35
Elemental analysis, 42, 47
Elemental analysis of eukaryotic cells, 48
Elemental mapping using EDS or EELS, 44
Elongation, 228
Endoplasmic reticulum, 49
Energy filter, 70
Energy-minimization, 303
Envelope function, 263
Equally sloped tomography, 272
Error in defocus determination, 271
Expectation maximization, 243
Exposure filtering, 78
Extended acquisition scheme, 271
Extract peaks, 252
F
Falciparum, P., 296–298
False positives, 240
Fast Rotational Matching, 244
Feature-tracking, 14
FIB-SEM, 265
Fiducial locations, 77
Fiducial markers, 14, 51, 220
Field emission guns, 69
Filaments, 308
Filopodia, 294, 295
Filters, 79
First projection image, 76
Flagellar motor, 251
Flexible control of semi-convergence angle and
probe size, 51
Focal gradient, 223
Focused ion beam, 8, 67
Focus gradient, 24
Fourier ring correlations, 229
Fourier Shell Correlation (FSC), 80, 288
Fourier space, 4, 283, 285, 288, 298
Fourier transforms, 65, 285
Free software options, 71
Freeze-substitution, 7, 152, 156
Frequency space reconstruction, 209, 213
Frequency truncation, 286, 287
Frozen-hydrated, 4
Fully automated, 86
Fuzzy set theory, 304
320
Index