Buzz Words (Transmission Electron Microscopy)
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1 Buzz Words (Transmission Electron Microscopy) Airy disk amplitude contrast angular aperture anticontaminator aperture contrast astigmatism barrel distortion BFEM (Bright Field EM) blind imaging Bragg reflection C c (chromatic aberration coefficient) camera constant camera length CCD (charge coupled device) chromatic aberration circle of least confusion classical optics close to focus coherent illumination column alignment condenser aperture condenser lens constructive interference contamination converging (positive) lens cryo shield cryo tomography C s (spherical aberration coefficient) C s corrector CTF (Contrast Transfer Function) depth of field depth of focus destructive interference DFEM (Dark Field EM) diffraction lens diffraction limited resolution diverging (negative) lens DQE (detective quantum efficiency) ED (electron diffraction) elastic scattering electromagnetic lens electron diffusion electron dose EM (electron microscopy/micrograph) electron wavelength electrostatic lens empty magnification emulsion speed energy filter equipotentials eucentric stage exact focus FEG (Field Emission Gun) field of view filament saturation flux density focal pair interference contrast intermediate lens IVEM (Intermediate Voltage EM) latent image lattice resolution test lens formula (thin lens equation) lens hysteresis lens normalization light wavelength low dose magnetic flux minimal dose monochromatic radiation MTF (modulation transfer function) multiple scattering N.A. (numerical aperture) near focus near point negative (diverging) lens nominal magnification objective aperture objective lens Omega filter optical density paraxial ray phase contrast photographic graininess physical optics pincushion distortion point separation test PSF (point spread function) positive (converging) lens pre-irradiation projection image projector lens radiation damage ray diagram Rayleigh limit/criteria of resolution real image real lens remanence replica grating resolution resolution limit resolving power SAD (selected area diffraction) scattering contrast search mode self-biased electron gun semi-angular aperture silver grain single hit process Snell s Law of Refraction spatial coherence spherical aberration spiral distortion spot scan imaging
2 focal series stigmator focus wobbler TEM (Transmission EM) Fraunhofer diffraction pattern temporal coherence Fresnel fringe/diffraction thermal drift gamma thermionic electron source geometrical optics thermionic emission gun anode thin lens equation (lens formula) gun cathode tomography gun crossover true focus high vacuum unbiased electron gun HVEM (High Voltage EM) virtual image ideal lens Wehnelt shield incoherent illumination work function inelastic scattering µ metal
3 Buzz Words (Biological Specimen Preparation) anionic stain cationic stain collodion support film critical dose cryo-negative staining cryo protectant cryo-sectioning cryo transfer cryogen cubic ice devitrification temperature diamond knife EM forceps EM grid ethane slush finder grid Formvar support film freeze fracture freeze substitution frozen-hydrated glass knife glow discharge glutaraldehyde hexagonal ice holey carbon film ice contamination ice thickness liquid ethane liquid helium liquid nitrogen metal shadow negative stain osmium tetroxide Parlodion support film Quantifoil grid RFFSE (Rapid-Freeze, Freeze- Substitution & Embed) sample homogeneity spray droplet technique thin section ultramicrotome vitrification Vitrobot
4 Buzz Words (Image Processing and 3D Reconstruction) absolute hand angular reconstitution anisotropic/isotropic resolution anti-aliasing Argand diagram asu (asymmetric unit) atomic docking atomic fitting atomic modeling auto correlation blobology Babinet s Principle Bragg's law Bravais lattices common lines conical tilt reconstruction contour level contour threshold convolution theorem cross common lines cross correlation cryo-tomogram crystal lattice crystal structure crystallization in silico CTF (contrast transfer function) CTF correction CTF nodes cubic symmetry/point group cyclic symmetry/point group C α backbone denoising difference density difference map dihedral symmetry/point group divide and conquer approach EMAN program package Euler angles FFT (Fast Fourier Transform) Fourier average Fourier filtering Fourier transform Fraunhofer pattern Friedel s Law FSC (Fourier Shell Correlation) glide plane symmetry helical pitch helical selection rule Hermann-Mauguin (H-M) notation hi-pass Fourier filter histogram equalization image averaging image padding image segmentation IMAGIC program package improper rotation inversion (i) symmetry lattice LEGINON program package local averaging lo-pass Fourier filter Miller indices mirror (m) symmetry missing cone missing density missing information missing pyramid missing wedge model-based refinement molecular envelope molecular replacement motif MSA (Multivariate Statistical Analysis) MTF (modulation transfer function) multiplication (sampling) non-crystallographic symmetry normal mode analysis Nyquist frequency Nyquist limit optical diffraction optical filtering orientation search/refinement origin search/refinement PFT (polar Fourier transform) PSF (point spread function) phase difference phase origin phasing model pixel pixel resolution pixel size projection theorem quasi-equivalent random conical tilt reference free alignment reflection (m) symmetry ribbon diagram rotational filtering rotational (n) symmetry sampling (multiplication) S/N (signal-to-noise) Schoenflies (S) notation screw-axis symmetry Shannon sampling theorem SPIDER program package symmetry element symmetry mismatch symmetry operator/operation T symmetry (triangulation symmetry) voxel Wiener filter
5
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