scholarly journals Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation

IUCrJ ◽  
2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Benjamin Himes ◽  
Nikolaus Grigorieff
Keyword(s):  
Electron Microscopy ◽  
Matched Filter ◽  
Mathematical Formulation ◽  
High Resolution Electron Microscopy ◽  
Mean Free Path ◽  
Specimen Thickness ◽  
Environment Modeling ◽  
Cellular Environment ◽  
Resolution Electron ◽  
Open Source Software Package

Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The `frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.

scholarly journals Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation

2021 ◽  
Author(s):  
Benjamin A. Himes ◽  
Nikolaus Grigorieff
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Imaging System ◽  
Matched Filter ◽  
Mathematical Formulation ◽  
Mean Free Path ◽  
Specimen Thickness ◽  
Environment Modeling ◽  
Cellular Environment ◽  
Transmission Electron

AbstractImage simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness, and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g., simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. To do so, we introduce the “Frozen-Plasmon” method which explicitly models spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. Taken in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, we also demonstrate how the matched-filter concept can be used to quantitatively compare model and experiment. The simulator is available as a standalone program, implemented in C++ with multi-threaded parallelism using the computational imaging system for Transmission Electron Microscopy (cisTEM.)

Recent Applications of High Resolution Electron Microscopy to Crystalline Arrays of Virus Particles

1978 ◽  
Vol 36 (3) ◽  
pp. 470-482 ◽  
Author(s):  
R.W. Horne
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
Analytical Techniques ◽  
Staining Technique ◽  
High Resolution Electron Microscopy ◽  
Optical Diffraction ◽  
Full Potential ◽  
Virus Particles ◽  
Resolution Electron ◽  
Wide Range

The technique of surrounding virus particles with a neutralised electron dense stain was described at the Fourth International Congress on Electron Microscopy, Berlin 1958 (see Home & Brenner, 1960, p. 625). For many years the negative staining technique in one form or another, has been applied to a wide range of biological materials. However, the full potential of the method has only recently been explored following the development and applications of optical diffraction and computer image analytical techniques to electron micrographs (cf. De Hosier & Klug, 1968; Markham 1968; Crowther et al., 1970; Home & Markham, 1973; Klug & Berger, 1974; Crowther & Klug, 1975). These image processing procedures have allowed a more precise and quantitative approach to be made concerning the interpretation, measurement and reconstruction of repeating features in certain biological systems.

One Million Direct Magnification Microscopy

1971 ◽  
Vol 29 ◽  
pp. 166-167
Author(s):  
J. A. Hugo ◽  
V. A. Phillips
Keyword(s):  
Electron Microscopy ◽  
High Resolution Electron Microscopy ◽  
Illumination Level ◽  
Level Of Detail ◽  
Photographic Emulsion ◽  
Low Contrast ◽  
Fluorescent Screen ◽  
Resolution Electron ◽  
Lattice Images ◽  
Electron Microscopes

A continuing problem in high resolution electron microscopy is that the level of detail visible to the microscopist while he is taking a picture is inferior to that obtainable by the microscope, readily readable on a photographic emulsion and visible in an enlargement made from the plate. Line resolutions, of 2Å or better are now achievable with top of the line 100kv microscopes. Taking the resolution of the human eye as 0.2mm, this indicates a need for a direct viewing magnification of at least one million. However, 0.2mm refers to optimum viewing conditions in daylight or the equivalent, and certainly does not apply to a (colored) image of low contrast and illumination level viewed on a fluorescent screen through a glass window by the dark-adapted eye. Experience indicates that an additional factor of 5 to 10 magnification is needed in order to view lattice images with line spacings of 2 to 4Å. Fortunately this is provided by the normal viewing telescope supplied with most electron microscopes.

Structural analysis of the surface-layer protein of spirillum serpens by high-resolution electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 738-739
Author(s):  
W. H. Wu ◽  
R. M. Glaeser
Keyword(s):  
Electron Microscopy ◽  
Surface Layer ◽  
Structural Analysis ◽  
High Resolution ◽  
Low Dose ◽  
High Resolution Electron Microscopy ◽  
Optical Diffraction ◽  
Surface Layer Protein ◽  
Morphological Unit ◽  
Resolution Electron

Spirillum serpens possesses a surface layer protein which exhibits a regular hexagonal packing of the morphological subunits. A morphological model of the structure of the protein has been proposed at a resolution of about 25 Å, in which the morphological unit might be described as having the appearance of a flared-out, hollow cylinder with six ÅspokesÅ at the flared end. In order to understand the detailed association of the macromolecules, it is necessary to do a high resolution structural analysis. Large, single layered arrays of the surface layer protein have been obtained for this purpose by means of extensive heating in high CaCl2, a procedure derived from that of Buckmire and Murray. Low dose, low temperature electron microscopy has been applied to the large arrays.As a first step, the samples were negatively stained with neutralized phosphotungstic acid, and the specimens were imaged at 40,000 magnification by use of a high resolution cold stage on a JE0L 100B. Low dose images were recorded with exposures of 7-9 electrons/Å2. The micrographs obtained (Fig. 1) were examined by use of optical diffraction (Fig. 2) to tell what areas were especially well ordered.

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

Quality films from carbon fiber evaporation for thorough coverage of TEM grids

1988 ◽  
Vol 46 ◽  
pp. 418-419
Author(s):  
N. Tempel ◽  
M. C. Ledbetter
Keyword(s):  
Electron Microscopy ◽  
High Resolution Electron Microscopy ◽  
Carbon Films ◽  
Low Noise ◽  
Vacuum Evaporation ◽  
High Yield ◽  
Good Adhesion ◽  
Noise Structure ◽  
Resolution Electron ◽  
Carbon Foils

Carbon films have been a support of choice for high resolution electron microscopy since the introduction of vacuum evaporation of carbon. The desirable qualities of carbon films and methods of producing them has been extensively reviewed. It is difficult to get a high yield of grids by many of these methods, especially if virtually all of the windows must be covered with a tightly bonded, quality film of predictable thickness. We report here a method for producing carbon foils designed to maximize these attributes: 1) coverage of virtually all grid windows, 2) freedom from holes, wrinkles or folds, 3) good adhesion between film and grid, 4) uniformity of film and low noise structure, 5) predictability of film thickness, and 6) reproducibility.Our method utilizes vacuum evaporation of carbon from a fiber onto celloidin film and grid bars, adhesion of the film complex to the grid by carbon-carbon contact, and removal of the celloidin by acetone dissolution. Materials must be of high purity, and cleanliness must be rigorously maintained.

High resolution electron microscopy of lanthanum phosphate crystals

1978 ◽  
Vol 36 (1) ◽  
pp. 274-275
Author(s):  
J. C. Wheatley ◽  
J. M. Cowley
Keyword(s):  
Electron Microscopy ◽  
Catalytic Activity ◽  
High Resolution ◽  
Petroleum Industry ◽  
High Resolution Electron Microscopy ◽  
Lanthanum Phosphate ◽  
Good Catalyst ◽  
Resolution Electron ◽  
Good Catalytic Activity ◽  
Physical And Chemical

Rare-earth phosphates are of particular interest because of their catalytic properties associated with the hydrolysis of many aromatic chlorides in the petroleum industry. Lanthanum phosphates (LaPO4) which have been doped with small amounts of copper have shown increased catalytic activity (1). However the physical and chemical characteristics of the samples leading to good catalytic activity are not known.Many catalysts are amorphous and thus do not easily lend themselves to methods of investigation which would include electron microscopy. However, the LaPO4, crystals are quite suitable samples for high resolution techniques.The samples used were obtained from William L. Kehl of Gulf Research and Development Company. The electron microscopy was carried out on a JEOL JEM-100B which had been modified for high resolution microscopy (2). Standard high resolution techniques were employed. Three different sample types were observed: 669A-1-5-7 (poor catalyst), H-L-2 (good catalyst) and 27-011 (good catalyst).

Possible applications of fraunhofer holography in high resolution electron microscopy

1978 ◽  
Vol 36 (1) ◽  
pp. 222-223 ◽  
Author(s):  
N. Bonnet ◽  
M. Troyon ◽  
P. Gallion
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Transfer Function ◽  
Radiation Damage ◽  
High Resolution Electron Microscopy ◽  
Far Field ◽  
Field Region ◽  
Crystalline Materials ◽  
Resolution Electron ◽  
The Ideal

Two main problems in high resolution electron microscopy are first, the existence of gaps in the transfer function, and then the difficulty to find complex amplitude of the diffracted wawe from registered intensity. The solution of this second problem is in most cases only intended by the realization of several micrographs in different conditions (defocusing distance, illuminating angle, complementary objective apertures…) which can lead to severe problems of contamination or radiation damage for certain specimens.Fraunhofer holography can in principle solve both problems stated above (1,2). The microscope objective is strongly defocused (far-field region) so that the two diffracted beams do not interfere. The ideal transfer function after reconstruction is then unity and the twin image do not overlap on the reconstructed one.We show some applications of the method and results of preliminary tests.Possible application to the study of cavitiesSmall voids (or gas-filled bubbles) created by irradiation in crystalline materials can be observed near the Scherzer focus, but it is then difficult to extract other informations than the approximated size.

The observation of solutions in Ni3Nb

1988 ◽  
Vol 46 ◽  
pp. 540-541
Author(s):  
Z.M. Wang ◽  
J.P. Zhang
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Phase Modulation ◽  
High Resolution Electron Microscopy ◽  
Antiphase Domain ◽  
Boundary Area ◽  
Matrix Type ◽  
Resolution Electron ◽  
Domain Boundaries ◽  
Kontorova Model

High resolution electron microscopy reveals that antiphase domain boundaries in β-Ni3Nb have a hexagonal unit cell with lattice parameters ah=aβ and ch=bβ, where aβ and bβ are of the orthogonal β matrix. (See Figure 1.) Some of these boundaries can creep “upstairs” leaving an incoherent area, as shown in region P. When the stepped boundaries meet each other, they do not lose their own character. Our consideration in this work is to estimate the influnce of the natural misfit δ{(ab-aβ)/aβ≠0}. Defining the displacement field at the boundary as a phase modulation Φ(x), following the Frenkel-Kontorova model [2], we consider the boundary area to be made up of a two unit chain, the upper portion of which can move and the lower portion of the β matrix type, assumed to be fixed. (See the schematic pattern in Figure 2(a)).

Atomic structure imaging of the Si/SiO2 interface with high-resolution electron microscopy

1986 ◽  
Vol 44 ◽  
pp. 390-391
Author(s):  
J.L. Batstone ◽  
J.M. Gibson ◽  
Alice.E. White ◽  
K.T. Short
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Atomic Structure ◽  
High Resolution Electron Microscopy ◽  
Medium Voltage ◽  
Voltage Electron ◽  
Resolution Electron ◽  
Structural Image ◽  
Electron Microscopes ◽  
Point To Point

High resolution electron microscopy (HREM) is a powerful tool for the determination of interface atomic structure. With the previous generation of HREM's of point-to-point resolution (rpp) >2.5Å, imaging of semiconductors in only <110> directions was possible. Useful imaging of other important zone axes became available with the advent of high voltage, high resolution microscopes with rpp <1.8Å, leading to a study of the NiSi2 interface. More recently, it was shown that images in <100>, <111> and <112> directions are easily obtainable from Si in the new medium voltage electron microscopes. We report here the examination of the important Si/Si02 interface with the use of a JEOL 4000EX HREM with rpp <1.8Å, in a <100> orientation. This represents a true structural image of this interface.

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