scholarly journals Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

2017 ◽  
Author(s):  
Nikhil Biyani ◽  
Sebastian Scherer ◽  
Ricardo D. Righetto ◽  
Julia Kowal ◽  
Mohamed Chami ◽  
...  
Keyword(s):  
Image Processing ◽  
High Resolution ◽  
3D Structure ◽  
Adenosine Monophosphate ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Oxide Semiconductor ◽  
Electron Crystallography ◽  
Contrast Transfer Function ◽  
2D Crystals

Abstract2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming. However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases. We have developed image-processing algorithms allowing to generate a high resolution 3D structure from cryo-electron crystallography images of badly ordered crystals. These include movie-mode unbending, refinement over sub-tiles of the images in order to locally refine the sample tilt geometry; implementation of different CTF correction schemes; and an iterative method to apply known constraints in the real and reciprocal space to approximate amplitudes and phases in the so-called missing cone regions. These algorithms applied to a dataset of the potassium channel MloK1 show significant resolution improvements to approximately 5Å.Abbreviations2Dtwo dimensions / dimensional3Dthree dimensions / dimensionalAmpamplitudecAMPcyclic adenosine monophosphateCCDcharge coupled devicesCMOScomplementary metal-oxide-semiconductorCNBDcyclic nucleotide-binding domaincryo-EMcryo-electron microscopyCTFcontrast transfer functionDEDdirect electron detectorDQEdetector quantum efficiencyEMelectron microscopeFOMfigure-of-meritPhaphaseSNRsignal-to-noise ratio

scholarly journals Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

Imaging and Characterization of Microporous Carbonates Using Confocal and Electron Microscopy of Epoxy Pore Casts

SPE Journal ◽  
2019 ◽  
Vol 24 (03) ◽  
pp. 1220-1233 ◽  
Author(s):  
A.. Hassan ◽  
V.. Chandra ◽  
M. P. Yutkin ◽  
T. W. Patzek ◽  
D. N. Espinoza
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Oil Recovery ◽  
Laser Scanning ◽  
Two Dimensions ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser ◽  
Improved Oil Recovery ◽  
Imaging Approach

Summary Microporous carbonates contain perhaps 50% of the oil left behind in current projects in the giant carbonate fields in the Middle East and elsewhere. Pore geometry, connectivity, and wettability of the micropore systems in these carbonates are of paramount importance in finding new improved-oil-recovery methods. In this study, we present a robust pore-imaging approach that uses confocal laser scanning microscopy (CLSM) to obtain high-resolution 3D images of etched epoxy pore casts of the highly heterogeneous carbonates. In our approach, we have increased the depth of investigation for carbonates 20-fold, from 10 µm reported by Fredrich (1999) and Shah et al. (2013) to 200 µm. In addition, high-resolution 2D images from scanning electron microscopy (SEM) have been correlated with the 3D models from CLSM to develop a multiscale imaging approach that covers a range of scales, from millimeters in three dimensions to micrometers in two dimensions. The developed approach was implemented to identify various pore types [e.g., intercrystalline microporosity (IM), intragranular microporosity (IGM), and interboundary sheet pores (SPs)] in limestone and dolomite samples.

scholarly journals Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

2018 ◽  
Vol 203 (2) ◽  
pp. 120-134 ◽  
Author(s):  
Nikhil Biyani ◽  
Sebastian Scherer ◽  
Ricardo D. Righetto ◽  
Julia Kowal ◽  
Mohamed Chami ◽  
...  
Keyword(s):  
Image Processing ◽  
High Resolution ◽  
Structure Determination ◽  
Image Processing Techniques ◽  
High Resolution Structure ◽  
Processing Techniques ◽  
2D Crystals ◽  
Resolution Structure

High-resolution work on zeolites

1990 ◽  
Vol 48 (4) ◽  
pp. 828-829
Author(s):  
V. Alfredsson
Keyword(s):  
Image Processing ◽  
Electron Beam ◽  
High Resolution ◽  
Transfer Function ◽  
Image Intensifier ◽  
False Information ◽  
Contrast Transfer Function ◽  
The Stability ◽  
Short Time ◽  
Dark Contrast

Zeolites are aluminosilicates with very open frameworks . The structures are characterized by the presence of tunnels or large cavities. The Si and Al sit in the centre of oxygen tetrahedra which are linked together.HREM work on zeolites has two big disadvantages. The greatest problem is the beam sensitivity of the crystals. After a short time in the electron beam they become amorphous. To improve the stability, the zeolites are made with as high Si/Al ratio as possible, the microscope is run with a very spread electron beam and at low magnification. A TV-camera with an image intensifier is used for focusing. Higher accelerating voltage has also proved to enhance the lifetime of the crystals in the beam. Secondly, an artefact caused by the shape of the contrast transfer function (CTF), gives false information to the images creating dark contrast in areas where there are no atoms. Two different solutions to this problem have been worked out. The first is to change the shape of the CTF by changing the focus and the second by removing the artifact effect caused by the CTF by means of image processing.

High-resolution (centimetre-scale) GPS/GIS-based 3D mapping and spatial analysis of in situ fossils in two horned-dinosaur bonebeds in the Dinosaur Park Formation (Upper Cretaceous) at Dinosaur Provincial Park, Alberta, Canada

2020 ◽  
pp. 1-22
Author(s):  
Caleb M. Brown ◽  
Sean Herridge-Berry ◽  
Kentaro Chiba ◽  
Allison Vitkus ◽  
David A. Eberth
Keyword(s):  
Information Systems ◽  
Geographic Information Systems ◽  
High Resolution ◽  
Spatial Data ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Geographic Information ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Digital Map

Mapping of fossil sites represents an important aspect of palaeontology, because the data collected are required for interpreting the taphonomic and depositional history of the site, as well as the palaeoecology and behavior of the organisms. Methods for mapping and documenting certain vertebrate fossil sites, such as trackways, have drastically changed in recent years, with the integrated technologies of photogrammetry, laser scanning, and geographic information systems becoming standard practice, and providing digital, three-dimensional, and georeferenced data for analyses. Contrasting this technological revolution, the methods for mapping vertebrate bone accumulations, such as bonebeds, have changed little in recent decades, and are largely limited to two dimensions, are non-georeferenced, and produce static maps. Here, we present a novel test case in the mapping of two ceratopsid (Dinosauria: Ornithischia) monodominant bonebeds (mass death assemblages) that are documented digitally, fully georeferenced, and in three dimensions, using a combination of high-resolution (at centimetre-scale) global positioning system, photogrammetry, and geographic information systems. Importantly, accompanying spatial data (i.e., size and orientation) are collected in the field in the traditional manner and directly compared with values calculated from the digital map. Parameters describing bone length and orientation exported from the digital map are largely reflective of measured field data, with both size and orientation distributions being statistically indistinguishable, but with disproportionate error for elements smaller than 10 cm. Protocols and methods tested here will hopefully add to the discussion about the future of fossil bonebed mapping, specifically incorporating digital, three-dimensional, and fully georeferenced data into a powerful analytical tool.

scholarly journals Preparation of single-layered enzyme 2D crystals for electron crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1065-C1065
Author(s):  
Matthew Johnson ◽  
Yusuf Uddin ◽  
Maureen Metcalfe ◽  
Ingeborg Schmidt-Krey
Keyword(s):  
Image Processing ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Electron Diffraction Data ◽  
Two Dimensional ◽  
Electron Crystallography ◽  
Negative Stain ◽  
Wide Range ◽  
Tubular Crystals ◽  
2D Crystals

Electron crystallography allows for a wide range of membrane proteins to be studied once conditions for two-dimensional (2D) crystallization have been identified. Two-dimensional crystallization is most frequently achieved via the dialysis approach, where the detergent-solubilized membrane protein is reconstituted into a lipid bilayer [1]. Vesicles, planar-tubular crystals, and sheets are the three most common 2D crystal morphologies. Vesicle and planar-tubular morphologies are observed for the largest percentage of 2D crystals of membrane proteins. Upon negative stain as well as electron cryo-microscopy (cryo-EM) grid preparation, each planar-tubular and vesicle 2D crystal will result in two ordered bilayers that can be analyzed separately by image processing. If any of these morphologies, however, contains a larger number of stacked crystals, data of tilted crystal stacks in particular can currently not be analyzed. Sheets constitute the most desirable morphology, allowing for the preparation of very flat samples for cryo-EM [2]. This is at present the only type of morphology that may be amenable to collection and analysis of electron diffraction data of highly ordered samples [3]. We could reproducibly induce single-layered sheet formation in the large majority of 2D crystals of two different enzyme samples and are working towards a general protocol applicable to other membrane protein 2D crystals.

Comparison of Conventional and Electron Spectroscopic Imaging in the Fixed Beam Electron Microscope of Ordered Protein Arrays

1985 ◽  
Vol 43 ◽  
pp. 74-75
Author(s):  
E. L. Buhle ◽  
U. Aebi
Keyword(s):  
Image Processing ◽  
Electron Microscope ◽  
High Resolution ◽  
Image Plane ◽  
Electron Spectroscopic Imaging ◽  
Protein Arrays ◽  
Beam Electron ◽  
Average Unit ◽  
Fixed Beam ◽  
Energy Components

CTEM brightfield images are formed by a combination of relatively high resolution elastically scattered electrons and unscattered and inelastically scattered electrons. In the case of electron spectroscopic images (ESI), the inelastically scattered electrons cause a loss of both contrast and spatial resolution in the image. In the case of ESI imaging on the Zeiss EM902, the transmited electrons are dispersed into their various energy components by passing them through a magnetic prism spectrometer; a slit is then placed in the image plane of the prism to select the electrons of a given energy loss for image formation. The purpose of this study was to compare CTEM with ESI images recorded on a Zeiss EM902 of ordered protein arrays. Digital image processing was employed to analyze the average unit cell morphologies of the two types of images.

Defocus ramp correction in spot-scan imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 130-131
Author(s):  
Kenneth H. Downing
Keyword(s):  
Computer Control ◽  
Three Dimensional ◽  
Sufficient Accuracy ◽  
Objective Lens ◽  
Electron Crystallography ◽  
Contrast Transfer Function ◽  
Tilt Axis ◽  
Specimen Height ◽  
The Difference ◽  
Envelope Functions

Three-dimensional structures of a number of samples have been determined by electron crystallography. The procedures used in this work include recording images of fairly large areas of a specimen at high tilt angles. There is then a large defocus ramp across the image, and parts of the image are far out of focus. In the regions where the defocus is large, the contrast transfer function (CTF) varies rapidly across the image, especially at high resolution. Not only is the CTF then difficult to determine with sufficient accuracy to correct properly, but the image contrast is reduced by envelope functions which tend toward a low value at high defocus.We have combined computer control of the electron microscope with spot-scan imaging in order to eliminate most of the defocus ramp and its effects in the images of tilted specimens. In recording the spot-scan image, the beam is scanned along rows that are parallel to the tilt axis, so that along each row of spots the focus is constant. Between scan rows, the objective lens current is changed to correct for the difference in specimen height from one scan to the next.

High-Resolution electron crystallography of the light-harvesting chlorophyll-a/b protein complex from chloroplast membranes

1990 ◽  
Vol 48 (1) ◽  
pp. 610-610
Author(s):  
Werner Kühlbrandt ◽  
Da Neng Wang ◽  
K.H. Downing
Keyword(s):  
High Resolution ◽  
Electron Diffraction ◽  
Chlorophyll A ◽  
Protein Complex ◽  
Structural Integrity ◽  
Light Harvesting ◽  
Lhc Ii ◽  
Diffraction Patterns ◽  
Difference Fourier ◽  
2D Crystals

The light-harvesting chlorophyll-a/b protein complex (LHC-II) is the most abundant membrane protein in the chloroplasts of green plants where it functions as a molecular antenna of solar energy for photosynthesis. We have grown two-dimensional (2d) crystals of the purified, detergent-solubilized LHC-II . The crystals which measured 5 to 10 μm in diameter were stabilized for electron microscopy by washing with a 0.5% solution of tannin. Electron diffraction patterns of untilted 2d crystals cooled to 130 K showed sharp spots to 3.1 Å resolution. Spot-scan images of 2d crystals were recorded at 160 K with the Berkeley microscope . Images of untilted crystals were processed, using the unbending procedure by Henderson et al . A projection map of the complex at 3.7Å resolution was generated from electron diffraction amplitudes and high-resolution phases obtained by image processing .A difference Fourier analysis with the same image phases and electron diffraction amplitudes recorded of frozen, hydrated specimens showed no significant differences in the 3.7Å projection map. Our tannin treatment therefore does not affect the structural integrity of the complex.

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