scholarly journals FastTomo: A SerialEM Script for Collecting Electron Tomography Data

2021 ◽  
Author(s):  
Albert Xu ◽  
Chen Xu
Keyword(s):  
Target Tracking ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Field Of View ◽  
Proportional Control ◽  
Transmission Electron ◽  
Tilt Series ◽  
Electron Microscopes ◽  
Tomography Data ◽  
Separate Calibration

AbstractFastTomo is a SerialEM script for collecting tilted specimen images in transmission electron microscopes to be further used in tomographic reconstruction. It achieves a speedup over conventional tracking methods by minimizing the usage of off-target tracking shots, and instead applies proportional control to the specimen images. Movement in the Z coordinate is estimated prior to each tilt series in a separate calibration routine. Overall, this method is fast and reliable when the field of view is at least 1 um, and can tolerate minor errors in setting eucentric height. The implemented tilt series schemes include the unidirectional, bidirectional, and dose-symmetric schemes.

Computer-Controlled Transmission Electron Microscopy: Automated Tomography

2001 ◽  
Vol 7 (S2) ◽  
pp. 968-969
Author(s):  
Theo van der Krift ◽  
Ulrike Ziese ◽  
Willie Geerts ◽  
Bram Koster
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
User Interfaces ◽  
Electron Tomography ◽  
Imaging Method ◽  
Optical Elements ◽  
Computer Screen ◽  
Transmission Electron ◽  
Computer Controlled ◽  
Electron Microscopes

The integration of computers and transmission electron microscopes (TEM) in combination with the availability of computer networks evolves in various fields of computer-controlled electron microscopy. Three layers can be discriminated: control of electron-optical elements in the column, automation of specific microscope operation procedures and display of user interfaces. The first layer of development concerns the computer-control of the optical elements of the transmission electron microscope (TEM). Most of the TEM manufacturers have transformed their optical instruments into computer-controlled image capturing devices. Nowadays, the required controls for the currents through lenses and coils of the optical column can be accessed by computer software. The second layer of development is aimed toward further automation of instrument operation. For specific microscope applications, dedicated automated microscope-control procedures are carried out. in this paper, we will discuss our ongoing efforts on this second level towards fully automated electron tomography. The third layer of development concerns virtual- or telemicroscopy. Most telemicroscopy applications duplicate the computer-screen (with accessory controls) at the microscope-site to a computer-screen at another site. This approach allows sharing of equipment, monitoring of instruments by supervisors, as well as collaboration between experts at remote locations.Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. with electron tomography a series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments.

scholarly journals Atomically resolved tomographic reconstruction of nanoparticles from Single Projection: influence of amorphous carbon support

2020 ◽  
Author(s):  
Pritam Banerjee ◽  
Chiranjit Roy ◽  
Subhra Kanti De ◽  
Antonio J. Santos ◽  
Francisco M. Morales ◽  
...  
Keyword(s):  
Amorphous Carbon ◽  
Tomographic Reconstruction ◽  
Carbon Film ◽  
Carbon Support ◽  
Atomic Scale ◽  
Structure Property ◽  
Transmission Electron ◽  
Wide Range ◽  
Correlation Information ◽  
Electron Microscopes

Abstract Nanoparticles have a wide range of applications due to their unique geometry and arrangement of atoms. For a precise structure-property correlation, information regarding atomically resolved 3D structures of nanoparticles is utmost beneficial. Though modern aberration-corrected transmission electron microscopes can resolve atoms with sub-angstrom resolution, an atomic-scale 3D reconstruction of nanoparticle is a challenge using tilt series tomography due to high radiation damage. Instead, inline 3D holography based tomographic reconstructions from single projection registered at low electron doses are more suitable for defining atoms dispositions at nanostructures. Nanoparticles are generally supported on amorphous carbon film for TEM experiments. However, neglecting the influence of carbon film on the tomographic reconstruction of the nanoparticle may lead to ambiguity. In order to address this issue, the effect of amorphous carbon support was quantitatively studied using simulations and experiments.

scholarly journals Transmission Electron Microscopy Tilt-Series Data from In-Situ Chondrocyte Primary Cilia

Data ◽  
2021 ◽  
Vol 6 (11) ◽  
pp. 118
Author(s):  
Michael J. Jennings ◽  
Timothy C. A. Molteno ◽  
Robert J. Walker ◽  
Jennifer J. Bedford ◽  
John P. Leader ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Primary Cilia ◽  
Tomographic Reconstruction ◽  
Physical Structure ◽  
Eukaryotic Cells ◽  
Series Data ◽  
Transmission Electron ◽  
Tilt Series

The primary cilium has recently become the focus of intensive investigations into understanding the physical structure and processes of eukaryotic cells. This paper describes two tilt-series image datasets, acquired by transmission electron microscopy, of in situ chick-embryo sternal-cartilage primary cilia. These data have been released under an open-access licence, and are well suited to tomographic reconstruction and modelling of the cilium.

scholarly journals CURT1A and CURT1C mediate distinct stages of plastid conversion in Arabidopsis

2021 ◽  
Author(s):  
Zizhen Liang ◽  
Wai Tsun Yeung ◽  
Keith Ka Ki Mai ◽  
Juncai Ma ◽  
Zhongyuan Liu ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Chloroplast Biogenesis ◽  
Chemical Fixation ◽  
Cubic Crystal ◽  
Zinc Blende ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Type Lattice ◽  
Curved Membrane

AbstractThe crystalline structure of prolamellar bodies (PLBs) and light-induced etioplasts-to-chloroplasts transformation have been investigated with electron microscopy methods. However, these studies suffer from chemical fixation artifacts and limited volumes of tomographic reconstruction. We have examined Arabidopsis thaliana cotyledon samples preserved by high-pressure freezing with scanning transmission electron tomography to visualize larger volumes in etioplasts and their conversion into chloroplasts. PLB tubules were arranged in a zinc blende-type lattice like carbon atoms in diamonds. Within 2 hours after illumination, the lattice collapsed from the PLB exterior and the disorganized tubules merged to form fenestrated sheets that eventually matured into lamellar thylakoids. These planar thylakoids emerging from PLBs overlapped or folded into grana stacks in PLBs’ vicinity. Since the nascent lamellae had curved membrane at their tips, we examined the localization of CURT1 proteins. CURT1A transcript was most abundant in de-etiolating cotyledon samples, and CURT1A concentrated at the peripheral PLB. In curt1a mutant etioplasts, thylakoid sheets were swollen and failed to develop stacks. In curt1c mutant, however, PLBs had cracks in their lattices, indicating that CURT1C contributes to cubic crystal growth under darkness. Our data provide evidence that CURT1A and CURT1C play distinct roles in the etioplast and chloroplast biogenesis.

Two- or three-way observations of the identical cell elements within the same sections by LM, TEM and/or SEM

1978 ◽  
Vol 36 (2) ◽  
pp. 82-83 ◽  
Author(s):  
Nakazo Watari ◽  
Yasuaki Hotta ◽  
Yoshio Mabuchi
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Fine Structure ◽  
Light Microscopy ◽  
Thin Sections ◽  
Transmission Electron ◽  
Identical Cell ◽  
Electron Microscopes ◽  
Scanning Electron

It is very useful if we can observe the identical cell elements within the same sections by light microscopy (LM), transmission electron microscopy (TEM) and/or scanning electron microscopy (SEM) sequentially, because, the cell fine structure can not be indicated by LM, while the color is; on the other hand, the cell fine structure can be very easily observed by EM, although its color properties may not. However, there is one problem in that LM requires thick sections of over 1 μm, while EM needs very thin sections of under 100 nm. Recently, we have developed a new method to observe the same cell elements within the same plastic sections using both light and transmission (conventional or high-voltage) electron microscopes.In this paper, we have developed two new observation methods for the identical cell elements within the same sections, both plastic-embedded and paraffin-embedded, using light microscopy, transmission electron microscopy and/or scanning electron microscopy (Fig. 1).

Removing Substrate Background in TEM Microanalysis

1974 ◽  
Vol 32 ◽  
pp. 568-569
Author(s):  
John C. Russ ◽  
Nicholas C. Barbi
Keyword(s):  
Electrical Conductivity ◽  
Rapid Growth ◽  
Organic Film ◽  
Absolute Concentration ◽  
Background Signal ◽  
X Ray ◽  
Elemental Concentrations ◽  
Transmission Electron ◽  
Electron Microscopes ◽  
The Continuum

The rapid growth of interest in attaching energy-dispersive x-ray analysis systems to transmission electron microscopes has centered largely on microanalysis of biological specimens. These are frequently either embedded in plastic or supported by an organic film, which is of great importance as regards stability under the beam since it provides thermal and electrical conductivity from the specimen to the grid.Unfortunately, the supporting medium also produces continuum x-radiation or Bremsstrahlung, which is added to the x-ray spectrum from the sample. It is not difficult to separate the characteristic peaks from the elements in the specimen from the total continuum background, but sometimes it is also necessary to separate the continuum due to the sample from that due to the support. For instance, it is possible to compute relative elemental concentrations in the sample, without standards, based on the relative net characteristic elemental intensities without regard to background; but to calculate absolute concentration, it is necessary to use the background signal itself as a measure of the total excited specimen mass.

The Theoretical Contrast in Scanning and Conventional High Resolution Microscopes

1969 ◽  
Vol 27 ◽  
pp. 170-171
Author(s):  
E. Zeitler ◽  
M. G. R. Thomson
Keyword(s):  
Small Volume ◽  
Volume Element ◽  
Optical Processing ◽  
Image Construction ◽  
Object Interaction ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Optical Treatment ◽  
Electron Microscopes ◽  
Intensity Contrast

In the formation of an image each small volume element of the object is correlated to an areal element in the image. The structure or detail of the object is represented by changes in intensity from element to element, and this variation of intensity (contrast) is determined by the interaction of the electrons with the specimen, and by the optical processing of the information-carrying electrons. Both conventional and scanning transmission electron microscopes form images which may be considered in this way, but the mechanism of image construction is very different in the two cases. Although the electron-object interaction is the same, the optical treatment differs.

7-beam lattice images of (110) oriented Ge

1978 ◽  
Vol 36 (1) ◽  
pp. 290-291
Author(s):  
J.R. Parsons ◽  
C.W. Hoelke
Keyword(s):  
Image Features ◽  
Objective Lens ◽  
Lattice Plane ◽  
Lattice Image ◽  
Crystalline Defects ◽  
Transmission Electron ◽  
Lattice Images ◽  
Electron Microscopes ◽  
Structural Aspects ◽  
Beam Lattice

The direct imaging of a crystal lattice has intrigued electron microscopists for many years. What is of interest, of course, is the way in which defects perturb their atomic regularity. There are problems, however, when one wishes to relate aperiodic image features to structural aspects of crystalline defects. If the defect is inclined to the foil plane and if, as is the case with present 100 kV transmission electron microscopes, the objective lens is not perfect, then terminating fringes and fringe bending seen in the image cannot be related in a simple way to lattice plane geometry in the specimen (1).The purpose of the present work was to devise an experimental test which could be used to confirm, or not, the existence of a one-to-one correspondence between lattice image and specimen structure over the desired range of specimen spacings. Through a study of computed images the following test emerged.

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