scholarly journals Entropy-regularized deconvolution of cellular cryotransmission electron tomograms

2021 ◽  
Vol 118 (50) ◽  
pp. e2108738118
Author(s):  
Matthew Croxford ◽  
Michael Elbaum ◽  
Muthuvel Arigovindan ◽  
Zvi Kam ◽  
David Agard ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Biological Macromolecules ◽  
Back Projection ◽  
Signal To Noise ◽  
Transmission Electron ◽  
Cryo Electron Tomography

Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).

scholarly journals Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms

2021 ◽  
Author(s):  
Matthew Croxford ◽  
Michael Elbaum ◽  
Muthuvel Arigovindan ◽  
Zvi Kam ◽  
David A Agard ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Biological Macromolecules ◽  
Data Sets ◽  
Back Projection ◽  
Signal To Noise ◽  
Transmission Electron ◽  
Cryo Electron Tomography

Cryo-electron tomography (cryo-ET) allows for the high resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy regularized deconvolution to cryo-ET data generated from transmission electron microscopy and reconstructed using weighted back projection. We applied DC to several in situ cryo-ET data sets, and assess the results by Fourier analysis and subtomogram analysis.

scholarly journals Contrast Transfer Function-Based Exit-Wave Reconstruction and Denoising of Atomic-Resolution Transmission Electron Microscopy Images of Graphene and Cu Single Atom Substitutions by Deep Learning Framework

Nanomaterials ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1977
Author(s):  
Jongyeong Lee ◽  
Yeongdong Lee ◽  
Jaemin Kim ◽  
Zonghoon Lee
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Transfer Function ◽  
Signal To Noise Ratio ◽  
Atomic Resolution ◽  
Single Atom ◽  
Monolayer Graphene ◽  
Signal To Noise ◽  
Contrast Transfer Function ◽  
Transmission Electron

The exit wave is the state of a uniform plane incident electron wave exiting immediately after passing through a specimen and before the atomic-resolution transmission electron microscopy (ARTEM) image is modified by the aberration of the optical system and the incoherence effect of the electron. Although exit-wave reconstruction has been developed to prevent the misinterpretation of ARTEM images, there have been limitations in the use of conventional exit-wave reconstruction in ARTEM studies of the structure and dynamics of two-dimensional materials. In this study, we propose a framework that consists of the convolutional dual-decoder autoencoder to reconstruct the exit wave and denoise ARTEM images. We calculated the contrast transfer function (CTF) for real ARTEM and assigned the output of each decoder to the CTF as the amplitude and phase of the exit wave. We present exit-wave reconstruction experiments with ARTEM images of monolayer graphene and compare the findings with those of a simulated exit wave. Cu single atom substitution in monolayer graphene was, for the first time, directly identified through exit-wave reconstruction experiments. Our exit-wave reconstruction experiments show that the performance of the denoising task is improved when compared to the Wiener filter in terms of the signal-to-noise ratio, peak signal-to-noise ratio, and structural similarity index map metrics.

New Frontiers in Cryo-electron Tomography with Zernike Phase Contrast Imaging for Transmission Electron Microscopy

2008 ◽  
Vol 14 (S2) ◽  
pp. 1072-1073
Author(s):  
B Armbruster ◽  
J Brink ◽  
H Furukawa ◽  
TC Isabell ◽  
M Kawasaki ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
New Mexico ◽  
Phase Contrast ◽  
Electron Tomography ◽  
Phase Contrast Imaging ◽  
Contrast Imaging ◽  
Transmission Electron ◽  
Cryo Electron Tomography

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008

Three Dimensional Energy Filtered Transmission Electron Microscopy (3D-EFTEM)

2001 ◽  
Vol 7 (S2) ◽  
pp. 1162-1163
Author(s):  
M Weyland ◽  
P.A. Midgley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
Physical Sciences ◽  
Flexible Tool ◽  
Spatially Resolved ◽  
Transmission Electron

Energy filtered transmission electron microscopy (EFTEM) has been developed in recent years to be a highly flexible tool for spatially resolved microanalysis. The basic technique has been extended to allow fully quantitative mapping of single elements, or a large range of elements using an image-spectroscopy approach . All these techniques are still limited by the nature of the TEM as a structure projector; any elemental map is only a 2D projection of what is in reality a 3D structure. A fully 3D approach to EFTEM analysis would offer additional insights into many materials problems and make possible meaningful analysis of certain systems for the first time. Three-dimensional electron microscopy (electron tomography) offers one path for the reconstruction of 3D structures from 2D projections. Although this has been well developed for solving the structure of biological macromolecules and viruses its use in the physical sciences is quite new.

scholarly journals In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

2020 ◽  
Author(s):  
Sylvain Trépout
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Trypanosoma Brucei ◽  
Cell Body ◽  
Electron Tomography ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Attachment Zone

SummaryThe flagellum of Trypanosoma brucei is a 20 µm-long organelle responsible for locomotion and cell morphogenesis. The flagellum attachment zone (FAZ) is a multi-protein complex whose function is to attach the flagellum to the cell body but also to guide cytokinesis. Cryo-transmission electron microscopy is a tool of choice to access the structure of the FAZ in a close-to-native state. However, because of the large dimension of the cell body, the whole FAZ cannot be structurally studied in situ at high resolution in 3D using classical transmission electron microscopy approaches. In the present work, cryo-scanning transmission electron tomography, a new method capable of investigating cryo-fixed thick biological samples, has been used to study whole T. brucei cells at the bloodstream stage. The method has been used to visualise and characterise the structure and organisation of the FAZ filament. It is composed of an array of cytoplasmic stick-like structures. These sticks are heterogeneously distributed between the posterior part and the anterior tip of the cell. This cryo-STET investigation provides new insights in the structure the FAZ filament. In combination with protein structure predictions, this work proposes a new model for the elongation of the FAZ.HighlightsFlagellar and cellular membranes are in close contact next to the FAZ filamentSticks are heterogeneously distributed along the FAZ filament lengthThin appendages are present between the FAZ filament sticks to neighbouring microtubulesFAZ elongation could originate from the force exerted by dynein motors on subpellicular microtubules

Epitaxy and texture analysis of Bi-Sr-Ca-Cu-O thin films on (100) MgO using Transmission Electron Microscopy

1990 ◽  
Vol 48 (4) ◽  
pp. 68-69
Author(s):  
J. T. Sizemore ◽  
D. G. Schlom ◽  
Z. J. Chen ◽  
J. N. Eckstein ◽  
I. Bozovic ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Thin Films ◽  
Transmission Electron Microscopy ◽  
Critical Currents ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Cell Axis ◽  
Transmission Electron ◽  
Synthesis Procedure

Investigators observe large critical currents for superconducting thin films deposited epitaxially on single crystal substrates. The orientation of these films is often characterized by specifying the unit cell axis that is perpendicular to the substrate. This omits specifying the orientation of the other unit cell axes and grain boundary angles between grains of the thin film. Misorientation between grains of YBa2Cu3O7−δ decreases the critical current, even in those films that are c axis oriented. We presume that these results are similar for bismuth based superconductors and report the epitaxial orientations and textures observed in such films.Thin films of nominally Bi2Sr2CaCu2Ox were deposited on MgO using molecular beam epitaxy (MBE). These films were in situ grown (during growth oxygen was incorporated and the films were not oxygen post-annealed) and shuttering was used to encourage c axis growth. Other papers report the details of the synthesis procedure. The films were characterized using x-ray diffraction (XRD) and transmission electron microscopy (TEM).

Transmission Electron Microscopy of Epitaxial silicides grown by ultra high vacuum deposition

1989 ◽  
Vol 47 ◽  
pp. 462-463
Author(s):  
D. Loretto ◽  
J. M. Gibson ◽  
S. M. Yalisove
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Electron Diffraction ◽  
High Vacuum ◽  
High Energy ◽  
Energy Electron ◽  
Ultra High Vacuum ◽  
Ex Situ ◽  
Transmission Electron

The silicides CoSi2 and NiSi2 are both metallic with the fee flourite structure and lattice constants which are close to silicon (1.2% and 0.6% smaller at room temperature respectively) Consequently epitaxial cobalt and nickel disilicide can be grown on silicon. If these layers are formed by ultra high vacuum (UHV) deposition (also known as molecular beam epitaxy or MBE) their thickness can be controlled to within a few monolayers. Such ultrathin metal/silicon systems have many potential applications: for example electronic devices based on ballistic transport. They also provide a model system to study the properties of heterointerfaces. In this work we will discuss results obtained using in situ and ex situ transmission electron microscopy (TEM).In situ TEM is suited to the study of MBE growth for several reasons. It offers high spatial resolution and the ability to penetrate many monolayers of material. This is in contrast to the techniques which are usually employed for in situ measurements in MBE, for example low energy electron diffraction (LEED) and reflection high energy electron diffraction (RHEED), which are both sensitive to only a few monolayers at the surface.

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