Contour-based segmentation and visualization of electron tomographic volumes

1995 ◽  
Vol 53 ◽  
pp. 1082-1083
Author(s):  
M. Marko ◽  
A. Leith ◽  
K. Buttle ◽  
Y. Li
Keyword(s):  
Spatial Frequency ◽  
High Voltage ◽  
Structural Information ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Structural Elements ◽  
Frequency Range ◽  
Low Contrast ◽  
Tremendous Amount

Electron tomography is increasingly employed to obtain highly-detailed 3-D structural information from complex biological specimens, when such information cannot be obtained otherwise. Thick sections (ca. 0.25-3 μm), which require an intermediate- or high-voltage EM, are often used so that an appreciable portion of the structure of interest can be contained within the section. Because of this relatively large amount of material, volumes made by tomographic reconstruction are often filled with a tremendous amount of detail, not all of which is of interest. Often, in the absence of special stains, the structures of interest have low contrast compared to surrounding or adjoining structures. Typically, all the structures are embedded in the "ground cytoplasm", which has nonuniformlydispersed small structural elements that have the same density and spatial-frequency range as the structures of interest. In addition, the density of a given structure may vary within an image due to non-uniform staining. In these situations, the segmentation of the volume to isolate the interesting portions of the structure presents a formidable problem.

“High Resolution High Voltage Electron Microscopy”

1968 ◽  
Vol 26 ◽  
pp. 326-327
Author(s):  
Benjamin M. Siegel
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Voltage ◽  
Full Potential ◽  
Contrast Imaging ◽  
High Voltage Electron Microscopy ◽  
Low Contrast ◽  
Voltage Electron ◽  
Critical Areas ◽  
High Voltage Electron

The potential advantages of high voltage electron microscopy for extending the limits of resolution and contrast in imaging low contrast objects, such as biomolecular specimens, is very great. The results of computations will be presented showing that at accelerating voltages of 500-1000 kV it should be possible to achieve spacial resolutions of 1 to 1.5 Å and using phase contrast imaging achieve adequate image contrast to observe single atoms of low atomic number.The practical problems associated with the design and utilization of the high voltage instrument are, optimistically, within the range of competence of the state of the art. However, there are some extremely important and critical areas to be systematically investigated before we have achieved this competence. The basic electron optics of the column required is well understood, but before the full potential of an instrument capable of resolutions of better than 1.5 Å are realized some very careful development work will be required. Of great importance for the actual achievement of high resolution with a high voltage electron microscope is the fundamental limitation set by the characteristics of the high voltage electron beam that can be obtained from the accelerator column.

Density-based discrimination of protein and RNA in the ribosome

1992 ◽  
Vol 50 (1) ◽  
pp. 464-465
Author(s):  
Joachim Frank
Keyword(s):  
Transfer Function ◽  
Spatial Frequency ◽  
Three Dimensional ◽  
Wiener Filter ◽  
Dark Field Image ◽  
Dark Field ◽  
Frequency Range ◽  
Bright Field ◽  
Contrast Transfer Function ◽  
Pass Filter

Cryo-electron microscopy combined with single-particle reconstruction techniques has allowed us to form a three-dimensional image of the Escherichia coli ribosome.In the interior, we observe strong density variations which may be attributed to the difference in scattering density between ribosomal RNA (rRNA) and protein. This identification can only be tentative, and lacks quantitation at this stage, because of the nature of image formation by bright field phase contrast. Apart from limiting the resolution, the contrast transfer function acts as a high-pass filter which produces edge enhancement effects that can explain at least part of the observed variations. As a step toward a more quantitative analysis, it is necessary to correct the transfer function in the low-spatial-frequency range. Unfortunately, it is in that range where Fourier components unrelated to elastic bright-field imaging are found, and a Wiener-filter type restoration would lead to incorrect results. Depending upon the thickness of the ice layer, a varying contribution to the Fourier components in the low-spatial-frequency range originates from an “inelastic dark field” image. The only prospect to obtain quantitatively interpretable images (i.e., which would allow discrimination between rRNA and protein by application of a density threshold set to the average RNA scattering density may therefore lie in the use of energy-filtering microscopes.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

Practical electron tomography

1995 ◽  
Vol 53 ◽  
pp. 742-743
Author(s):  
C.L. Woodcock
Keyword(s):  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3D Shape ◽  
Computational Resources ◽  
Shape Of Particles

Despite the potential of the technique, electron tomography has yet to be widely used by biologists. This is in part related to the rather daunting list of equipment and expertise that are required. Thanks to continuing advances in theory and instrumentation, tomography is now more feasible for the non-specialist. One barrier that has essentially disappeared is the expense of computational resources. In view of this progress, it is time to give more attention to practical issues that need to be considered when embarking on a tomographic project. The following recommendations and comments are derived from experience gained during two long-term collaborative projects.Tomographic reconstruction results in a three dimensional description of an individual EM specimen, most commonly a section, and is therefore applicable to problems in which ultrastructural details within the thickness of the specimen are obscured in single micrographs. Information that can be recovered using tomography includes the 3D shape of particles, and the arrangement and dispostion of overlapping fibrous and membranous structures.

METHODS AND ALGORITHMS FOR THE COMPLETE PROCESSING OF A POSTDETECTOR LOW-CONTRAST OPTICAL IMAGE

2018 ◽  
pp. 99-107
Author(s):  
V. V. Lavrov ◽  
R. S. Luchkin ◽  
O. I. Nemykin ◽  
M. E. Prokhorov ◽  
Yu. G. Ryndin ◽  
...  
Keyword(s):  
Optical Image ◽  
Structural Elements ◽  
Filtration Process ◽  
Low Contrast ◽  
Information Object ◽  
Detection Stage ◽  
Metric Structures ◽  
Spot 5 ◽  
Integrated Indicators ◽  
Complete Processing

Methods and algorithms for the complete processing of a post-detector low-contrast optical image (OI) of an unknown remote object obtained by ground-based optical means of observation under conditions of a complex background situation are considered. The purpose of processing is to separate and interpret at least with the help of the analyst, of the main constructive elements using the integrated indicators introduced in [6] and the characteristics of the analyzed OI, which are connected by the information, topological and metric structures of the OI. The stages of processing the OI include extracting the image-containing information object of the image portion (detection) and filtration of the OI, using recursive rank filtering. The final stages of processing include the segmentation of the OI and the allocation on it constructive elements using the apparatus of graph theory. An example of image processing of a Spot-5 spacecraft obtained in real conditions is given. It is shown that in this case at the detection stage it is possible to reduce the volume of information processed at subsequent stages by 8 times, in the filtration process to increase the compactness of the OI and to increase its connectivity in comparison with the post-detection OI. As a result of segmentation and allocation of constructive elements, three structural elements that can be interpreted as a spacecraft case and two remote panels can be identified with the analyst’s participation.

High-voltage synthetic inductor for vibration damping in resonant piezoelectric shunt

2020 ◽  
pp. 107754632095261
Author(s):  
Kevin Dekemele ◽  
Patrick Van Torre ◽  
Mia Loccufier
Keyword(s):  
Piezoelectric Material ◽  
High Voltage ◽  
State Of The Art ◽  
Vibration Damping ◽  
Operational Amplifiers ◽  
Frequency Range ◽  
Resonant Condition ◽  
Passive Components ◽  
Resonance Frequencies ◽  
Resonant Shunt

Resonant piezoelectric shunts are a well-established way to reduce vibrations of mechanical systems suffering from resonant condition. The vibration energy is transferred to the electrical domain through the bonded piezoelectric material where it is dissipated in the shunt. Typically, electrical and mechanical resonance frequencies are several orders apart. As such, finding a suitable high inductance component for the resonant shunt is not feasible. Therefore, these high inductance values are mimicked through synthetic impedances, consisting of operational amplifiers and passive components. A downside of these synthetic impedances is that standard operational amplifiers can only handle up to 30 V peak to peak and the state-of-the-art amplifiers up to 100 Vpp. However, as mechanical structures tend to become lighter and more flexible, the order induced voltages over the piezoelectric material electrode voltages increase above these limitations. In this research, a high-voltage synthetic inductor is proposed and built by combining the bridge amplifier configuration and the output voltage boost configuration around a single operational amplifier gyrator circuit, effectively quadrupling the range of the synthetic inductor to 400 Vpp. The impedance of the circuit over a frequency range is numerically and experimentally investigated. The synthetic inductor is then connected to a piezoelectric material bonded to a cantilever beam. Numerical and experimental investigation confirms the high-voltage operation of the implemented circuit and its suitability as a vibration damping circuit.

Spatial frequency analsis in early visual processing

1980 ◽  
Vol 290 (1038) ◽  
pp. 11-22 ◽  
Keyword(s):  
Spatial Frequency ◽  
Visual Processing ◽  
Spatial Information ◽  
Multiple Channels ◽  
Low Contrast ◽  
Local Sign ◽  
Early Visual Processing ◽  
Low Luminance ◽  
Lowered Sensitivity ◽  
Prior Adaptation

The existence of multiple channels, or multiple receptive field sizes, in the visual system does not commit us to any particular theory of spatial encoding in vision. However, distortions of apparent spatial frequency and width in a wide variety of conditions favour the idea that each channel carries a width- or frequency-related code or ‘label’ rather than a ‘local sign’ or positional label. When distortions of spatial frequency occur without prior adaptation (e.g. at low contrast or low luminance) they are associated with lowered sensitivity, and may be due to a mismatch between the perceptual labels and the actual tuning of the channels. A low-level representation of retinal space could be constructed from the spatial information encoded by the channels, rather than being projected intact from the retina.

scholarly journals Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

2020 ◽  
Author(s):  
Jonathan Bouvette ◽  
Hsuan-Fu Liu ◽  
Xiaochen Du ◽  
Ye Zhou ◽  
Andrew P. Sikkema ◽  
...  
Keyword(s):  
Data Collection ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Beam Image ◽  
Geometrical Constraints ◽  
Order Of Magnitude ◽  
Biological Environment ◽  
Map Resolution ◽  
Resolution Single

ABSTRACTTomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by an order of magnitude and improve map resolution by ~1-3 Å compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved.

scholarly journals A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

2017 ◽  
Vol 2017 ◽  
pp. 1-17 ◽  
Author(s):  
C. O. S. Sorzano ◽  
J. Vargas ◽  
J. Otón ◽  
J. M. de la Rosa-Trevín ◽  
J. L. Vilas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
Iterative Algorithms ◽  
Projection Methods ◽  
Particle Analysis ◽  
Reconstruction Algorithms ◽  
Large Families ◽  
Key Steps

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

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