Computer Visualization of Volume Data in Electron Tomography

The complex environment of biological cells and tissues has motivated development of three-dimensional (3D) imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper source post facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryoscanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles and then in representative cryotomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.

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Critical Comparison of Volume Data Obtained by Different Electron Tomography Techniques

Macromolecules ◽

10.1021/ma901998r ◽

2010 ◽

Vol 43 (3) ◽

pp. 1444-1448 ◽

Cited By ~ 14

Author(s):

Kangbo Lu ◽

Erwan Sourty ◽

Ralph Guerra ◽

Georg Bar ◽

Joachim Loos

Keyword(s):

Electron Tomography ◽

Volume Data ◽

Critical Comparison

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Automated electron tomography: from data collection to image processing

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100136507 ◽

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.

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Practical electron tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140087 ◽

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.

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Three-Dimensional reconstruction of isolated centrosomes by automated electron tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100169286 ◽

1994 ◽

Vol 52 ◽

pp. 310-311

Author(s):

M.B. Braunfeld ◽

M. Moritz ◽

B.M. Alberts ◽

J.W. Sedat ◽

D.A. Agard

Keyword(s):

Electron Tomography ◽

Three Dimensional ◽

Vital Role ◽

Complex Nature ◽

Animal Cells ◽

Microtubule Organizing Center ◽

Nucleation Sites ◽

Dimensional Reconstruction ◽

Organizing Center ◽

Resolution Model

In animal cells, the centrosome functions as the primary microtubule organizing center (MTOC). As such the centrosome plays a vital role in determining a cell's shape, migration, and perhaps most importantly, its division. Despite the obvious importance of this organelle little is known about centrosomal regulation, duplication, or how it nucleates microtubules. Furthermore, no high resolution model for centrosomal structure exists.We have used automated electron tomography, and reconstruction techniques in an attempt to better understand the complex nature of the centrosome. Additionally we hope to identify nucleation sites for microtubule growth.Centrosomes were isolated from early Drosophila embryos. Briefly, after large organelles and debris from homogenized embryos were pelleted, the resulting supernatant was separated on a sucrose velocity gradient. Fractions were collected and assayed for centrosome-mediated microtubule -nucleating activity by incubating with fluorescently-labeled tubulin subunits. The resulting microtubule asters were then spun onto coverslips and viewed by fluorescence microscopy.

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On the Use of POCS for Restoring the “Missing Wedge” in Electron Tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010018135x ◽

1990 ◽

Vol 48 (1) ◽

pp. 520-521

Author(s):

Neng-Yu Zhang ◽

Bruce F. McEwen ◽

Joachim Frank

Keyword(s):

Function Space ◽

Convex Sets ◽

Electron Tomography ◽

Spinal Ganglion ◽

Fourier Space ◽

Missing Information ◽

Voltage Electron ◽

High Voltage Electron Microscope ◽

Energy Bound ◽

Spatial Boundedness

Reconstructions of asymmetric objects computed by electron tomography are distorted due to the absence of information, usually in an angular range from 60 to 90°, which produces a “missing wedge” in Fourier space. These distortions often interfere with the interpretation of results and thus limit biological ultrastructural information which can be obtained. We have attempted to use the Method of Projections Onto Convex Sets (POCS) for restoring the missing information. In POCS, use is made of the fact that known constraints such as positivity, spatial boundedness or an upper energy bound define convex sets in function space. Enforcement of such constraints takes place by iterating a sequence of function-space projections, starting from the original reconstruction, onto the convex sets, until a function in the intersection of all sets is found. First applications of this technique in the field of electron microscopy have been promising.To test POCS on experimental data, we have artificially reduced the range of an existing projection set of a selectively stained Golgi apparatus from ±60° to ±50°, and computed the reconstruction from the reduced set (51 projections). The specimen was prepared from a bull frog spinal ganglion as described by Lindsey and Ellisman and imaged in the high-voltage electron microscope.

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Electron tomography

AccessScience ◽

10.1036/1097-8542.801290 ◽

2015 ◽

Keyword(s):

Electron Tomography

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Analisis Kinerja dan Pengaruh Pelebaran Jalan serta Pembuatan Median Jalan (Studi Kasus Jalan Temanggung Tilung Kota Palangkaraya)

Media Ilmiah Teknik Sipil ◽

10.33084/mits.v7i1.685 ◽

2018 ◽

Vol 7 (1) ◽

pp. 51-60

Author(s):

Fitri Wulandari ◽

Nirwana Puspasari ◽

Noviyanthy Handayani

Keyword(s):

Data Retrieval ◽

Service Level ◽

Traffic Volume ◽

Primary Data ◽

Volume Data ◽

Saturation Degree ◽

The Road ◽

Before And After ◽

Road Widening ◽

The Way

Jalan Temanggung Tilung is a 2/2 UD type road (two undirected two-way lanes) with a road width of 5.5 meters, which is a connecting road between two major roads, namely the RTA road. Milono and the path of G. Obos. Over time, the volume of traffic through these roads increases every year, plus roadside activities that also increase cause congestion at several points of the way. To overcome this problem, the local government carried out road widening to increase the capacity and level of road services. The study was conducted to determine the amount of traffic volume, performance, service level of the Temanggung Tilung road section at peak traffic hours before and after road widening. Data retrieval is done by the direct survey to the field to obtain primary data in the form of geometric road data, two-way traffic volume data, and side obstacle data. Performance analysis refers to the 1997 Indonesian Road Capacity Manual (MKJI) for urban roads. From the results of data processing, before increasing the road (Type 2/2 UD), the traffic volume that passes through the path is 842 pcs/hour and after road widening (Type 4/2 UD) the traffic volume for two directions is 973 pcs/hour, with route A equaling 528 pcs/hour and direction B equaling 445 pcs/hour. Based on the analysis of road performance before road enhancement, the capacity = 2551 pcs/hour, saturation degree = 0.331, and the service level of the two-way road are level B. Based on the analysis of the performance of the way after increasing the way, the direction capacity A = 2686 pcs/hour and direction B = 2674 pcs /hour, saturation degree for direction A = 0.196 and direction B = 0.166, service level for road direction A and direction B increase to level A

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