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.

scholarly journals Focus: The interface between data collection and data processing in cryo-EM

2017 ◽  
Author(s):  
Nikhil Biyani ◽  
Ricardo D. Righetto ◽  
Robert McLeod ◽  
Daniel Caujolle-Bert ◽  
Daniel Castano-Diez ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Data Processing ◽  
Electron Tomography ◽  
Single Particles ◽  
Transmission Electron ◽  
Computer Image Processing ◽  
Elemental Image ◽  
User Friendly ◽  
High Throughput Manner

We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.

scholarly journals Cryo-electron tomography: an ideal method to study membrane-associated proteins

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160210 ◽  
Author(s):  
Michelle A. Dunstone ◽  
Alex de Marco
Keyword(s):  
Image Processing ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Macromolecular Complexes ◽  
Membrane Pores ◽  
Cryo Electron Tomography ◽  
Associated Proteins ◽  
Ideal Method

Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

Structural studies of small amorphous volumes by electron diffraction

1990 ◽  
Vol 48 (4) ◽  
pp. 122-123
Author(s):  
Pierre Moine
Keyword(s):  
Electron Diffraction ◽  
Born Approximation ◽  
Structural Information ◽  
Fundamental Relation ◽  
X Rays ◽  
Structural Studies ◽  
Diffraction Experiment ◽  
Transmission Electron ◽  
Amorphous Structures ◽  
Diffraction Patterns

Qualitatively, amorphous structures can be easily revealed and differentiated from crystalline phases by their Transmission Electron Microscopy (TEM) images and their diffraction patterns (fig.1 and 2) but, for quantitative structural information, electron diffraction pattern intensity analyses are necessary. The parameters describing the structure of an amorphous specimen have been introduced in the context of scattering experiments which have been, so far, the most used techniques to obtain structural information in the form of statistical averages. When only small amorphous volumes (< 1/μm in size or thickness) are available, the much higher scattering of electrons (compared to neutrons or x rays) makes, despite its drawbacks, electron diffraction extremely valuable and often the only feasible technique.In a diffraction experiment, the intensity IN (Q) of a radiation, elastically scattered by N atoms of a sample, is measured and related to the atomic structure, using the fundamental relation (Born approximation) : IN(Q) = |FT[U(r)]|.

EMCAT: An automatic image-processing system for electron-microscopic tomography

1994 ◽  
Vol 52 ◽  
pp. 418-419
Author(s):  
Weiping Liu ◽  
John W. Sedat ◽  
David A. Agard
Keyword(s):  
Image Processing ◽  
Structural Information ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Processing System ◽  
Electron Microscopic ◽  
Data Set ◽  
Ordered Structures ◽  
Automatic Image Processing ◽  
Em Tomography

Any real world object is three-dimensional. The principle of tomography, which reconstructs the 3-D structure of an object from its 2-D projections of different view angles has found application in many disciplines. Electron Microscopic (EM) tomography on non-ordered structures (e.g., subcellular structures in biology and non-crystalline structures in material science) has been exercised sporadically in the last twenty years or so. As vital as is the 3-D structural information and with no existing alternative 3-D imaging technique to compete in its high resolution range, the technique to date remains the kingdom of a brave few. Its tedious tasks have been preventing it from being a routine tool. One keyword in promoting its popularity is automation: The data collection has been automated in our lab, which can routinely yield a data set of over 100 projections in the matter of a few hours. Now the image processing part is also automated. Such automations finish the job easier, faster and better.

Three-Dimensional Dispersion of Nano-Fillers in Soft Composite as Revealed by Transmission Electron Microscopy/Electron Tomography (3D-TEM)

2006 ◽  
Vol 514-516 ◽  
pp. 353-358 ◽  
Author(s):  
Shinzo Kohjiya
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Carbon Black ◽  
Natural Rubber ◽  
Structural Information ◽  
Electron Tomography ◽  
Nano Composites ◽  
Nano Structure ◽  
Transmission Electron ◽  
Particulate Silica

. Generally rubber products are a typical soft material, and a composite of a nano-filler (typically, carbon black or particulate silica) and a rubber (natural rubber and various synthetics are used). The properties of these soft nano-composites have been well known to depend on the dispersion of the nano-filler in the rubbery matrix. The most powerful tool for the elucidation of it has been transmission electron microscopy (TEM). The microscopic techniques are based on the projection of 3-dimensional (3D) body on a plane (x, y plane), thus the structural information along the thickness (z axis) direction of the sample is difficult to obtain. This paper describes our recent results on the dispersion of carbon black (CB) and particulate silica in natural rubber (NR) matrix observed by TEM combined with electron tomography (3D-TEM) technique, which enabled us to obtain images of 3D nano-structure of the sample. Thus, 3D images of CB and silica in NR matrix are visualized and analyzed in this communication. These results are precious ones for the design of soft nano-composites, and the technique will become an indispensable one in nanotechnology.

Automated data collection for electron tomography

1992 ◽  
Vol 50 (2) ◽  
pp. 1044-1045
Author(s):  
D.A. Agard ◽  
A.J. Koster ◽  
M.B. Braunfeld ◽  
J.W. Sedat
Keyword(s):  
Data Collection ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Ccd Camera ◽  
Higher Order ◽  
Projection Data ◽  
Voltage Electron ◽  
Digital Format ◽  
Central Interest ◽  
Focus Variation

Three-dimensional imaging has become an important addition to the variety of methods available for research on biological structures. Non-crystalline samples can be examined by high resolution electron tomography which requires that projection data be collected over a large range of specimen tilts. Practical limitations of tomography are set by the large number of micrographs to be processed, and by the required (and tedious) recentering and refocusing of the object during data collection; especially for dose sensitive specimens. With automated electron tomography a number of these problems can be overcome. First, the images are recorded directly in digital format, using a cooled slow scan CCD camera, and, with automatic tracking and correction for image shift and focus variation, a pre-aligned dataset is obtained, with every image recorded under well defined imaging conditions.At UCSF, we use intermediate voltage electron tomography to study higher-order chromatin structure. Of central interest is elucidating the higher-order arrangement of the 30nm chromatin fiber within condensed chromosomes through several phases of the cell cycle and, in collaboration with Chris Woodcock, the structure of the 30 nm fiber.

scholarly journals Recent Advances in Electron Tomography: TEM and HAADF-STEM Tomography for Materials Science and Semiconductor Applications

2005 ◽  
Vol 11 (5) ◽  
pp. 378-400 ◽  
Author(s):  
Christian Kübel ◽  
Andreas Voigt ◽  
Remco Schoenmakers ◽  
Max Otten ◽  
David Su ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
Electron Tomography ◽  
Semiconductor Devices ◽  
Three Dimensional ◽  
Crystalline Materials ◽  
Transmission Electron ◽  
Stem Tomography

Electron tomography is a well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life sciences applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution three-dimensional (3D) structural information in physical sciences. In this article, we evaluate the capabilities and limitations of transmission electron microscopy (TEM) and high-angle-annular-dark-field scanning transmission electron microscopy (HAADF-STEM) tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1–2 nm can be resolved in three dimensions by electron tomography. For partially crystalline materials with small single crystalline domains, bright-field TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

scholarly journals Improvements on marker-free images alignment for electron tomography

2020 ◽  
Author(s):  
C.O.S. Sorzano ◽  
F. de Isidro-Gómez ◽  
E. Fernández-Giménez ◽  
D. Herreros ◽  
S. Marco ◽  
...  
Keyword(s):  
Structural Information ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Reconstruction Process ◽  
New Approach ◽  
Alignment Procedure ◽  
Transmission Electron ◽  
Marker Free ◽  
Stem Tomography

AbstractElectron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.

scholarly journals ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography

2019 ◽  
Vol 75 (2) ◽  
pp. 138-150 ◽  
Author(s):  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Go Ueno ◽  
Yoshiaki Kawano ◽  
Kazuya Hasegawa ◽  
...  
Keyword(s):  
Data Collection ◽  
Structural Information ◽  
Protein Crystal ◽  
Quality Data ◽  
Collection System ◽  
Automated Data Collection ◽  
Automatic Data ◽  
Data Collection System ◽  
Automatic Data Collection ◽  
Processing Techniques

Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.

A Novel Method of Data Collection for Automated Electron Tomography Based upon Pre-cal1bration of Image Shifts and Defocus Changes

2001 ◽  
Vol 7 (S2) ◽  
pp. 78-79
Author(s):  
Ulrike Ziese ◽  
Ries Janssen ◽  
Willie Geerts ◽  
Theo van der Krift ◽  
Auke van Balen ◽  
...  
Keyword(s):  
Data Collection ◽  
3D Reconstruction ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Current Status ◽  
Imaging Method ◽  
Major Step ◽  
Experimental Conditions ◽  
Digital Format ◽  
Tilt Series

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. For the 3D-reconstruction, the images of the tilt series are aligned relative to each other and the 3D-reconstruction is computed. Electron tomography is the only technique that can provide 3D information with nm-scale resolution of individual and unique samples. Routine application of electron tomography will comprise a major step forward in the characterization of complex materials and cellular arrangements. When collecting tilt series for electron tomography image shifts and defocus changes have to be corrected for by the human operator. The repetitive correction of these changes is highly time consuming, error prone and very hard to carry out under low-dose imaging conditions.Many practical problems are overcome when electron tomography data collection is performed in an automated fashion. Automation includes the (a) image acquisition on a (digital) CCD camera, which implies that (b) changes in image position and defocus can be detected by on-line image processing and (c) immediately be corrected for by computer control of the microscope, (d) Finally, tilt series are directly available in digital format for subsequent processing. Typically, carrying out such an experiment would take a day, and the actual data collection 2-4 hours. in spite of the enormous progress made in terms of data collection speed during the last few years, the current status of automated tomography still does not meet the requirements that would make it a routinely applicable tool. For a great number of biological assays and research projects, results obtained under different experimental conditions have to be compared, and series of experiments have to be carried out. Therefore, we propose a novel approach for recording a tilt series that significantly increases data collection speed, and widens the applicability of the technique.

Sign in / Sign up

Export Citation Format

Share Document