Improved Three-Dimensional (3D) Resolution of Electron Tomograms Using Robust Mathematical Data-Processing Techniques

2017 ◽  
Vol 23 (6) ◽  
pp. 1121-1129 ◽  
Author(s):  
Toby Sanders ◽  
Ilke Arslan
Keyword(s):  
Data Processing ◽  
Electron Tomography ◽  
Full Range ◽  
Center Of Mass ◽  
Three Dimensional ◽  
Pt Nanoparticles ◽  
Specimen Preparation ◽  
Reconstruction Algorithms ◽  
Data Set ◽  
Tilt Series

AbstractElectron tomography has become an essential tool for three-dimensional (3D) characterization of nanomaterials. In recent years, advances have been made in specimen preparation and mounting, acquisition geometries, and reconstruction algorithms. All of these components work together to optimize the resolution and clarity of an electron tomogram. However, one important component of the data-processing has received less attention: the 2D tilt series alignment. This is challenging for a number of reasons, namely because the nature of the data sets and the need to be coherently aligned over the full range of angles. An inaccurate alignment may be difficult to identify, yet can significantly limit the final 3D resolution. In this work, we present an improved center-of-mass alignment model that allows us to overcome discrepancies from unwanted objects that enter the imaging area throughout the tilt series. In particular, we develop an approach to overcome changes in the total mass upon rotation of the imaging area. We apply our approach to accurately recover small Pt nanoparticles embedded in a zeolite that may otherwise go undetected both in the 2D microscopy images and the 3D reconstruction. In addition to this, we highlight the particular effectiveness of the compressed sensing methods with this data set.

scholarly journals A Simple Preparation Method for Full-Range Electron Tomography of Nanoparticles and Fine Powders

2017 ◽  
Vol 23 (6) ◽  
pp. 1150-1158 ◽  
Author(s):  
Elliot Padgett ◽  
Robert Hovden ◽  
Jessica C. DaSilva ◽  
Barnaby D. A. Levin ◽  
John L. Grazul ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Bulk Material ◽  
Automatic Segmentation ◽  
Full Range ◽  
Three Dimensional ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Preparation Methods ◽  
Tomographic Images ◽  
Fine Powders

AbstractElectron tomography has become a valuable and widely used tool for studying the three-dimensional nanostructure of materials and biological specimens. However, the incomplete tilt range provided by conventional sample holders limits the fidelity and quantitative interpretability of tomographic images by leaving a “missing wedge” of unknown information in Fourier space. Imaging over a complete range of angles eliminates missing wedge artifacts and dramatically improves tomogram quality. Full-range tomography is usually accomplished using needle-shaped samples milled from bulk material with focused ion beams, but versatile specimen preparation methods for nanoparticles and other fine powders are lacking. In this work, we present a new preparation technique in which powder specimens are supported on carbon nanofibers that extend beyond the end of a tungsten needle. Using this approach, we produced tomograms of platinum fuel cell catalysts and gold-decorated strontium titanate photocatalyst specimens. Without the missing wedge, these tomograms are free from elongation artifacts, supporting straightforward automatic segmentation and quantitative analysis of key materials properties such as void size and connectivity, and surface area and curvature. This approach may be generalized to other samples that can be dispersed in liquids, such as biological structures, creating new opportunities for high-quality electron tomography across disciplines.

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).

A Novel Method for Automated Acquisition of Tilt Series for Electron Tomography Based on Pre-Calibration of the Specimen Stage

2000 ◽  
Vol 6 (S2) ◽  
pp. 1148-1149
Author(s):  
U. Ziese ◽  
A.H. Janssen ◽  
T.P. van der Krift ◽  
A.G. van Balen ◽  
W.J. de Ruijter ◽  
...  
Keyword(s):  
High Resolution ◽  
3D Reconstruction ◽  
Cell Biology ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Imaging Method ◽  
3D Images ◽  
Tilt Series ◽  
3D Information ◽  
Structural Arrangements

Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. Conventional TEM images are in first approximation mere 2D-projections of a 3D sample under investigation. With electron tomographya series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments (so called tilt-series). For the subsequent 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 true 3D information with nm-scale resolution of individual and unique samples. For (cell) biology and material science applications the availability of high-resolution 3D images of structural arrangements within individual samples provides unique architectural information that cannot be obtained otherwise. Routine application of electron tomography will comprise a major revolutionary step forward in the characterization of complex materials and cellular arrangements.

Automation of Tilt Series Acquisition in Transmission Electron Microscopy for Applications in Biology and Materials Science

2001 ◽  
Vol 7 (S2) ◽  
pp. 88-89
Author(s):  
Ingo Daberkow ◽  
Bernhard Feja ◽  
Peter Sparlinek ◽  
Hans R. Tietz
Keyword(s):  
3D Reconstruction ◽  
Data Acquisition ◽  
San Francisco ◽  
High Speed ◽  
Materials Science ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Max Planck ◽  
Automatic Data ◽  
Tilt Series

During the last decade, computation of a three-dimensional image from a tilt series (3D reconstruction) has become a well established method, of which a variety of implementations are available. The term “electron tomography” is now generally used for this type of data acquisition and 3D reconstruction. An overview over the techniques involved is given in.With the introduction of micro-processor-controlled TEMs and cooled slow-scan CCD cameras and with the progress in performance of high-speed computers, automation of complex imaging procedures became mainly a task of developing appropriate software, using the control facilities of the microscope. in this way, automated electron tomography was realized in 1990 at the Max- Planck-Institute for Biochemistry in Martinsried, and at about the same time at the University of California in San Francisco (UCSF). New techniques for automatic focusing and alignment, developed somewhat earlier , have been integrated in these automated tomography procedures. in the following we discuss the requirements of automatic data acquisition and the present implementation for several TEMs.

scholarly journals 6D electron microscopy: combining real-space and reciprocal-space tomography

2014 ◽  
Vol 70 (a1) ◽  
pp. C368-C368 ◽  
Author(s):  
Alexander Eggeman ◽  
Robert Krakow ◽  
Paul Midgley
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Real Space ◽  
Dark Field ◽  
Reciprocal Space ◽  
Data Set ◽  
Wide Range ◽  
The Matrix ◽  
Precession Electron Diffraction ◽  
Tilt Series

STEM and TEM-based tomography has been used widely to study the 3D morphology of a wide range of materials. Similarly reciprocal space tomography in which a tilt-series of diffraction patterns are acquired offers a powerful method for the analysis of the atomic structure of crystalline materials. The natural progression is to combine these techniques into a complete three dimensional morphology and crystallography data set, allowing both features to be studied simultaneously. Using a tilt series of scanning precession electron diffraction measurements from a commercially available Ni-base superalloy as an example, the complete reciprocal lattice orientation for a number of components embedded within the matrix could be determined. It was straightforward to identify reciprocal lattice vectors that allowed dark-field images representing each phase to be produced post-acquisition. In turn these were combined using geometric tomography methods to yield a 3-D tomogram of the superalloy. Imaging these phases using conventional ADF STEM tomography would potentially be challenging given the compositional similarity between the different phases. From the combined dataset the spatial distribution of the component phases could be easily recovered but more importantly the orientational relationships between these different components could be unambiguously determined. In this way the thermo-mechanical history of the sample could be inferred from the arrangement of coherent and semi-coherent interfaces and a previously unreported crystallographic registry between metal carbide (MC) and the matrix f.c.c. phases could been identified. The possibilities for development and applications of this technique will be discussed further.

VALIDATION OF MRI-BASED MEASUREMENTS OF SUPRASPINATUS MORPHOLOGY

2003 ◽  
Vol 07 (01) ◽  
pp. 15-23
Author(s):  
Tomotaka Nakajima ◽  
Richard E. Hughes ◽  
Kai-Nan An
Keyword(s):  
Data Processing ◽  
Spin Echo ◽  
Three Dimensional ◽  
Image Data ◽  
Supraspinatus Tendon ◽  
Fast Spin Echo ◽  
Acquisition Time ◽  
Data Set ◽  
Tendon Length ◽  
Voxel Data

The goal of this study was to visualize the supraspinatus tendon three-dimensionally using fast spin-echo (FSE) MRI and validate the accuracy of measuring the dimensions of the supraspinatus tendon based on 3D reconstructed images. Nine cadaver shoulders (51–84 y/o, mean 70.0 y/o) were imaged at conventional T2-weighted spin-echo (CSE), gradient echo (GRE), and 3D T2-weighted FSE sequences. Each "object" of the supraspinatus muscle, tendon and scapula was three-dimensionally reconstructed using ANALYZE™ image data processing software. The FSE images revealed significantly higher contrast of the tendon and contrast-to-noise ratios of the fat-to-tendon and fat-to-muscle. The length of the anterior, middle, and posterior portions of the tendon were measured in two ways: (1) from the three-dimensional reconstructed images, and (2) directly from the cadaver specimen using calipers. No statistically significant differences were found between the ANALYZE™ and caliper measurements using a paired t-test for the anterior (p = 0.55), middle (p = 0.57) and posterior (p = 0.44) portions of the supraspinatus. The 3D FSE sequence exhibits higher spatial resolution, spends shorter acquisition time, and constructs a voxel data set. These advantages can prevent blurring artifacts when imaging the supraspinatus tendon of a human body. Tendon length measurements derived from three-dimensional reconstructions using ANALYZE™ were found to be good estimates of actual tendon length. Therefore, the combination of FSE sequence and 3D image data processing provides a method for noninvasive quantitative analysis of supraspinatus tendon morphology. The results lay the groundwork for future quantitative studies of cuff pathology.

scholarly journals Electron Tomography

2002 ◽  
Vol 10 (2) ◽  
pp. 3-5
Author(s):  
Stephen W. Carmichael
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Specimen Preparation ◽  
Two Dimensional Image ◽  
Transmission Electron ◽  
Different Depths ◽  
Depth Dimension ◽  
Pass Through

The transmission electron microscope (TEM) was invented in the 1930's, and developments in specimen preparation in the 1950's led to its widespread use as a tool to study structure in biologic systems. Similar in principle to the light microscope, but utilizing a much shorter wavelength for better resolution, the TEM has the image-forming beam pass through the specimen. This results in a two-dimensional image which can be difficult to interpret because features from different depths of the three dimensional specimen are superimposed. Traditionally this was dealt with by cutting sections of plastic-embedded specimens so thin (in the 40 to SO nanometer range) that they effectively had only two dimensions. To allow biologists to examine structures in three dimensions, serial sections are stacked and structures reconstructed. Even though computers have made reconstruction easier, the reality is that resolution in the depth dimension is limited by the section thickness. The technique of electron tomography is emerging as a way to overcome this limitation.

scholarly journals Current data processing strategies for cryo-electron tomography and subtomogram averaging

2021 ◽  
Vol 478 (10) ◽  
pp. 1827-1845
Author(s):  
Euan Pyle ◽  
Giulia Zanetti
Keyword(s):  
Data Processing ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Current Data ◽  
Processing Strategies ◽  
Cryo Electron Tomography ◽  
Subtomogram Averaging ◽  
The Individual

Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from tomograms, aligned, and averaged in a process called subtomogram averaging (STA). STA overcomes the low signal to noise ratio within the individual subtomograms to generate structures of the particle(s) of interest. In recent years, cryo-ET with STA has increasingly been capable of reaching subnanometer resolution due to improvements in microscope hardware and data processing strategies. There has also been an increase in the number and quality of software packages available to process cryo-ET data with STA. In this review, we describe and assess the data processing strategies available for cryo-ET data and highlight the recent software developments which have enabled the extraction of high-resolution information from cryo-ET datasets.

Three-Dimensional Analysis of Carbon Nanotube Networks in Interconnects by Electron Tomography without Missing Wedge Artifacts

2010 ◽  
Vol 16 (2) ◽  
pp. 210-217 ◽  
Author(s):  
Xiaoxing Ke ◽  
Sara Bals ◽  
Daire Cott ◽  
Thomas Hantschel ◽  
Hugo Bender ◽  
...  
Keyword(s):  
Focused Ion Beam ◽  
Electron Tomography ◽  
Ion Beam ◽  
Full Range ◽  
Three Dimensional ◽  
X Ray ◽  
Quantitative Studies ◽  
Transmission Electron ◽  
Carbon Nanotube Networks ◽  
Semiconductor Contact

AbstractThe three-dimensional (3D) distribution of carbon nanotubes (CNTs) grown inside semiconductor contact holes is studied by electron tomography. The use of a specialized tomography holder results in an angular tilt range of ±90°, which means that the so-called “missing wedge” is absent. The transmission electron microscopy (TEM) sample for this purpose consists of a micropillar that is prepared by a dedicated procedure using the focused ion beam (FIB) but keeping the CNTs intact. The 3D results are combined with energy dispersive X-ray spectroscopy (EDS) to study the relation between the CNTs and the catalyst particles used during their growth. The reconstruction, based on the full range of tilt angles, is compared with a reconstruction where a missing wedge is present. This clearly illustates that the missing wedge will lead to an unreliable interpretation and will limit quantitative studies.

scholarly journals Three-dimensional Organization of Basal Bodies from Wild-Type and δ-Tubulin Deletion Strains of Chlamydomonas reinhardtii

2003 ◽  
Vol 14 (7) ◽  
pp. 2999-3012 ◽  
Author(s):  
Eileen T. O'Toole ◽  
Thomas H. Giddings ◽  
J. Richard McIntosh ◽  
Susan K. Dutcher
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Basal Body ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Specimen Preparation ◽  
Basal Bodies ◽  
Wild Type ◽  
Tubulin Isoforms ◽  
Striated Fiber ◽  
And Function

Improved methods of specimen preparation and dual-axis electron tomography have been used to study the structure and organization of basal bodies in the unicellular alga Chlamydomonas reinhardtii. Novel structures have been found in both wild type and strains with mutations that affect specific tubulin isoforms. Previous studies have shown that strains lacking δ-tubulin fail to assemble the C-tubule of the basal body. Tomographic reconstructions of basal bodies from the δ-tubulin deletion mutant uni3-1 have confirmed that basal bodies contain mostly doublet microtubules. Our methods now show that the stellate fibers, which are present only in the transition zone of wild-type cells, repeat within the core of uni3-1 basal bodies. The distal striated fiber is incomplete in this mutant, rootlet microtubules can be misplaced, and multiflagellate cells have been observed. A suppressor of uni3-1, designated tua2-6, contains a mutation in α-tubulin. tua2-6; uni3-1 cells build both flagella, yet they retain defects in basal body structure and in rootlet microtubule positioning. These data suggest that the presence of specific tubulin isoforms in Chlamydomonas directly affects the assembly and function of both basal bodies and basal body-associated structures.

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