bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secondary Electron Image Contrast in the Scanning Electron Microscope
Authors: Suga Hiroshi , Fujiwara Takafumi , Kanai Nobuhiro , Kotera Masatoshi 
Published: June 2020

An image contrast given in the scanning electron microscope(SEM) is due to differences in a detected number of secondary electrons (SE) coming from the specimen surface. The difference arises from the topographic, compositional and voltage features at the specimen surface. Two kinds of approaches have been taken for the quantification of SE images. One is to simulate electron trajectories in vacuum toward the detector, assuming the typical angular and energy distributions of electrons emitted from the specimen surface. However, the typical angular and energy distributions are not always applicable if a topographic or a compositional feature is present at the surface. The other is to simulate electron trajectory in the specimen. It is possible to obtain angular, energy, and spatial distributions of electrons emitted from the specimen surface. However, in order to discuss the SEM contrast based on these data, one has to assume that, for example, all slow electrons (<50eV) may be collected by the SE detector, or fast electrons ((>50eV) electrons may take a straight trajectory in the vacuum specimen chamber of the SEM. In a practical SEM picture of, for example, an etch-pit, different crystallographic plane surface shows different contrast even if the angle of the primary electron incidence toward all those surfaces is the same. This is because of the acceptance of the signal detection system. In a present study we combined two electron trajectory simulations mentioned above and calculated electron trajectories both in and out of the specimen, to simulate the trajectory from the point of the signal generated until the signal is detected.Although several simulation models of electron scatterings in a specimen have been reported to estimate the SE intensity at the surface, the model should be available to trace low energy (<50eV) electron trajectories. The model used here is basically the same as that reported in previous papers, and only a brief explanation is given in the following. Here, we made several assumptions as; [l]the energy loss of the primary and excited fast electrons is proportion to the number of SEs generated in the specimen, [2]the generated SE has an energy distribution as described by the Streitwolf equation, [3]the energy of the generated SEs are transferred to free electrons of the atom by the elastic-binary-collision, then one SE excited by the primary electron produces a ternary electron after the collision, and each one of the SE and the ternary electron produces higher order electrons in a cascade fashion. The simulation continues until the energy of each electron is less than the surface potential barrier. Angular and energy distributions and number of electrons emitted at the surface agree quite well with each experimental result in a typical case.
Object Restoration in 3D Electron Microscopy and Inverse Problems
Authors: Barth Martin 
Published: June 2020

Standard 3D object reconstructions in electron microscope applications may be described as the solution of a forward problem: a series of projections is processed to collect reciprocal space data and a usually subsequent inverse Fourier transform yields a 3D objects representation. The resulting structure is commonly impaired by a convolution with an effective pointspread function that results fro an instrumental transfer function and the sampling character of the data.Corresponding artificial features in the reconstruction may be reduced, if not eliminated, by approaching object restorations as solution of an inverse problem. In particular the problem with unevenly sampled data or "missing data" may considerably be alleviated.With undersampled or unevenly sampled data the inverse problem tends to be ill-posed, i.e. the reconstruction as solution of the inverse problem tends to be non unique and sensitive to errors in the data such as noise. This ambiguity and sensitivity needs control by regularisation techniques. We discuss some general techniques such as projections onto convex sets (POCS), Maximum Entropy and Bayesian estimation with emphasis on applications to electron microscope data.
Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers
Authors: Carazo Jose-Maria , Benavides I. , Marco S. , Carrascosa J.L. , Zapata E.L. 
Published: June 2020

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.
Angular Calibration of Ribosomal Subuntts in Factor Space
Authors: Pujari Minakhi , Frank Joachim 
Published: June 2020

In single-particle analysis of macromolecule images with the electron microscope, variations of projections are often observed that can be attributed to the changes of the particle’s orientation on the specimen grid (“rocking”). In the multivariate statistical analysis (MSA) of such projections, a single factor is often found that expresses a large portion of these variations. Successful angle calibration of this “rocking factor” would mean that correct angles can be assigned to a large number of particles, thus facilitating three-dimensional reconstruction.In a study to explore angle calibration in factor space, we used 40S ribosomal subunits, which are known to rock around an axis approximately coincident with their long axis. We analyzed micrographs of a field of these particles, taken with 20° tilt and without tilt, using the standard methods of alignment and MSA. The specimen was prepared with the double carbon-layer method, using uranyl acetate for negative staining. In the MSA analysis, the untilted-particle projections were used as active, the tilted-particle projections as inactive objects. Upon tilting, those particles whose rocking axes are parallel to the tilt axis will change their appearance in the same way as under the influence of rocking. Therefore, each vector, in factor space, joining a tilted and untilted projection of the same particle can be regarded as a local 20-degree calibration bar.
Feasibility of the Common-Axis Method for Alignment Prior to 3D Reconstruction in Dark-Held Electron Microscopy
Authors: Farrow Neil A , Peter Ottensmeyer F 
Published: June 2020

Dark field electron microscopy has allowed the atomic modelling of the 3D structure of a number of biological molecules from images of single molecules and protein complexes. A prerequisite for such determinations has been knowledge as to the projection directions yielding the various images. The determination of these directions has relied on either the correlation of the dark field images with known biochemical data or with structures determined by x-ray crystallography. The use of information from such sources allows orientation of the different dark field images relative to each other. It will often be the case however that no other information is available as to the structure of the molecule under investigation. It then becomes necessary to use the images alone to determine their orientation relative to each other prior to using 3D reconstruction techniques.A number of methods are available to determine projection directions from a set of images of a given object. Most notable among these methods are the method of moments and the common axis method. The common axis method uses the fact that any two views of the same object share a common line projection. Thus by comparing line projections of three images it is possible to orientate these images relative to each other in space.
The Contribution of Intermediate-Voltage, High-Resolution Electron Microscopy In Materials Science: An Appraisal
Authors: Hutchison John L. 
Published: June 2020

Over the past five years or so the development of a new generation of high resolution electron microscopes operating routinely in the 300-400 kilovolt range has produced a dramatic increase in resolution, to around 1.6 Å for “structure resolution” and approaching 1.2 Å for information limits. With a large number of such instruments now in operation it is timely to assess their impact in the various areas of materials science where they are now being used. Are they falling short of the early expectations? Generally, the manufacturers’ claims regarding resolution are being met, but one unexpected factor which has emerged is the extreme sensitivity of these instruments to both floor-borne and acoustic vibrations. Successful measures to counteract these disturbances may require the use of special anti-vibration blocks, or even simple oil-filled dampers together with springs, with heavy curtaining around the microscope room to reduce noise levels. In assessing performance levels, optical diffraction analysis is becoming the accepted method, with rotational averaging useful for obtaining a good measure of information limits. It is worth noting here that microscope alignment becomes very critical for the highest resolution.In attempting an appraisal of the contributions of intermediate voltage HREMs to materials science we will outline a few of the areas where they are most widely used. These include semiconductors, oxides, and small metal particles, in addition to metals and minerals.
Microanalysis At Intermediate Voltages
Authors: Williams David B. , Michael Zemyan S. 
Published: June 2020

Microanalysis using x-ray emission spectrometry (XES) or electron energy-loss spectrometry (EELS) at intermediate voltages should offer advantages over 100kV instruments. Brightness increases linearly with kV (for thermionic sources), but the inelastic scattering cross section decreases. Potential improvements in detectability limit and spatial resolution in both XES and EELS have been major factors spurring the development of intermediate voltage AEMs.The x-ray peak to background ratio increases with kV (Figure 1), and improvements in detectability limits have been reported at 300kV. The variation of detectability with spatial resolution is discussed elsewhere in these proceedings. Beam spreading should decrease linearly with kV, but experimentally the spatial resolution (Figure 2a,2b) does not show the expected improvement. This may be due to increased beam broadening from fast secondary electrons. The smallest probe size consistent with generating sufficient signal (i.e. an FEG) is better than increased kV for improved spatial resolution3. Increased kV has seen the return of the ‘hole count’ problem in XES. Higher voltage electrons generate harder x-rays at the C aperture, and current aperture design cannot sufficiently restrict the xray flux. The flux at 300kV can contribute up to 10% of the characteristic x-ray signal, which severely compromises the microanalysis quality. An FEG with reduced source size may help. At intermediate voltages, intrinsic Ge (IG) detectors can be used for analysis of Kα, lines from high atomic number elements. K line analysis gives improved accuracy compared with L and M line analysis for which Cliff- Lorimer k factors, (both experimental and theoretical) are extremely variable, possibly due to fast secondaries also. IG detectors can detect Au K lines, resolve Kα1Kα2 lines, (see Figure 3) offer improved energy resolution (~120eV) over Si(Li) detectors, and may be more stable under electron irradiation. Continued improvement in IG detectors may result in their displacing Si(Li) detectors from most AEMs.
High-resolution Study of DNA in Vitrified Sections
Authors: Richter Karsten , Dubochet Jacques 
Published: June 2020

Water in biological specimens, when cooled at a very high rate can be immobilized in a metastable, amorphous, so-called vitreous state. Kept vitreous at temperatures below 130 K, the vapour presure of water is so low, that the specimens will not dry when observed directly in the EM. Therefore, cryo-EM of vitrified biological specimens ommits artifacts due to dehydration and chemical fixation.One field of interest in the application of this technique is the study of the structural organisation of genomic material in situ.The objects to be studied, i.e. isolated nuclei, culture cells, or tissues are all too large to allow investigation as a whole in the TEM; they must be observed as ultrathin sections. While the cutting of vitrified bulk specimens into ultrathin sections is possible, the cutting process provokes severe deformation: The sections are compressed along the cutting direction by ca 50% and correspondingly, the section thickness doubles in respect to the actual advance of the microtome, which indicates important displacements of material takeing place during sectioning. Nevertheless structural information even in small range order can be conserved.
Structure of The Z Disk of Sectioned Bee Flight Muscle
Authors: Deatherage J.F. , Cheng N. 
Published: June 2020

Information from oblique thin sections and from 3-D reconstructions of tilted transverse thin sections has been combined to determine the 3-D structure of the honeybee flight muscle Z disk at 7øÅ resolution. The overall symmetry and structure of the Z disk and its relationship to the rest of the myofibril have been determined by tracing filaments and connecting elements on electron images of oblique sections which have been enhanced by a local crystallographic averaging technique .The 3-D structure of the central region of the Z disk of honeybee flight muscle has been determined by crystallographic 3-D reconstruction from electron micrographs of tilted thin sections. The reconstructions show a complex network in which actin filaments terminate and are crosslinked together (Figure 1); a number of structural domains are resolved in the network.The central region of the Z disk contains two sets of overlapping actin filaments of opposite polarity, which originate in the sarcomeres adjacent to the Z disk, and connections between these filaments. The filaments are deflected by the attachment of crosslinks; spacings between filaments change by over 1øøÅ during their passage through the Z disk. Each actin filament is linked by connecting structures to four filaments of opposite polarity and two filaments of the same polarity.
Electron Microscope Tomography (Emt): Reconstruction Algorithms, Imaging and Mass Loss of Thick Sections
Authors: Olins A.L. , Levy H. A. , Shah M. B. , Lamprecht G. G. , Olins D. E. 
Published: June 2020

We previously reported EMT reconstructions of thick (>0.5 μm) sections using electron spectroscopic imaging at the most probable electron energy loss (ΔEp). We2 calculated values of contrast and signal-to-noise ratio (SNR) for images formed with electrons taken throughout the spectrum. We observed maximal SNR just below ΔEp, and found that changes in the electron beam voltage and mass thickness (t/λ) led to predictable changes in the EELS.We have begun a study of mass loss due to electron exposure of thick epon sections. Uranyl and lead stained sections were put on formvar covered grids and carbon coated on each side. Clear epon regions were analyzed. During each exposure series the beam was kept at crossover; the beam current was changed from its lowest value (0.5 μamp) to its highest value (55 μamp). As reported elsewhere, mass loss occurs early and plateaus. Calculations were based on EELS collected at different times during each series (Figure 1a). Measured positions of ΔEp at different times (min) of maximum beam current irradiation are shown in Figure 1 b. Mass thickness, t/λ = In (total area/zero loss area), shows a linear relationship with ΔEp (Figure 1c). Using λ = 115 nm in epon, we calculate the initial thickness of the sections to be 0.5, 0.75, 1.0 μm and the mass loss to be ∼37 nm. If mass loss is independent of the specimen thickness, then the 50% loss observed with thinner specimen becomes a trivial 4-7% loss in sections of 0.5 to 1.0 μm.
Instrument Design and Image Reconstruction For A Laboratory X-Ray Microtomograph
Authors: Johnson Roger H. , Nelson Alan C. , Burns David H. 
Published: June 2020

X-ray microscopy has received considerable attention over the years, since it has the potential of producing high-resolution images of thick specimens in air. We are developing an x-ray microtomograph for three-dimensional imaging of small biological specimens. The instrument, shown in Figure 1, has much in common with projection x-ray microscopes of decades past, but incorporates several technological advances of recent years to partially overcome the limitations of the older instruments. The most important of these are the use of a planar solid-state detector and the provision for volume reconstruction. We describe the design for a relatively low-cost instrument intended for 3-D imaging of biological specimens up to ten cubic millimeters in size.The x-ray source for the microtomograph consists of a modified SEM. The electron beam, in spot mode and focused to about ten nanometers, impinges on a thin foil target to produce an emergent, low-intensity cone beam of characteristic and Bremsstrahlung x-rays. The foil resides in close proximity to an optional aluminum filter and a thin beryllium window which terminates the evacuated electron column. The specimen is mounted on a precision rotating shaft within two millimeters of the target foil. A two-dimensional detector is placed ten to forty centimeters from the sample, providing direct projection magnifications of up to 200 times. Two-dimensional projection views are collected at each of many angular orientations as the sample is rotated through 360 degrees. Cone beam backprojection algorithms are then applied to reconstruct a threedimensional data set.
A Metastable Crystalline Phase Coexisted with the Decagonal Quasicrystals in Rapidly Solidified Al-Ir Al-Pd and Al-Pt Alloys
Authors: Rong Wang , Lina Ma , Kuo K.H. 
Published: June 2020

Up to now, decagonal quasicrystals have been found in the alloys of whole Al-Pt group metals [1,2]. The present paper is concerned with the TEM study of a hitherto unreported hexagonal phase in rapidly solidified Al-Ir, Al-Pd and Al-Pt alloys.The ribbons of Al5Ir, Al5Pd and Al5Pt were obtained by spun-quenching. Specimens cut from the ribbons were ion thinned and examined in a JEM 100CX electron microscope. In both rapidly solidified Al5Ir and Al5Pd alloys, the decagonal quasicrystal, with rosette or dendritic morphologies can be easily identified by its electron diffraction patterns(EDPs). The EDPs of the decagonal phase for the two alloys are quite similar. However, the existance of decagonal quasicrystal in the Al-Pt alloy has not been verified by our TEM study. It is probably for the reason that the cooling rate is not great enough for the Al5Pt alloy to form the decagonal phase. During the TEM study, a metastable hexagonal phase has been observed in the Al5Ir, Al5Pd and Al5Pt alloys. The lattic parameters calculated from the X-ray powder data of this phase are a=1.229 and c=2.647nm(Al-Pd) and a=1.231 and c=2.623nm(Al-Ir). The composition of this phase was determined by EDS analysis as Al4(Ir, Pd or Pt). It coexists with the decagonal phase in the alloys and transformed to other stable crystalline phases on heating to high temperature. A comparison between the EDPs of the hexagonal and the decagonal phase are shown in Fig.l. Fig. 1(a) is the EDPs of the decagonal phase in various orientions and the EDPs of the hexagonal phase are shown in Fig.1(b), in a similar arrangement as Fig.1(a). It can be clearly seen that the EDPs of the hexagonal phase, especially the distribution of strong spots, are quite similar to their partners of the decagonal quasicrystal in Fig.1(a). All the angles, shown in Fig.l, between two corresponding EDPs are very close to each other. All of these seem strongly to point out that a close structural relationshipexists between these two phases:[110]//d10 [001]//d2(D) //d2 (P)The structure of α-AlFeSi is well known [3] and the 54-atom Mackay icosahedron with double icosahedral shells in the α-AlFeSi structure [4] have been used to model the icosahedral quasicrystal structure. Fig.2(a) and (b) show, respectively, the [110] and [001] projections of the crystal structure of α- AlFeSi, and decagon-pentagons can easily be identified in the former and hexagons in the latter. In addition, the optical transforms of these projections show clearly decagons and hexagons of strong spots, quite similar to those in [110] and [001] EDPs in Fig.1(b). This not only proves the Al(Ir, Pt, Pd) metastable phase being icostructural with the α-AlFeSi phase but also explains the orientation relationship mentioned above.
Mickey, A Computer Helping Hand for the Everyday use of the T.E.M.
Authors: Pierre Chemelle , Bernard Muller , Michel Crouillère 
Published: June 2020

The efficiency of transmission electron microscopy investigations is drastically impaired by the time required for photographic plate development, measurements and interpretation. Very often, the operator has to go back to the microscope to complete his analysis. The evolution of the TEM, through the automation of an increasing number of operating parameters and the increasing use of small computers has led to a variety of performance improvements.The outline of the microscope facility that we developed is shown in Figure 1. The TEM/STEM EM400T PHILIPS microscope is linked simultaneously to the EDAX PDP devoted to X-ray microanalysis and to a DEC μPDP for diffraction analysis. This second computer, operating in a multitask RSX environment can be used for on-line and off-line analysis of patterns, microanalysis data and crystallographic calculations. The μPDP is coupled to the microscope via ADC/DAC converters and the Hybrid Diffraction STEM apparatus. The two computers are connected through a serial line for data transmission (i.e. spectra and chemical analysis). As a whole, this facility is integrated in a DEC ETHERNET network connected to a mainframe VAX computer. Several image workstations, are among the other nodes of the network.