bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relation Between the Phase of the Electron Wave (Which is Lost When an Em Image is Recorded) and the Preserved Crystallographic Structure Factor Phases
Authors: Hovmöller Sven , Zou Xiaodong 
Published: July 2020

Abstract
The phase problem in X-ray crystallography is one of the most interesting and most studied mathematical problems that exist. There is still today no general solution of the phase problem, but partial solutions have resulted in at least 8 Nobel Prizes, even though one of the most prominent solutions, the Patterson function, was not awarded the Prize.
It has frequently been claimed that there should be a phase problem also in electron microscopy. It may be more correct to say that there is no phase problem, only a phase confusion problem in electron microscopy. The phase confusion problem has arisen since the word phase is used for (at least) two very different physical entities in the field of electron microscopy. When crystallographers speak about phases, they mean the crystallographic structure factor phases, while physicists mean the wave front phases. In order to resolve the phase confusion problem, it is necessary to define clearly which phases are meant.
Direct Phasing Determination of Si(111)-(3X1)-Ag Surface Reconstruction
Authors: Bailey GW , Dimlich RVW , Alexander KB , McCarthy JJ , Pretlow TP , Grozea D , Collazo-Davila C , Marks L D 
Published: July 2020

Abstract
The Si(111)-(3x1) reconstruction, observed for submonolayer coverage of all alkali metals and Ag, has been an attractive subject to study. Their almost identical low-energy electron diffraction (LEED) I-V curves suggest a similar surface structure, adsorbate size-independent. Moreover, filled-state scanning tunneling microscopy for Li, Na, Ag show similar features, double rows of maxima, resembling zigzag chains, and a pi surface unit cell symmetry. The atomic structure of this reconstruction is still controversial. Several models, most of them based on a π-bonded silicon chain, such as the Seiwatz or extended Pandey chain, have been proposed. This study attempts to determine this structure using direct phasing of transmission electron diffraction (TED) patterns.
Transmission electron microscopy silicon samples were cleaned and the Si(111)-(3x1)-Ag structure obtained in a surface science system, SPEAR, under ultrahigh vacuum conditions. Using the attached Hitachi UHV H-9000 microscope, through exposure series diffraction patterns were recorded and reduced with a cross-correlation technique.
Structure of the TiO2(100)-1X3 Surface Determined by Direct Methods
Authors: Bailey GW , Dimlich RVW , Alexander KB , McCarthy JJ , Pretlow TP , Landree E , Marks L D , Zschack P 
Published: July 2020

Abstract
An atomic model of the TiO2(100)-1x3 surface has been determined based on Grazing Incidence X-Ray Diffraction (GIXD) data analyzed by direct methods coupled with χ2 minimization. The final model has every surface octahedral site occupied, and resembles the NaCl structure, in contrast to the normal structure of bulk rutile which has half of the sites occupied (Fig. 1). This structure is non-stoichiometric which is consistent with the observed spectroscopic data that indicates that the surface is titanium rich. The structure contains edge and face sharing octahedra, present in other known defect structures in TiO2, and appear consistent with what has been observed in Scanning Tunneling Microscopy.
The data consisted of 19 measured structure factors acquired from GIXD. The phases for the measured beams were calculated using a Sayre equation with Unitary Structure factors and a Genetic Algorithm global search technique. Based upon the calculated phases, charge density maps were constructed and used to determine the positions of titanium atoms within the unit cell (Fig. 2).
Current State of the Art of Digital Imaging in TEM
Authors: Fan G Y , Ellisman M H 
Published: July 2020

Abstract
The increasingly wide use of digital computers, the world-wide-web and electronic publishing has had a fundamental impact on the way scientists conduct research in every discipline of science. Electron microscopy is no exception. A considerable amount of effort has been devoted to the development of digital imaging acquisition systems for transmission electron microscopy (TEM). Digital image acquisition systems for TEM, including complete systems, have been produced by several companies, including: Advanced Microscopy Techniques (Rowley, MA), JEOL (Peabody, MA), Gatan (Warrendale, PA), Princeton Instruments (Trenton, NJ) and Tietz-Video (Herbststrasse, Gauting, Germany). While most systems are CCD-based, JEOL has also offered a system which is based on the Imaging Plate technology.
The Imaging Plate has the same size as, and is compatible with the camera system for, the 8.09 cm × 99.6 cm electron microscope film. As with film, a latent image is formed on the plate when exposed to electrons. A stack of exposed imaging plates are then taken out of the microscope and scanned by a laser beam in a readout device which converts the latent image to a digital form.
Measurement of Point-Spread Function of IP-System
Authors: Oikawa T , Hosokawa F , Taniyama A , Shindo D , Kersker M 
Published: July 2020

Abstract
For the resolution estimation of the Imaging Plate (IP)-system, several methods were carried out. One of them is the measurement of the modulation transfer function (MTF) from the phase contrast transfer function taken with an amorphous Ge film specimen. One of another is the measurement of the point-spread function (PSF) from the auto-correlation of the Poison noise obtained by the IP-system.
In this experiment, the PSF of the IP-system were measured from the intensity distribution recorded with a 1.6 μm-diameter electron probe on the IP.
When recording the electron intensity with a small enough electron probe as compared with the pixel size of the IP (25 μm × 25 μm), a single pixel detects the electron signal in case of ideal IP-resolution which is limited only by the pixel size. However, practical IP-resolution is limited by the electron diffusion, x-ray emission and the laser beam diffusion in the IP, and so on. Therefore, it is possible to measure the PSF from the intensity distributions of the patterns recorded with a small enough electron probe.
Approaches for High Resolution Cryo-Electron Tomography of Biological Specimens
Authors: Agard DA , Braunfeld MB , Chen Hans , McQuitty Rebecca , Sedat John 
Published: July 2020

Abstract
Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. Use of intermediate voltage electron microscopes extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety cellular organelles and assemblies such as centrosomes (Moritz et al.,1995a,b), kinetochores (McEwen, 1993) and chromatin (Woodcock, 1994), have clearly demonstrated the power of this method for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significant new insights into biological function.
Although the information that tomography provides is unique, its use as a general tool in the biological community has been limited due to the complexities involved in data collection and processing.
We are simultaneously trying to make this approach accessible through automation as well as trying to extend the resolution and accuracy of the reconstructions. Significant, has been the use of low-dose cryo-electron microscopic automated data collection methods.
Automated CCD Data Collection and 3D Reconstruction of Aleutian Mink Disease Parvovirus
Authors: Olson NH , Chipman PR , Bloom ME , McKenna R , Agbandje-McKenna M , Booth TF , Baker TS 
Published: July 2020

Abstract
Acquisition of CCD image data from frozen-hydrated specimens provides several advantages compared with the use of photographic film. CCD cameras possess excellent linearity, sensitivity and dynamic range. The CCD also allows one to pre-check the quality of a cryo sample much easier than with a TV rate camera or on film. However, the limited field of view (IK2 pixels) of the CCD makes data collection difficult. Gatan, Inc. has produced a LowDose software package, in conjunction with their DigitalMicrograph™ environment, that automates this process and allows for efficient collection of larger amounts of data. This software, along with our own image analysis software, has facilitated the computation of a three-dimensional reconstruction (3D) from images of baculo-expressed, VP2 particles of Aleutian mink disease parvovirus (ADV).
ADV has a capsid (∼28.5 nm diam.) that contains two proteins (VP1-2) of which ∼90% is VP2. ADV infections lead to plasmacytosis in mink and are a significant problem worldwide.
Three-Dimensional Time-Lapse Digital Movie Analysis of the Developing Fruit Fly Eye in Organ Culture
Authors: Archie Pollock John , Maneckshana Bejon T , Leonardo Teresa E 
Published: July 2020

Abstract
The compound eye of the fruit fly, Drosophila melanogaster, is composed of a highly ordered array of facets (FIG. 1), each containing a precise set of neurons and supporting cells. The eye arises during the third larval instar from an undifferentiated epithelium, the eye imaginai disc, which is connected to the brain via the optic stalk (FIG. 2). During eye development, movement of the morphogenetic furrow, progressive recruitment of specific cell types and the growth of photoreceptor axons into the brain are each dynamic processes that are routinely studied indirectly in fixed tissues. While stereotyped development and the ‘crystalline’ like structure of the eye facilitates this analysis, certain experiments are hindered by the inability to observe developmental processes as they occur. To overcome this limitation, we have combined organ culture with advanced microscopy tools to enable the observation of eye development in living tissue.
Bioimage: Towards a New Data Base of Biological Volumes
Authors: José María Carazo 
Published: July 2020

Abstract
This presentation introduces the current work of the Bioimage Corsortium and its international collaborators in the setting up of a new data base containing volumes of biological specimens.
The scope of the data that we will be organizing during the next three years is very broad, ranging from macromolecules to larger structures or even entire cells. The approach is designed to combine the desire to break many undesired formal barriers between the type of volume information produced at the different resolution levels whith, at the same time, the clear need of implementational flexibility required to appropriately handle different types of data.
The internal organization of the Bioimage Consortium clearly reflects the objectives presented above. In the first place, partners in the consortium have the scientific knowledge and projection in areas ranging from macromolecular structure to cell dynamics. These partners are then nucleated around two well-defined “servers”, one in Madrid, responsible for the work on macromolecular structures, and the other in Heildeberg, responsible for data more in the area of cell biology.
3D Reconstruction from Single Particles: Improved Orientation Determination from Noisy Images
Authors: Ottensmeyer FP , Timmer M , Allen K , Fernandes AB , Moremen KW 
Published: July 2020

Abstract
The correct reconstruction of the 3D structure from electron micrographs of sets of individual macromolecules or macromolecular assemblies depends crucially on the alignment and orientation determination of the individual images. The lateral alignment from one image to the next is generally easily accomplished by calculating the centre of mass of the individual molecular micrographs. For relatively noise-free pairs of images of unknown structures the sinogram correlation function provides common axes which can determine a correct angular orientation for any set of three images, building consecutively to a complete orientation determination for all images [1]. Low-dose images, however, are inherently noisy. For noisy images the angle determination becomes more problematical, since any fourth noisy image will have three different orientations, each with respect to one of the three possible pairs of three previously oriented noisy images. As more noisy images are added to the set, the number of possible orientations for any given image grow factorially.
Inorganic Crystal Structures Solved from EM Images and Refined to 0.02 À Accuracy Against Electron Diffraction Data
Authors: Hovmöller Sven , Zou Xiaodong , Weirich Thomas 
Published: July 2020

Abstract
Single crystal X-ray diffraction is the traditional method for accurate crystal structure determination. A major difficulty in X-ray crystallography is the phase problem; diffracted intensities contain amplitude information but no phases. In order to solve a structure, the phases of at least the strongest reflections must be estimated by Patterson techniques, so-called direct methods or in any other way. Once the structure has been solved (i.e. the atoms found to within about 0.2 Ångström of their correct positions), then refinement is rather straight-forward for single crystal data. Typically, single crystals diffract to about 1 Â resolution. After refinement, the atomic co-ordinates are obtained with an accuracy of about 0.01 Â for organic molecules and down to 0.001 Â for inorganic structures. One limitation of single crystal X-ray diffraction is that the crystals need to be at least about 10μm in all dimensions in order to diffract, even if the radiation source is a synchrotron.
Quantitative Information from Image Processing in ADF Stem
Authors: Nellist PD , Pennycook SJ 
Published: July 2020

Abstract
Annular dark-field (ADF) imaging in the scanning transmission electron microscope (STEM) at atomic resolution can be regarded as being almost perfect incoherent imaging, which has two major advantages over conventional high-resolution transmission electron microscopy (HRTEM), which is close to being perfectly coherent: Firstly, the images formed are direct structure images of the projected atomic structure, with regions of intensity located at the positions of the atomic columns. Secondly, the images can be written as the convolution between two real and positive functions: a point-spread function given by the intensity of the STEM probe, and an object function that consists of narrow, almost &lt;5-function-like, peaks located exactly over the nuclei of the atomic columns. Thus there is no phase problem in ADF STEM imaging, unlike in conventional HRTEM where phase retrieval techniques such as holography are often employed.
The lack of a phase problem in ADF STEM imaging creates immediate opportunities for image processing.
Extracting Structure Information from Cbed Patterns
Authors: Zuo JM 
Published: July 2020

Abstract
The advance of digital recording and energy filtering now makes it possible to extract quantitative crystal structure information in an accuracy close to or better than the x-ray method. The extraction of structure information employs the refinement technique by comparing theory and experiment using chisquare criteria of

For the unit cell or crystal orientation determination, the experiment yx is the line equation of Kikuchi or HOLZ lines, and/or positions of convergent beam disks or diffraction spots. Lines, or disks, can be measured directly from the digitally recorded two-dimensional patterns using techniques of image processing and transformation such as Hough. A practical method for measuring unit cell parameters was described by [1]. For the determination of atomic positions, the experiment yx is the diffracted intensities of medium and high order reflections. For the measurement of charge density, the yx is the energy-filtered diffracted intensities of low order reflections or high order reflections coupled with a low order reflections.
Electron Holography at Atomic Dimensions
Authors: Lichte Hannes 
Published: July 2020

Abstract
Many of the problems of transmission electron microscopy (TEM) are due to the fact that wave optics which governs the interaction of electrons with the specimen and the imaging process definitely is brought to an end with the detection of the final electron image. Unfortunately, resolution is limited by an increasing number of aberrations. Furthermore, wave optical tools in the electron microscope which are needed for example to produce phase contrast better than that given by the phase contrast transfer function, for distinction of amplitude contrast and phase contrast, or to measure phases in Fourier space, are only poorly developed. Since subsequent image processing of electron diffraction patterns or real space images can never compensate for the loss of phase information, the phase has to be recorded also, i.e. one has to work holographically to collect and reconstruct all data of the object structure.
On-Line Aberration Measurement and Correction in STEM
Authors: Krivanek Ondrej L , Dellby Niklas , Spence Andrew J , Camps Roger A , Michael Brown L 
Published: July 2020

Abstract
Aberration correction in electron microscopy is a subject with a 60 year history dating back to the fundamental work of Scherzer. There have been several partial successes, such as Deltrap's spherical aberration (Cs) corrector which nulled Cs over 30 years ago. However, the practical goal of attaining better resolution than the best uncorrected microscope operating at the same voltage remains to be fulfilled. Combining well-known electron-optical principles with stable electronics, versatile computer control, and software able to diagnose and correct aberrations on-line is at last bringing this goal within reach.
We are building a quadrupole-octupole Cs corrector with automated aberration diagnosis for a VG HB5 dedicated scanning transmission electron microscope (STEM). A STEM with no spherical aberration will produce a smaller probe size with a given beam current than an uncorrected STEM, and a larger beam current in a given size probe.
Field of View and Image Distortion : A Review of Low Magnification Imaging In the Environmental and Conventional Scanning Electron Microscopes (SEM)
Authors: Griffin Brendan J 
Published: July 2020

Abstract
Most scanning electron microscopy is performed at low magnification; applications utilising the large depth of field nature of the SEM image rather than the high resolution aspect. Some environmental SEMs have a particular limitation in that the field of view is restricted by a pressure limiting aperture (PLA) at the beam entry point of the specimen chamber. With the original ElectroScan design, the E-3 model ESEM utilised a 500 urn aperture which gave a very limited field of view (∼550um diameter at a 10mm working distance [WD]). An increase of aperture size to ∼lmm provided an improved but still unsatisfactory field of view. The simplest option to increase the field of view in an ESEM was noted to be a movement of the pressure and field, limiting aperture back towards the scan coils1. This approach increased the field of view to ∼2mm, at a 10mm WD. A commercial low magnification device extended this concept and indicated the attainment of conventional fields of view.
Comparison of Amplification and Imaging Behaviours of Several Gases In The Environmental Sem
Authors: Thiel BL , Fletcher AL , Donald AM 
Published: July 2020

Abstract
We have investigated the amplification properties of several imaging gases in the Environmental SEM (ESEM) with the intent of forming a set of general guidelines for the selection of gases. In the ElectroScan ESEM, a gas ionisation cascade is used to amplify the secondary electron signals emanating from the specimen surface. The presence of gas in the chamber also gives rise to a pressure dependent background signal derived from ionisation events between gas molecules and high energy primary beam and backscattered electrons. The fraction of secondary electron signal decreases as the pressure is raised. This point is illustrated in figures la and lb which show the calculated fraction of signal contributed by secondary, backscattered, and primary electrons as a function of pressure in helium and water vapour. Helium yields a very pure secondary electron signal over the entire range of pressures shown. Unfortunately, helium does not provide a great deal of signal amplification compared to water vapour (figure 2).
A New Mechanism for the Imaging of Crystal Structure in Non-Conductive Materials: An Application of Charge-Induced Contrast in the Environmental Scanning Electron Microscope (ESEM)
Authors: Griffin Brendan J 
Published: July 2020

Abstract
The mechanism of the contrast in ‘environmental’ or ‘gaseous’ secondary electron images in the environmental scanning electron microscope is at best poorly understood. The original theory suggested a simple gas amplification model in which emitted secondary electrons ionise the chamber gas, leading to signal amplification and finally measurement at a biased detector. This theory is being advanced but little attention has as yet been paid to the factors which influence the actual secondary emission, although unusual contrast effects have been noted in one case. The conven-tional view is that the positive ion product of the gas-electron interaction results in charge neu-tralisation at the sample surface.
The implantation and trapping of charge in non-conductive materials was recently described, in reference to electron range measurements. This work demonstrated that trapped charge influ-enced the secondary electron yield, with enhanced secondary electron emission above the region of trapped charge. The consequence is that the distribution of the trapped charge is seen as a bright circle on the surface of the specimen, centred on the point of beam exposure (Fig.l).
Application of ESEM/Eds to Pharmaceutical Synthesis
Authors: Carlton R A , Orton E , Lyman C E 
Published: July 2020

Abstract
Solid phase synthesis (SPS) is used for the discovery and optimization of biologically active substances for the pharmaceutical and agricultural industries. Large numbers of novel organic compounds are generated by successively adding functional groups onto a solid substrate - usually polystyrene. Several techniques have been applied to the qualitative and quantitative analysis of these polymer-bound compounds with varying success. Environmental scanning electron microscopy (ESEM) with energy dispersive x-ray spectrometry (EDS) offers a unique approach to the qualitative analysis of SPS resins. Heteroatoms (such as Cl, Br, and S) are added either as a part of the synthesis or as a marker for analysis. Heavier atoms, such as these, are easily detected by EDS. The advantages of EDS are speed, sensitivity, and small required weight of the sample. The advantages of the ESEM are that it eliminates the need for a conductive coating and the vacuum conditions are not as severe on the specimen as with a conventional SEM.