Abstract: Publication date: Available online 24 April 2017 Source:Advances in Imaging and Electron Physics Author(s): John C.H. Spence The recent invention of the X-ray laser (XFEL), with its high spatial coherence and ability to outrun radiation damage, has provided unprecedented new opportunities for structural biology. Here, we review the challenges and advances which have occurred over the past 7 years since the first beamtimes, provide their historical context, and describe the underlying principles of the new techniques used and the XFEL. The main focus is on the achievements and prospects for imaging protein dynamics at near-atomic spatial resolution under physiological and controlled chemical conditions, in the correct thermal bath, and a summary of the many approaches to this aim. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mixing jets, caged molecules, pH jump, and other reaction initiation methods, and the thermodynamics of molecular machines are all discussed, in addition to data analysis methods for all the instrumental modes. The ability of the XFEL to separate chemical reaction effects in dynamical imaging from radiation-induced effects (by minimizing these), while imaging at the physiological temperatures required for molecular machines, is highlighted.

Abstract: Publication date: Available online 20 April 2017 Source:Advances in Imaging and Electron Physics Author(s): Christopher J. Edgcombe A brief survey is given of prespecimen plates used to generate vortex beams, followed by some details of postspecimen plates as now used to provide image intensity modulation from phase objects. Spectral transfer theory applied to some simple model systems shows that the maximum size of object that can be imaged accurately with the Zernike plate depends not only on the object diameter but also on the system parameters. Further analysis suggests that when a Hilbert plate is located exactly on the cylindrical axis, the usual choice of an added phase of π minimizes the linear response of intensity to the phase of a weak-phase object. A linear response may be available if the added phase is reduced to π/2.

Authors:Inder Jeet Taneja Abstract: Publication date: Available online 20 March 2017 Source:Advances in Imaging and Electron Physics Author(s): Inder Jeet Taneja In the literature on information theory, there exist many divergence measures. These are known by Jensen difference divergence measure, J-Divergence, and arithmetic and geometric mean divergence. These are symmetric in pair of probability distributions. There is an interesting inequality relating these measures. These are with logarithmic expressions. Still there are measures without logarithmic expressions, known as, Hellinger's distance, triangular discrimination, etc. All these measures can be unified in three different parametric generalizations having much more particular cases. On the other sides, arithmetic, geometric, harmonic, square-root means, etc. are also well famous mathematics. In parametric situation, generalized Gini-mean is also known in literature. We can create new measures by using the idea of difference of means arising due to inequalities among these means. The same can also be done with difference of divergence measures. The aim of this work is to relate these differences arising due to inequalities among the divergence measures and means, and to find relations among them. Refinement inequalities are also studied.

Authors:Ivan Lazić; Eric G.T. Bosch Abstract: Publication date: Available online 11 March 2017 Source:Advances in Imaging and Electron Physics Author(s): Ivan Lazić, Eric G.T. Bosch Scanning transmission electron microscopy (STEM) imaging, which has been in use for many decades, is analyzed mathematically for thin nonmagnetic samples. The result is a closed-form description of a general STEM image, showing that STEM imaging is, in general, nonlinear (contrast transfer is sample dependent), except when an ideal first moment detector is used. The closed-form description is subsequently used to optimize STEM imaging. We distinguish between STEM techniques using symmetric scalar detectors and antisymmetric vector detectors and show that for both cases practical experimental techniques can be defined that are approximately linear. The case of antisymmetric vector detectors yields the newly introduced integrated differential phase contrast (iDPC-STEM) technique. For this technique we show experimental results, showing that it is capable of imaging light and heavy elements together as well as giving full low-frequency transfer. We demonstrate that it can be used under low-dose conditions.

Authors:Mai Xu; Jie Ren; Zulin Wang Abstract: Publication date: Available online 6 March 2017 Source:Advances in Imaging and Electron Physics Author(s): Mai Xu, Jie Ren, Zulin Wang This chapter addresses the problem of identifying and interpreting the components (e.g., balconies and windows) of the 3D model of a building. First, a voting scheme is presented for solving the problem of component identification in the 3D model. It is intuitive that interferences, such as occlusions, rarely happen at the same place nor at different times, when a person looks at a scene from different directions. In the spirit of this intuition, the voting scheme combines the information from various multiple view images to identify and segment the components of a building. For the component identification task, we use (from 3 to 11 views per building) multiple view images with short baselines in our experiments. Here, a priori 3D building model with a set of perpendicular and rectangular planes is set up for the identification task. The experimental results show the effectiveness of our scheme in identifying the components of 3D models of several buildings. With the identified components, we can proceed to the interpreting stage using the proposed tower of knowledge (ToK) approach, which automatically labels 3D components of buildings. Specifically, ToK is designed for discovering and encoding the logic rules (such as functionalities) for labeling components of the 3D model of a building. Then, we show how to make decisions on labeling components using ToK and utility theory. In order to deal with the case of lacking training data for making such decisions, we introduce a recursive version of ToK. Finally, a prototype of labeling components of building scenes is employed for validating the proposed ToK approach.

Authors:Igor A. Kopaev; Dmitry Grinfeld; Mikhail A. Monastyrskiy; Roman S. Ablizen; Sergei S. Alimpiev; Andrei A. Trubitsyn Abstract: Publication date: Available online 28 February 2017 Source:Advances in Imaging and Electron Physics Author(s): Igor A. Kopaev, Dmitry Grinfeld, Mikhail A. Monastyrskiy, Roman S. Ablizen, Sergei S. Alimpiev, Andrei A. Trubitsyn A variational approach is proposed for simulation of equilibrium ion distributions in radiofrequency low-vacuum ion traps with allowance for the Coulomb interaction and collisions of ions with the buffer gas molecules. A unimodal thermodynamic functional (potential) is introduced, the Euler equation for which is equivalent to the Poisson equation for Coulomb field and the Boltzmann distribution for ion density. The original problem is thus reduced to minimization of this thermodynamic potential in a functional space. By using the potential theory and Fourier analysis, the infinite-dimensional minimization problem is further reduced to a relevant finite-dimensional quadratic programming problem, which is numerically solved by means of the conjugate gradient method. Special emphasis is given to the physical grounds underlying the numerical method proposed. Examples of 2D and 3D calculations are presented and discussed.

Authors:Luiz H.G. Tizei; Mathieu Kociak Abstract: Publication date: Available online 28 February 2017 Source:Advances in Imaging and Electron Physics Author(s): Luiz H.G. Tizei, Mathieu Kociak Quantum optics is a very active field, with applications such as quantum cryptography which had once though impossible. Surprisingly, quantum engineering is becoming nevertheless a reality. The basic building blocks of this emerging field, such as single-photon emitters, are typically few nanometer in size, if not smaller. Therefore subwavelength techniques are necessary. In this chapter, we review the very recent developments of cathodoluminescence in scanning transmission electron microscopy applied to quantum nanooptics. This chapter is intended mainly to electron microscopists that have no specific knowledge in either quantum optics or cathodoluminescence. We therefore review basics quantities of interest in nanooptics such as the time-correlation function and how they can be measured in practice. We then describe the basics of electron/matter/photon interaction relevant to the field of nanooptics and finish by describing recent experiments in the field.

Authors:Michael Haschke; Stephan Boehm Abstract: Publication date: Available online 20 February 2017 Source:Advances in Imaging and Electron Physics Author(s): Michael Haschke, Stephan Boehm Micro-X-ray fluorescence is an established analytical method that is used for approx. 15 years for a sensitive elemental analysis. It could be developed due to the availability of X-ray optics, in particular polycapillary optics which can concentrate divergent tube radiation to spot sizes down to the 10μm range. After the introduction of separate μ-XRF instruments, this excitation possibility becomes interesting for scanning electron microscopes (SEMs). SEMs typically are equipped with an energy-dispersive detector. Therefore, the X-ray excitation would expand its analytical performance. In particular the sensitivity for trace elements could be increased and the characterization of layer systems will be possible. Additionally, sample preparation would be easier and the sample stress by irradiation with high energetic radiation is reduced. A special benefit is the use of both electron- and X-ray-excited spectra for a combined quantification, and thus, a more complete material characterization is possible. The combination of light element analysis and trace detection improves quantification results.

Authors:N. Chandra; S. Parida Pages: 1 - 164 Abstract: Publication date: 2016 Source:Advances in Imaging and Electron Physics, Volume 196 Author(s): N. Chandra, S. Parida This chapter presents a review of recent theoretical investigations which combine studies in electron spectroscopy of gaseous atoms and molecules with those in quantum information science (QIS). The basic ingredient of QIS—which differentiates it from classical information science—is the presence of nonintuitive, nonlocal correlation (called entanglement) in a system of more than one particle wherein each of them possesses at least two distinct states which are superposable and can be accessed with equal probabilities. Absorption of a single photon of appropriate energy by an atom or a molecule can cause ejection of one, or simultaneously of more, primary electrons from a single electronic state; radiative, or nonradiative, spontaneous emissions from electronic states other than that of primary ejection. Properties of the states of two or more of such liberated particles are analyzed using the tools developed in QIS, as well as their utilities to the protocols developed in the later are considered. In order to see the influence of the spin–orbit interaction on the entanglement properties of the states of the generated particles, the analysis has been performed also by taking into account only the Coulomb interaction present in an atom or a molecule. This hybridization of electron spectroscopy with QIS provides, hitherto, unknown insight about the nature of interactions present in atoms and molecules, as well as entangled states of particles, which are equally, if not more, useful in performing the studies proposed thus far in QIS.

Authors:Clough A.I.; Kirkland Abstract: Publication date: 2016 Source:Advances in Imaging and Electron Physics, Volume 198 Author(s): R. Clough, A.I. Kirkland It is now possible to use a variety of complementary metal oxide semiconductor sensors to directly detect primary electrons at intermediate voltages in transmission electron microscopy. These sensors offer significantly improved performance compared to traditional indirectly coupled devices. This has been been particularly significant in applications of cryo-electron microscopy in the life sciences. This review initially defines the relevant performance metrics for direct electron detectors and experimental methods for measuring them. Subsequently, we describe the different sensor geometries and readout modes available and finally offer a brief comparison of currently available detectors.

Authors:Ph. Sciau Abstract: Publication date: Available online 13 October 2016 Source:Advances in Imaging and Electron Physics Author(s): Ph. Sciau Transmission electron microscopy (TEM), with its various imaging modes and analytical abilities, is now an indispensable tool for chemical and structural characterization at the nanoscale of all types of materials. Cultural heritage materials do not differ fundamentally from other materials except that they are more heterogeneous, with a more complex and imperfect structure. In addition, many of them contain nanoparticles or have a nanoscale structuration, which plays a significant role in their physical properties or is rich in information concerning their manufacture. TEM techniques are thus well suited to investigate them, especially because the developments of these last decades afford both a more efficient sample preparation and faster data recording.

Authors:T. Tanigaki; T. Akashi; Y. Takahashi; T. Kawasaki; H. Shinada Abstract: Publication date: Available online 6 October 2016 Source:Advances in Imaging and Electron Physics Author(s): T. Tanigaki, T. Akashi, Y. Takahashi, T. Kawasaki, H. Shinada Advances in high-resolution electron microscopy were reviewed in this chapter, including a description of an innovation of the electron microscope, early efforts in lattice fringe imaging, developments of a cold field emission (cold-FE) electron source, high-voltage electron microscopy, realization and progress of the aberration corrector, and an aberration-corrected, 1.2-MV, high-voltage transmission electron microscope (TEM). The last one was developed through the FIRST Tonomura Program. Its point resolution was 43pm in TEM imaging mode. It also has a magnetic-field-free sample position, and a point resolution of 0.24nm was obtained at that position. These capabilities offer researchers a new way to observe magnetic fields at atomic scale, which has become particularly important for the development of technologies for controlling electrons by utilizing their spins.

Authors:R. Castañeda; G. Matteucci; R. Capelli Abstract: Publication date: Available online 28 September 2016 Source:Advances in Imaging and Electron Physics Author(s): R. Castañeda, G. Matteucci, R. Capelli Interference of light and material particles is described in this chapter with a unified model, which does not need to assume the superposition principle. A moving particle is associated with a region of spatial correlated points called a coherence cone. Its geometry depends on photon or material particle momentum and on the parameters of the experimental setup. The coherence cone geometry causes the spatial distribution of particles in preferential directions. After propagation, particles accumulate on the final observation plane to form interference peaks. In the context given here, the wave front superposition principle, wave–particle duality, and wave collapse are no longer significant. In addition, the present model describes light and material particle distributions in near- and far-field regions and in paraxial and nonparaxial approximations so that the paraxial Fourier and Wigner optics are included, as particular cases, in our more general model. Fits of observed single-electron and single-molecule interference patterns, together with the simulations of expected near-field molecule interferences, demonstrate the model validity. An interference experiment is suggested to realize molecular nanostructures with a vacuum sublimation process controlled by a shadow mask. A new scenario is envisaged to miniaturize electronic devices and to realize individual noninteracting nanodomains of well-chosen thickness.

Authors:K. Edee; J.-P. Plumey; B. Guizal Abstract: Publication date: Available online 28 September 2016 Source:Advances in Imaging and Electron Physics Author(s): K. Edee, J.-P. Plumey, B. Guizal The purpose of this chapter is to present a unified theory for the numerical implementation of modal methods for the analysis of electromagnetic phenomena with specific boundary conditions. All the fundamental concepts that form the basis of our study will be detailed. In plasmonics and photonics in general, solving Maxwell equations involving irregular functions is common. For example, when the relative permittivity is a piecewise constant function describing a dielectric–metal interface, the eigenmodes of the propagation equation are solutions of Maxwell's equations subject to specific boundary conditions at the interfaces between homogenous media. Prior knowledge about the eigenmodes allows one to define more appropriate expansion functions, and the rate of convergence of the numerical scheme will depend on the choice of these functions. In this chapter, we present and explain, a unified numerical formalism that allows one to build, from a set of subsectional functions defined on a set of subintervals, expansion functions defined on a global domain by enforcing certain stresses deduced from electromagnetic field properties. Then numerical modal analysis of a plasmonic device, such as a ring resonator, is presented as an example of an application.

Authors:A. Lubk; K. Vogel; D. Wolf; J. Krehl; F. Röder; L. Clark; G. Guzzinati; J. Verbeeck Abstract: Publication date: Available online 23 September 2016 Source:Advances in Imaging and Electron Physics Author(s): A. Lubk, K. Vogel, D. Wolf, J. Krehl, F. Röder, L. Clark, G. Guzzinati, J. Verbeeck The loss of the quantum phase information in the measurement process constitutes a fundamental limitation to transmission electron microscopy as the electron wave's phase often contains valuable information about the studied specimen. Phase retrieval from focal series is a holographic technique that seeks to recover the lost information from a set of images recorded at different defoci. In spite of its widespread use, especially for wave reconstruction at atomic resolution, a number of fundamental properties (e.g., regarding the conditions for a unique wave function reconstruction) the magnitude of the reconstruction error and the influence of inconsistencies or incomplete data are not well understood. Here, we elaborate on the fundamentals of the technique, making extensive use of the tomographic representation of a focal series as tilt series in phase space. Using this perspective, we discuss, among others, requirements for the focal series for a unique reconstruction, such as the focus interval ranging from the far field at underfocus to the far field at overfocus or the focus step size. We reveal that the prominent Gerchberg–Saxton iterative projection algorithm corresponds to a numerical integration of the quantum Hamilton–Jacobi equation in the small focus step limit. Moreover, we show that the topology of the starting guess divides the solution space of the Gerchberg–Saxton algorithm into equivalence classes, which mitigates the impact of the incompleteness of typical focal series data. To facilitate a focal series reconstruction meeting these theoretical requirements, such as the long range focus interval, we develop a dedicated calibration procedure facilitating the determination of unknown electron optical parameters such as the focal length of the principal imaging lens or the position of object and image planes. The findings are demonstrated with an example of a focal series reconstruction of an electron vortex beam.

Authors:V.G. Dyukov; S.A. Nepijko; G. Schönhense Pages: 165 - 246 Abstract: Publication date: Available online 3 August 2016 Source:Advances in Imaging and Electron Physics Author(s): V.G. Dyukov, S.A. Nepijko, G. Schönhense Based on a general approach, we consider the regularities of forming contrast imaging of static and dynamic potential distribution on the surface of an object investigated with a scanning electron microscope (SEM). The feasibility of using specialized secondary electron detectors was demonstrated. The calculations were performed, showing the functional parameters of three detectors with different types of electron spectrometers. The design of a detector is described, which provides measurement accuracy close to the theoretical limit. The results presented have been obtained with a SEM equipped with such a detector. The investigated samples exhibit static potential distributions with comparatively low gradients. These include metallic thin films with nanoscale islands and doped micro-regions with planar p–n junctions in Si crystals, prepared by ion implantation with subsequent annealing. The possibility to estimate a defect formation rate from the contrast is demonstrated. The ways to realize dynamic potential contrast without utilizing stroboscopy are presented, based on the frequency conversions using the non-linearity of the detector-retarding curve. The distinctive features of progressive waves on a piezoelectric crystal surface were investigated.

Authors:T.L. Kirk Pages: 247 - 326 Abstract: Publication date: Available online 25 June 2016 Source:Advances in Imaging and Electron Physics Author(s): T.L. Kirk The use of low-energy electrons in the analysis of materials at the nanoscale will play a significant role in many research areas including biological, medical, data storage, computing, and renewable energy. This recent trend in these fields is to employ low-energy primary electrons for better resolution and specificity of the resulting analysis. Here, we will discuss the method we have implemented that combines the essential functionalities of two types of microscopies; thereby, creating a quite compact instrument that can readily be integrated into ultrahigh vacuum scanning probe microscopy systems. The close proximity between the source and the object provides a means of overcoming the limitations of conventional scanning electron microscopes and opens the possibility to use lower primary beam energies (<50eV). We have named this technique “near field emission scanning electron microscopy,” and this chapter will summarize the developmental phases of the device.