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We report on the automatic alignment of a transmission electron microscope equipped with an orbital angular momentum sorter using a convolutional neural network. The neural network is able to control all relevant parameters of both the electron-optical setup of the microscope and the external voltage source of the sorter without input from the user. It can compensate for mechanical and optical misalignments of the sorter, in order to optimize its spectral resolution. The alignment is completed over a few frames and can be kept stable by making use of the fast fitting time of the neural network.

The key to optimizing spatial resolution in a state-of-the-art scanning transmission electron microscope is the ability to precisely measure and correct for electron optical aberrations of the probe-forming lenses. Several diagnostic methods for aberration measurement and correction with maximum precision and accuracy have been proposed, albeit often at the cost of relatively long acquisition times. Here, we illustrate how artificial intelligence can be used to provide near-real-time diagnosis of aberrations from individual Ronchigrams. The demonstrated speed of aberration measurement is important as microscope conditions can change rapidly, as well as for the operation of MEMS-based hardware correction elements that have less intrinsic stability than conventional electromagnetic lenses., Comment: 18 pages, 5 figures, 1 table

•A deep convolutional neural network is used to evaluate and correct the alignment of an orbital angular momentum sorter.•The convolutional neural network automatically analyses OAM spectra at a rate of 50 ms/spectrum, allowing for real time implementation.•The method is easily transferable to any programmable beam shaping technique. A convolutional neural network is used to align an orbital angular momentum sorter in a transmission electron microscope. The method is demonstrated using simulations and experiments. As a result of its accuracy and speed, it offers the possibility of real-time tuning of other electron optical devices and electron beam shaping configurations.

The orbital angular momentum (OAM) sorter is a new electron optical device for measuring an electron s OAM. It is based on two phase elements, which are referred to as the unwrapper and corrector and are placed in Fourier conjugate planes in an electron microscope. The most convenient implementation of this concept is based on the use of electrostatic phase elements, such as a charged needle as the unwrapper and a set of electrodes with alternating charges as the corrector. Here, we use simulations to assess the role of imperfections in such a device, in comparison to an ideal sorter. We show that the finite length of the needle and the boundary conditions introduce astigmatism, which leads to detrimental cross-talk in the OAM spectrum. We demonstrate that an improved setup comprising three charged needles can be used to compensate for this aberration, allowing measurements with a level of cross-talk in the OAM spectrum that is comparable to the ideal case.

How the Observation in a New Custom Basis Based on Orbital Angular Momentum Space Could Improve Our Dose Effective Reconstruction of the Protein Structure. - Filippo Troiani, Enzo Rotunno, Stefano Frabboni, Raimond Ravelli, Peter Peters, Ebrahim Karimi, Vincenzo Grillo

Electron energy-loss spectroscopy (EELS) is a powerful technique for measuring the energy state of electrons after scattering. It has had incredible success in measuring the atomic and chemical properties of materials, allowing chemical maps to be recorded with atomic spatial resolution. Energy information alone is often sufficient to obtain information about chemical species, plasmons or even phonon excitations, especially when using high-energy-resolution spectrometers and gun monochromators. However, it is sometimes desirable to add a second dispersion variable, either in the form of momentum and energy double-dispersion EELS, or by acquiring a spectrum for a given momentum transfer.

The theoretical possibility to use an electron microscope as a spin polarizer is studied. It turns out that a Bessel beam passing a standard magnetic objective lens is intrinsically spin polarized when post-selected on-axis. In the limit of infinitely small detectors, the spin polarisation tends to 100%. Increasing the detector size, the polarisation decreases rapidly, dropping below 10-4 for standard settings of medium voltage microscopes. For extremely low voltages, the Figure of Merit increases by two orders of magnitude, approaching that of existing Mott detectors. Our findings may lead to new desings of spin filters, an attractive option in view of its inherent combination with the electron microscope, especially at low voltage.

The propagation of an electron beam in the presence of transverse magnetic fields possessing integer topological charges is presented. The spin-magnetic interaction introduces a nonuniform spin precession of the electrons that gains a space-variant geometrical phase in the transverse plane proportional to the field's topological charge, whose handedness depends on the input electron's spin state. A combination of our proposed device with an electron orbital angular momentum sorter can be utilized as a spin-filter of electron beams in a mid-energy range. We examine these two different configurations of a partial spin-filter generator numerically. The results of this analysis could prove useful in the design of an improved electron microscope. © 2013 Elsevier B.V.

This paper reports on a novel approach to quantitatively reconstruct the column by column composition and the 3D distribution of guest atoms inside a host matrix by scanning transmission electron microscopy high angle annular dark field technique. We propose a new mathematical framework that allows to jointly analyze the information from a set of experiments with variable beam convergence and/or defocus. Our scheme allows to reconstruct the atomic distribution along the imaged columns from the measured intensity, for any dependence of the probe intensity on the depth. It is therefore well suited to incorporate channeling effects that are usually neglected in other approaches. As a case study, we focus here on the systematic variation of the beam convergence that permits to set the maximum of the channeling oscillations at different depths. We aim here to define the reliability and the limitation of this technique by the application of the method to accurate dynamic simulations in the case of the InGaN alloy. © 2014 Elsevier B.V.

We report a systematic treatment of the holographic generation of electron Bessel beams, with a view to applications in electron microscopy. We describe in detail the theory underlying hologram patterning, as well as the actual electro-optical configuration used experimentally. We show that by optimizing our nanofabrication recipe, electron Bessel beams can be generated with efficiencies reaching $37 \pm 3\%$. We also demonstrate by tuning various hologram parameters that electron Bessel beams can be produced with many visible rings, making them ideal for interferometric applications, or in more highly localized forms with fewer rings, more suitable for imaging. We describe the settings required to tune beam localization in this way, and explore beam and hologram configurations that allow the convergences and topological charges of electron Bessel beams to be controlled. We also characterize the phase structure of the Bessel beams generated with our technique, using a simulation procedure that accounts for imperfections in the hologram manufacturing process. Finally, we discuss a specific potential application of electron Bessel beams in scanning transmission electron microscopy.

The study of structured optical waves has enhanced our understanding of light and numerous experimental methods now enable the control of the angular momentum and radial distributions. Recently, these wavestructuring techniques have been successfully applied to the generation and shaping of electron beams, leading to promising practical and fundamental advances. Here, we discuss recent progress in the emerging field of electron beam shaping, and explore the unique attributes that distinguish electron beams from their photonic analogues.

Recent advances in transmission electron microscopy and specimen preparation now permit the revival of an old idea, originally pioneered by Marton, of using single crystals as amplitude division beam splitters. As a first step in the direction of realizing a three crystal electron interferometer, we present results obtained from a double crystal interferometer, in which the gap between the two crystals is under experimental control and perfect registry is obtained by using focused ion beam milling to fabricate the interferometer from a single Si crystal. Published version

Modern nanotechnology tools allowed us to prepare slits of 90 nm width and 450 nm spacing in a screen almost completely opaque to 200 keV electrons. Then by covering both slits with a layer of amorphous material and carrying out the experiment in a conventional transmission electron microscope equipped with an energy filter we can demonstrate that the diffraction pattern, taken by selecting the elastically scattered electrons, shows the presence of interference fringes, but with a bimodal envelope which can be accounted for by taking into account the non-constant thickness of the deposited layer. However, the intensity of the inelastically scattered electrons in the diffraction plane is very broad and at the limit of detectability. Therefore the experiment was repeated using an aluminum film and a microscope also equipped with a Schottky field emission gun. It was thus possible to observe also the image due to the inelastically scattered electron, which does not show interference phenomena both in the Fraunhofer or Fresnel regimes. If we assume that inelastic scattering through the thin layer covering the slits provides the dissipative process of interaction responsible for the localization mechanism, then these experiments can be considered a variant of the Feynman which-way thought experiment. (C) 2015 Elsevier B.V. All rights reserved.

Free electrons can possess an intrinsic orbital angular momentum, similar to those in an electron cloud, upon free-space propagation. The wavefront corresponding to the electron's wavefunction forms a helical structure with a number of twists given by the \emph{angular speed}. Beams with a high number of twists are of particular interest because they carry a high magnetic moment about the propagation axis. Among several different techniques, electron holography seems to be a promising approach to shape a \emph{conventional} electron beam into a helical form with large values of angular momentum. Here, we propose and manufacture a nano-fabricated phase hologram for generating a beam of this kind with an orbital angular momentum up to 200$\hbar$. Based on a novel technique the value of orbital angular momentum of the generated beam are measured, then compared with simulations. Our work, apart from the technological achievements, may lead to a way of generating electron beams with a high quanta of magnetic moment along the propagation direction, and thus may be used in the study of the magnetic properties of materials and for manipulating nano-particles., Comment: 4 pages, 4 figures - Supplementary Material (3 pages and 2 figures) accompanies this manuscript

A new graphical software (STEM_CELL) for analysis of HRTEM and STEM-HAADF images is here introduced in detail. The advantage of the software, beyond its graphic interface, is to put together different analysis algorithms and simulation (described in an associated article) to produce novel analysis methodologies. Different implementations and improvements to state of the art approach are reported in the image analysis, filtering, normalization, background subtraction. In particular two important methodological results are here highlighted: (i) the definition of a procedure for atomic scale quantitative analysis of HAADF images, (ii) the extension of geometric phase analysis to large regions up to potentially 1 μm through the use of under sampled images with aliasing effects.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

1. CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/a, I-41125 Modena, Italy 2. CNR-IMEM, Parco delle Scienze 37a, I-43100 Parma, Italy 3. Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5, Canada 4. CNR-IMM Bologna, Via P. Gobetti 101, 40129 Bologna, Italy 5. Dipartimento FIM, Universita di Modena e Reggio Emilia, Via G. Campi 213/a, 41125 Modena, Italy 6. Institute of Optics, University of Rochester, Rochester, New York 14627, USA

In this work the effects of strain on high-angle annular dark field (HAADF) images taken in zone axis conditions have been quantitatively studied. In particular, the presence of dark contrast zones in experimental HAADF images of InGaAs-GaAs interfaces is here interpreted in terms of strain relaxation at the surface. The consistence of this assumption is demonstrated by means of experiments and simulations performed for different In compositions, specimen tilt and thickness conditions. It is shown how the HAADF contrast mechanism is related to the bending of the lattice planes in the first surface region. Finally, a generalization of the 1s approximation that is able to qualitatively describe the effect of strain on HAADF images is presented.

Analysis of the Fourier components of through-focal images in scanning transmission electron microscopy with a high angle annular dark field detector is used to assess illumination defocus values. The method is based on a least squares fitting of the peculiar dependence of Fourier components of the high angle annular dark field image on defocus. The validity of the method has been checked against simulations and experiments obtaining a good level of accuracy on the defocus measurement (delta f = 2 nm) for simulated specimen thickness up to 40 nm. The difference between simulated and experimental Fourier coefficients for large defoci can be used to estimate the specimen thickness at least up to 30 nm but with decreasing precision for larger thickness. (c) 2006 Elsevier B.V. All rights reserved.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Alternative single-particle cryo-EM schemes are reviewed, in order to improve dose efficiency for obtaining more or complementary structure information within the limited lifetime of the sample., Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.

Competitive mechanisms contribute to image contrast from dislocations in annular dark-field scanningtransmission electron microscopy(ADF-STEM). A clear theoretical understanding of the mechanisms underlying the ADF-STEM contrast is therefore essential for correct interpretation of dislocation images. This paper reports on a systematic study of the ADF-STEM contrast from dislocations in a GaN specimen, both experimentally and computationally. Systematic experimental ADF-STEM images of the edge-character dislocations reveal a number of characteristic contrast features that are shown to depend on both the angular detection range and specific position of the dislocation in the sample. A theoretical model based on electron channelling and Bloch-wave scattering theories, supported by numerical simulations based on Grillo's strain-channelling equation, is proposed to elucidate the physical origin of such complex contrast phenomena.