Convexity constraints on linear background models for electron energy-loss spectra.

In this paper convexity constraints are derived for a background model of electron energy loss spectra (EELS) that is linear in the fitting parameters. The model outperforms a power-law both on experimental and simulated backgrounds, especially for wide energy ranges, and thus improves elemental quantification results. Owing to the model's linearity, the constraints can be imposed through fitting by quadratic programming. This has important advantages over conventional nonlinear power-law fitting such as high speed and a guaranteed unique solution without need for initial parameters. As such, the need for user input is significantly reduced, which is essential for unsupervised treatment of large datasets. This is demonstrated on a demanding spectrum image of a semiconductor device sample with a high number of elements over a wide energy range.

Deep reinforcement learning for data-driven adaptive scanning in ptychography.

We present a method that lowers the dose required for an electron ptychographic reconstruction by adaptively scanning the specimen, thereby providing the required spatial information redundancy in the regions of highest importance. The proposed method is built upon a deep learning model that is trained by reinforcement learning, using prior knowledge of the specimen structure from training data sets. We show that using adaptive scanning for electron ptychography outperforms alternative low-dose ptychography experiments in terms of reconstruction resolution and quality.

Synergistic use of gradient flipping and phase prediction for inline electron holography.

Inline holography in the transmission electron microscope is a versatile technique which provides real-space phase information that can be used for the correction of imaging aberrations, as well as for measuring electric and magnetic fields and strain distributions. It is able to recover high-spatial-frequency contributions of the phase effectively but suffers from the weak transfer of low-spatial-frequency information, as well as from incoherent scattering. Here, we combine gradient flipping and phase prediction in an iterative flux-preserving focal series reconstruction algorithm with incoherent background subtraction that gives extensive access to the missing low spatial frequencies. A procedure for optimizing the reconstruction parameters is presented, and results from Fe-filled C nanospheres, and MgO cubes are compared with phase images obtained using off-axis holography.

Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization.

The overdetermination of the mathematical problem underlying ptychography is reduced by a host of experimentally more desirable settings. Furthermore, reconstruction of the sample-induced phase shift is typically limited by uncertainty in the experimental parameters and finite sample thicknesses. Presented is a conjugate gradient descent algorithm, regularized optimization for ptychography (ROP), that recovers the partially known experimental parameters along with the phase shift, improves resolution by incorporating the multislice formalism to treat finite sample thicknesses, and includes regularization in the optimization process, thus achieving reliable results from noisy data with severely reduced and underdetermined information.

Inverse dynamical photon scattering (IDPS): an artificial neural network based algorithm for three-dimensional quantitative imaging in optical microscopy.

Inverse dynamical photon scattering (IDPS), an artificial neural network based algorithm for three-dimensional quantitative imaging in optical microscopy, is introduced. Because the inverse problem entails numerical minimization of an explicit error metric, it becomes possible to freely choose a more robust metric, to introduce regularization of the solution, and to retrieve unknown experimental settings or microscope values, while the starting guess is simply set to zero. The regularization is accomplished through an alternate directions augmented Lagrangian approach, implemented on a graphics processing unit. These improvements are demonstrated on open source experimental data, retrieving three-dimensional amplitude and phase for a thick specimen.

A novel quasi-one-dimensional topological insulator in bismuth iodide ß-Bi4I4.

Recent progress in the field of topological states of matter has largely been initiated by the discovery of bismuth and antimony chalcogenide bulk topological insulators (TIs; refs ,,,), followed by closely related ternary compounds and predictions of several weak TIs (refs ,,). However, both the conceptual richness of Z2 classification of TIs as well as their structural and compositional diversity are far from being fully exploited. Here, a new Z2 topological insulator is theoretically predicted and experimentally confirmed in the ß-phase of quasi-one-dimensional bismuth iodide Bi4I4. The electronic structure of ß-Bi4I4, characterized by Z2 invariants (1;110), is in proximity of both the weak TI phase (0;001) and the trivial insulator phase (0;000). Our angle-resolved photoemission spectroscopy measurements performed on the (001) surface reveal a highly anisotropic band-crossing feature located at the  point of the surface Brillouin zone and showing no dispersion with the photon energy, thus being fully consistent with the theoretical prediction.

Quantitative electron tomography: the effect of the three-dimensional point spread function.

The intensity levels in a three-dimensional (3D) reconstruction, obtained by electron tomography, can be influenced by several experimental imperfections. Such artifacts will hamper a quantitative interpretation of the results. In this paper, we will correct for artificial intensity variations by determining the 3D point spread function (PSF) of a tomographic reconstruction based on high angle annular dark field scanning transmission electron microscopy. The large tails of the PSF cause an underestimation of the intensity of smaller particles, which in turn hampers an accurate radius estimate. Here, the error introduced by the PSF is quantified and corrected a posteriori.

Atomic-scale determination of surface facets in gold nanorods.

It is widely accepted that the physical properties of nanostructures depend on the type of surface facets. For Au nanorods, the surface facets have a major influence on crucial effects such as reactivity and ligand adsorption and there has been controversy regarding facet indexing. Aberration-corrected electron microscopy is the ideal technique to study the atomic structure of nanomaterials. However, these images correspond to two-dimensional (2D) projections of 3D nano-objects, leading to an incomplete characterization. Recently, much progress was achieved in the field of atomic-resolution electron tomography, but it is still far from being a routinely used technique. Here we propose a methodology to measure the 3D atomic structure of free-standing nanoparticles, which we apply to characterize the surface facets of Au nanorods. This methodology is applicable to a broad range of nanocrystals, leading to unique insights concerning the connection between the structure and properties of nanostructures.

A holographic method to measure the source size broadening in STEM.

Source size broadening is an important resolution limiting effect in modern STEM experiments. Here, we propose an alternative method to measure the source size broadening making use of a holographic biprism to create interference patterns in an 'empty' Ronchigram. This allows us to measure the exact shape of the source size broadening with a much better sampling than previously possible. We find that the shape of the demagnified source deviates considerably from a Gaussian profile that is often assumed. We fit the profile with a linear combination of a Gaussian and a bivariate Cauchy distribution showing that even though the full width at half maximum is similar to previously reported measurements, the tails of the profile are considerable wider. This is of fundamental importance for quantitative comparison of STEM simulations with experiments as these tails make the image contrast dependent on the interatomic distance, an effect that cannot be reproduced by a single Gaussian profile of fixed width alone.

Method for retrieval of the three-dimensional object potential by inversion of dynamical electron scattering.

Dynamical scattering of fast electrons can be inverted by recasting the multislice algorithm as an artificial neural network, enabling the iterative retrieval of the three-dimensional object potential. This allows a nonheuristic treatment of the modulation transfer function of the CCD, partial spatial and temporal coherence, and inelastic scattering through an absorptive potential. Furthermore, prior knowledge about the atomic potential shape and the sparseness and positivity of the object can be used. The method is demonstrated on simulated bright field images recorded at 40 kV.

Introducing measure-by-wire, the systematic use of systems and control theory in transmission electron microscopy.

Transmission electron microscopes (TEMs) are the tools of choice for academic and industrial research at the nano-scale. Due to their increasing use for routine, repetitive measurement tasks (e.g., quality control in production lines) there is a clear need for a new generation of high-throughput microscopes designed to autonomously extract information from specimens (e.g., particle size distribution, chemical composition, structural information, etc.). To aid in their development, a new engineering perspective on TEM design, based on principles from systems and control theory, is proposed here: measure-by-wire (not to be confused with remote microscopy). Under this perspective, the TEM operator yields the direct control of the microscope's internal processes to a hierarchy of feedback controllers and high-level supervisors. These make use of dynamical models of the main TEM components together with currently available measurement techniques to automate processes such as defocus correction or specimen displacement. Measure-by-wire is discussed in depth, and its methodology is illustrated through a detailed example: the design of a defocus regulator, a type of feedback controller that is akin to existing autofocus procedures.

A practical method to determine the effective resolution in incoherent experimental electron tomography.

It is not straightforward to determine resolution for a 3D reconstruction when performing an electron tomography experiment. Different contributions such as missing wedge and misalignment add up and often influence the final resolution in an anisotropic manner. The conventional resolution measures can not be used for all of the reconstruction techniques, especially for iterative techniques which are more commonly used for electron tomography in materials science. Here we define a quantitative resolution measure that determines the resolution in three orthogonal directions of the reconstruction. As an application we use this measure to determine the optimum number of simultaneous iterative reconstruction technique (SIRT) iterations to reconstruct the gold nanoparticles, based on a high angle annular dark field STEM (HAADF-STEM) tilt series.