A software tool for automatic analysis of selected area diffraction patterns within Digital Micrograph™

Automatic center identification of electron diffraction with multi-scale transformer networks

Selected area electron diffraction (SAED) is a widely used technique for characterizing the structure and measuring lattice parameters of materials. An autonomous analytic method has become an urgent demand for the large-scale SAED data produced from in-situ experiments. In this work, we realize the automatic processing for center identification with a proposed deep segmentation model named the multi-scale Transformer (MS-Trans) network. This algorithm enables robust segmentation of the central spots by combining a novel gated axial-attention module and multi-scale feature fusion. The proposed MS-Trans model shows high precision and robustness, enabling autonomous processing of SAED patterns without any prior knowledge. The application on in-situ SAED data of the oxidation process of FeNi alloy demonstrates its capability of implementing autonomous quantitative processing. © 2017 Elsevier Inc. All rights reserved.

Classification of crystal structures using electron diffraction patterns with a deep convolutional neural network

Investigations have been made to explore the applicability of an off-the-shelf deep convolutional neural network (DCNN) architecture, residual neural network (ResNet), to the classification of the crystal structure of materials using electron diffraction patterns without prior knowledge of the material systems under consideration. The dataset required for training and validating the ResNet architectures was obtained by the computer simulation of the selected area electron diffraction (SAD) in transmission electron microscopy. Acceleration voltages, zone axes, and camera lengths were used as variables and crystal information format (CIF) files obtained from open crystal data repositories were used as inputs. The cubic crystal system was chosen as a model system and five space groups of 213, 221, 225, 227, and 229 in the cubic system were selected for the test and validation, based on the distinguishability of the SAD patterns. The simulated diffraction patterns were regrouped and labeled from the viewpoint of computer vision, i.e., the way how the neural network recognizes the two-dimensional representation of three-dimensional lattice structure of crystals, for improved training and classification efficiency. Comparison of the various ResNet architectures with varying number of layers demonstrated that the ResNet101 architecture could classify the space groups with the validation accuracy of 92.607%.

The off-the-shelf deep convolutional neural network architecture, ResNet, could classify the space group of materials with cubic crystal structures with the prediction accuracy of 92.607%, using the selected area electron diffraction patterns.

pycotem: An open source toolbox for online crystal defect characterization from TEM imaging and diffraction

We present a series of tools working together that facilitate the determination of dislocation Burgers vectors and slip planes, interface plane normals and misorientation between two crystals from a series of Transmission Electron Microscopy (TEM) micrographs and diffraction patterns. To that purpose, we developed graphical user interface programs that allow crystal orientation determination from spot diffraction patterns taken at various tilt angles or from Kikuchi patterns crystal representation from stereographic projection plots and determination of geometrical features from series of conventional images taken at different tilt angles. We present working examples that allow a faster and easier way to analyse data that can especially be retrieved during in situ straining experiments where dislocations and grain boundaries need to be characterized. More generally, these tools target material scientists interested in daily microstructural characterization in TEM.

τompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopy

τompas (TEM online multi-purpose analyzing system) is a free and integrated software tool designed to perform online crystallographic analysis in transmission electron microscopy (TEM) experiments. By using sample holder tilt angles as input, τompas can simultaneously simulate pole figures, Kikuchi patterns and feature projections, providing graphical views of the sample crystallography. These simulations are further employed to navigate sample tilting and to quickly interpret experimental Kikuchi patterns and images by image matching, giving self-consistent indices of features and crystal orientations. These functions are integrated with mouse operations to improve work efficiency. τompas is distributed as a small cross-platform program that can be installed on a microscope computer to cooperate with other tools.

A simple program for fast tilting electron-beam sensitive crystals to zone axes

Tilting crystals to proper zone axes is a necessary but tedious work in taking selected area electron diffraction patterns (SAED) and high-resolution images using transmission electron microscope (TEM). This process not only costs a lot of time but also limits the application of TEM in electron-beam sensitive materials. Therefore, it is desirable to develop a simple method for tilting crystals from random orientations to a specific zone axis quickly. Herein, we describe a novel program, Zones, which can index the electron diffraction pattern and calculate the tilting angles of a double-tilt sample holder from the current orientation to a desired zone axis. It can also bring crystals that are slightly deviated from a zone axis to the exact zone with the help of Laue ring in the diffraction pattern. This program has been successfully applied to studies of zeolites and metal-organic frameworks (MOFs), known as being electron-beam sensitive. The program shows its power not only in saving the operator's time but also in preventing the crystals from quick beam damages.

Pattern Center and Distortion Determined from Faint, Diffuse Electron Diffraction Rings from Amorphous Materials

Diffuse rings from amorphous materials sit on a steep background resulting in a monotonically decreasing intensity over scattering vector length, frequently with no clear local maximum that could be used to determine the center of the ring. The novelty of the method reported here is that it successful processes such weak patterns. It is based on separating the angular dependence of the positions of the maxima on the azimuthal angle in the measured two-dimensional pattern for a manually preselected peak. Both pattern center and elliptical distortion are simultaneously refined from this angular dependence. Both steps are based on nonlinear least square fitting, using the Levenberg-Marquardt method. It can be successfully applied to any amorphous patterns provided they were recorded with experimental conditions that facilitate dividing them into sectors with acceptable statistics. Patterns with the center shifted to the camera corner (recording a quadrant of a ring) can also be reliably evaluated, keeping precalibrated values of the elliptical distortion fixed during the fit. Finally, the limited number of counts in any pattern is overcome by cumulating many patterns (from equivalent areas) into a single pattern. Eliminating false effects is facilitated by masking out unwanted parts of any recorded pattern from processing.

Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographers

Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.).

Integrated approaches of x-ray absorption spectroscopic and electron microscopic techniques on zinc speciation and characterization in a final sewage sludge product

Integration of complementary techniques can be powerful for the investigation of metal speciation and characterization in complex and heterogeneous environmental samples, such as sewage sludge products. In the present study, we combined analytical transmission electron microscopy (TEM)-based techniques with X-ray absorption spectroscopy (XAS) to identify and characterize nanocrystalline zinc sulfide (ZnS), considered to be the dominant Zn-containing phase in the final stage of sewage sludge material of a full-scale municipal wastewater treatment plant. We also developed sample preparation procedures to preserve the organic and sulfur-rich nature of sewage sludge matrices for microscopic and spectroscopic analyses. Analytical TEM results indicate individual ZnS nanocrystals to be in the size range of 2.5 to 7.5 nm in diameter, forming aggregates of a few hundred nanometers. Observed lattice spacings match sphalerite. The ratio of S to Zn for the ZnS nanocrystals is estimated to be 1.4, suggesting that S is present in excess. The XAS results on the Zn speciation in the bulk sludge material also support the TEM observation that approximately 80% of the total Zn has the local structure of a 3-nm ZnS nanoparticle reference material. Because sewage sludge is frequently used as a soil amendment on agricultural lands, future studies that investigate the oxidative dissolution rate of ZnS nanoparticles as a function of size and aggregation state and the change of Zn speciation during post sludge-processing and soil residency are warranted to help determine the bioavailability of sludge-born Zn in the soil environment.

Simultaneous tetralin HDA and dibenzothiophene HDS reactions on NiMo bulk sulphide catalysts obtained from mixed oxides

Large selectivity differences were found between supported and unsupported NiMoS catalysts in dibenzothiophene HDS and tetralin HDA.