Huolin L. Xin

Robert Hovden, Yi Jiang, Huolin L. Xin et al.

The discrete Fourier transform is among the most routine tools used in high-resolution scanning / transmission electron microscopy (S/TEM). However, when calculating a Fourier transform, periodic boundary conditions are imposed and sharp discontinuities between the edges of an image cause a cross patterned artifact along the reciprocal space axes. This artifact can interfere with the analysis of reciprocal lattice peaks of an atomic resolution image. Here we demonstrate that the recently developed Periodic Plus Smooth Decomposition technique provides a simple, efficient method for reliable removal of artifacts caused by edge discontinuities. In this method, edge artifacts are reduced by subtracting a smooth background that solves Poisson's equation with boundary conditions set by the image's edges. Unlike the traditional windowed Fourier transforms, Periodic Plus Smooth Decomposition maintains sharp reciprocal lattice peaks from the image's entire field of view.

Lingli Kong, Zhengran Ji, Huolin L. Xin

The ionization edges encoded in the electron energy loss spectroscopy (EELS) spectra enable advanced material analysis including composition analyses and elemental quantifications. The development of the parallel EELS instrument and fast, sensitive detectors have greatly improved the acquisition speed of EELS spectra. However, the traditional way of core-loss edge recognition is experience based and human labor dependent, which limits the processing speed. So far, the low signal-noise ratio and the low jump ratio of the core-loss edges on the raw EELS spectra have been challenging for the automation of edge recognition. In this work, a convolutional-bidirectional long short-term memory neural network (CNN-BiLSTM) is proposed to automate the detection and elemental identification of core-loss edges from raw spectra. An EELS spectral database is synthesized by using our forward model to assist in the training and validation of the neural network. To make the synthesized spectra resemble the real spectra, we collected a large library of experimentally acquired EELS core edges. In synthesize the training library, the edges are modeled by fitting the multi-gaussian model to the real edges from experiments, and the noise and instrumental imperfectness are simulated and added. The well-trained CNN-BiLSTM network is tested against both the simulated spectra and real spectra collected from experiments. The high accuracy of the network, 94.9 %, proves that, without complicated preprocessing of the raw spectra, the proposed CNN-BiLSTM network achieves the automation of core-loss edge recognition for EELS spectra with high accuracy.

Huolin L. Xin, Mike Hu

Accurate decomposition of the mixed Mn oxidation states is highly important for characterizing the electronic structures, charge transfer, and redox centers for electronic, electrocatalytic, and energy storage materials that contain Mn. Electron energy loss spectroscopy (EELS) and soft X-ray absorption spectroscopy (XAS) measurements of the Mn L2,3 edges are widely used for this purpose. To date, although the measurement of the Mn L2,3 edges is straightforward given the sample is prepared properly, an accurate decomposition of the mix valence states of Mn remains non-trivial. For both EELS and XAS, 2+, 3+, 4+ reference spectra need to be taken on the same instrument/beamline and preferably in the same experimental session because the instrumental resolution and the energy axis offset could vary from one session to another. To circumvent this hurdle, in this study, we adopted a deep learning approach and developed a calibration-free and reference-free method to decompose the oxidation state of Mn L2,3 edges for both EELS and XAS. To synthesize physics-informed and ground-truth labeled training datasets, we created a forward model that takes into account plural scattering, instrumentation broadening, noise, and energy axis offset. With that, we created a 1.2 million-spectrum database with a three-element oxidation state composition label. The library includes a sufficient variety of data including both EELS and XAS spectra. By training on this large database, our convolutional neural network achieves 85% accuracy on the validation dataset. We tested the model and found it is robust against noise (down to PSNR of 10) and plural scattering (up to t/λ = 1). We further validated the model against spectral data that were not used in training.

Ruoqian Lin, Rui Zhang, Chunyang Wang et al.

Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional algorithms, such has thresholding, edge detection and clustering, can achieve reasonable performance in some predefined sceneries, they tend to fail when interferences from the background are strong and unpredictable. Particularly, for atomic-resolution STEM images, so far there is no well-established algorithm that is robust enough to segment or detect all atomic columns when there is large thickness variation in a recorded image. Herein, we report the development of a training library and a deep learning method that can perform robust and precise atom segmentation, localization, denoising, and super-resolution processing of experimental images. Despite using simulated images as training datasets, the deep-learning model can self-adapt to experimental STEM images and shows outstanding performance in atom detection and localization in challenging contrast conditions and the precision consistently outperforms the state-of-the-art two-dimensional Gaussian fit method. Taking a step further, we have deployed our deep-learning models to a desktop app with a graphical user interface and the app is free and open-source. We have also built a TEM ImageNet project website for easy browsing and downloading of the training data.

Doruk Aksoy, Huolin L. Xin, Timothy J. Rupert et al.

Automated detection of grain boundaries (GBs) in electron microscope images of polycrystalline materials could help accelerate the nanoscale characterization of myriad engineering materials and novel materials under scientific research. Accurate segmentation of interconnected line networks, such as GBs in polycrystalline material microstructures, poses a significant challenge due to the fragmented masks produced by conventional computer vision (CV) algorithms, including convolutional neural networks. These algorithms struggle with thin masks, often necessitating post-processing for effective contour closure and continuity. Previous approaches in this domain have typically relied on custom post-processing techniques that are problem-specific and heavily dependent on the quality of the mask obtained from a CV algorithm. Addressing this issue, this paper introduces a fast, high-fidelity post-processing technique that is universally applicable to segmentation masks of interconnected line networks. Leveraging domain knowledge about grain boundary connectivity, this method employs conditional random fields and perceptual grouping rules to refine segmentation masks of any image with a discernible grain structure. This approach significantly enhances segmentation mask accuracy by correctly reconstructing fragmented GBs in electron microscopy images of a polycrystalline oxide. The refinement improves the statistical representation of the microstructure, reflected by a 51 % improvement in a grain alignment metric that provides a more physically meaningful assessment of complex microstructures than conventional metrics. This method enables rapid and accurate characterization, facilitating an unprecedented level of data analysis and improving the understanding of GB networks, making it suitable for a range of disciplines where precise segmentation of interconnected line networks is essential.