A robust synthetic data generation framework for machine learning in High-Resolution Transmission Electron Microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate automated analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapidly generating complex nanoscale atomic structures, and develop an end-to-end workflow for creating large simulated databases for training neural networks. Construction Zone enables fast, systematic sampling of realistic nanomaterial structures, and can be used as a random structure generator for simulated databases, which is important for generating large, diverse synthetic datasets. Using HRTEM imaging as an example, we train a series of neural networks on various subsets of our simulated databases to segment nanoparticles and holistically study the data curation process to understand how various aspects of the curated simulated data -- including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions -- affect model performance across several experimental benchmarks. Using our results, we are able to achieve state-of-the-art segmentation performance on experimental HRTEM images of nanoparticles from several experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data.

Generalization Across Experimental Parameters in Machine Learning Analysis of High Resolution Transmission Electron Microscopy Datasets

Neural networks are promising tools for high-throughput and accurate transmission electron microscopy (TEM) analysis of nanomaterials, but are known to generalize poorly on data that is "out-of-distribution" from their training data. Given the limited set of image features typically seen in high-resolution TEM imaging, it is unclear which images are considered out-of-distribution from others. Here, we investigate how the choice of metadata features in the training dataset influences neural network performance, focusing on the example task of nanoparticle segmentation. We train and validate neural networks across curated, experimentally-collected high-resolution TEM image datasets of nanoparticles under controlled imaging and material parameters, including magnification, dosage, nanoparticle diameter, and nanoparticle material. Overall, we find that our neural networks are not robust across microscope parameters, but do generalize across certain sample parameters. Additionally, data preprocessing heavily influences the generalizability of neural networks trained on nominally similar datasets. Our results highlight the need to understand how dataset features affect deployment of data-driven algorithms.

Understanding the Influence of Receptive Field and Network Complexity in Neural-Network-Guided TEM Image Analysis

Trained neural networks are promising tools to analyze the ever-increasing amount of scientific image data, but it is unclear how to best customize these networks for the unique features in transmission electron micrographs. Here, we systematically examine how neural network architecture choices affect how neural networks segment, or pixel-wise separate, crystalline nanoparticles from amorphous background in transmission electron microscopy (TEM) images. We focus on decoupling the influence of receptive field, or the area of the input image that contributes to the output decision, from network complexity, which dictates the number of trainable parameters. We find that for low-resolution TEM images which rely on amplitude contrast to distinguish nanoparticles from background, the receptive field does not significantly influence segmentation performance. On the other hand, for high-resolution TEM images which rely on a combination of amplitude and phase contrast changes to identify nanoparticles, receptive field is a key parameter for increased performance, especially in images with minimal amplitude contrast. Our results provide insight and guidance as to how to adapt neural networks for applications with TEM datasets.