Machine Learning Pipeline for Segmentation and Defect Identification from High Resolution Transmission Electron Microscopy Data (2001.05022v2)

Abstract: In the field of transmission electron microscopy, data interpretation often lags behind acquisition methods, as image processing methods often have to be manually tailored to individual datasets. Machine learning offers a promising approach for fast, accurate analysis of electron microscopy data. Here, we demonstrate a flexible two step pipeline for analysis of high resolution transmission electron microscopy data, which uses a U-Net for segmentation followed by a random forest for detection of stacking faults. Our trained U-Net is able to segment nanoparticle regions from amorphous background with a Dice coefficient of 0.8 and significantly outperforms traditional image segmentation methods. Using these segmented regions, we are then able to classify whether nanoparticles contain a visible stacking fault with 86% accuracy. We provide this adaptable pipeline as an open source tool for the community. The combined output of the segmentation network and classifier offer a way to determine statistical distributions of features of interest, such as size, shape and defect presence, enabling detection of correlations between these features.