Machine Learning Pipeline for Segmentation and Defect Identification from High Resolution Transmission Electron Microscopy Data

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.

10 pages, 5 figures

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• scikit-image: Image processing in Python
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• A deep learning approach for determining the chiral indices of carbon nanotubes from high-resolution transmission electron microscopy images
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Cited by in corpus (8)

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• SAM-I-Am: Semantic Boosting for Zero-shot Atomic-Scale Electron Micrograph Segmentation
• Evaluating Stage Motion for Automated Electron Microscopy
• Quantifying Noise Limitations of Neural Network Segmentations in High-Resolution Transmission Electron Microscopy
• Lost Data in Electron Microscopy
• Revealing the Evolution of Order in Materials Microstructures Using Multi-Modal Computer Vision