October 29, 2022
Journal Article

A Deep Learning Approach for Semantic Segmentation of Unbalanced Data in Electron Tomography of Catalytic Materials


In computed TEM tomography, image segmentation represents one of the most basic tasks with implications not only for 3D volume visualization, but more importantly for quantitative 3D analysis. In case of large and complex 3D data sets, segmentation can be extremely difficult and laborious task, and thus has been one of the biggest hurdles for comprehensive 3D analysis. Heterogenous catalysts have complex surfaces and bulk structure, and often sparse distribution of catalytic nanoparticles with relatively poor intrinsic contrast, which possess a unique challenge for image segmentation, including the current state-of-the-art deep learning-based segmentation methods. To tackle this problem, we apply a deep learning-based approach for the multi-class semantic segmentation of a ?-Alumina/Pt catalytic material in a class imbalance situation. Specifically, we used the weighted focal loss as a loss function and attached it to the U-Net’s fully convolutional network architecture. We assessed the accuracy of our results using Dice similarity coefficient (DSC), recall, precision, and Hausdorff distance (HD) metrics on the overlap between the ground-truth and predicted segmentations. Our adopted U-Net model with the weighted focal loss function achieved an average DSC score of 0.96 ? 0.003 in the ?-Alumina support material and 0.84 ? 0.03 in the Pt NPs segmentation tasks. We report an average boundary-overlap error of less than 2 nm at the 90th percentile of HD for ?-Alumina and Pt NPs segmentations. The complex surface morphology of the ?-Alumina and its relation to the Pt NPs were visualized in 3D by the deep learning-assisted automatic segmentation of a large data set of high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography reconstructions.

Published: October 29, 2022


Genc A., L. Kovarik, and H.L. Fraser. 2022. A Deep Learning Approach for Semantic Segmentation of Unbalanced Data in Electron Tomography of Catalytic Materials. Scientific Reports 12, no. 1:Art. No. 16267. PNNL-SA-174381. doi:10.1038/s41598-022-16429-3