Automated Segmentation of Nanoparticles in BF TEM Images by U-Net Binarization and Branch and Bound

Abstract

Transmission electron microscopy (TEM) provides information about Inorganic nanoparticles that no other method is able to deliver. Yet, a major task when studying Inorganic nanoparticles using TEM is the automated analysis of the images, i.e. segmentation of individual nanoparticles. The current state-of-the-art methods generally rely on binarization routines that require parameterization, and on methods to segment the overlapping nanoparticles (NPs) using highly idealized nanoparticle shape models. It is unclear, however, that there is any way to determine the best set of parameters providing an optimal segmentation, given the great diversity of NPs characteristics, such as shape and size, that may be encountered. Towards remedying these barriers, this paper introduces a method for segmentation of NPs in Bright Field (BF) TEM images. The proposed method involves three main steps: binarization, contour evidence extraction, and contour estimation. For the binarization, a model based on the U-Net architecture is trained to convert an input image into its binarized version. The contour evidence extraction starts by recovering contour segments from a binarized image using concave contour points detection. The contour segments which belong to the same nanoparticle are grouped in the segment grouping step. The grouping is formulated as a combinatorial optimization problem and solved using the well-known branch and bound algorithm. Finally, the full contours of the NPs are estimated by an ellipse. The experiments on a real-world dataset consisting of 150 BF TEM images containing approximately 2,700 NPs show that the proposed method outperforms five current state-of-art approaches in the overlapping NPs segmentation.