In this example, we will cover the extraction of the structural model of a molecule of a bronze-type Niobium oxide, from HAADF-STEM micrographs (further background on this topic can be found in Chapter 5, High-Quality Image Formation by Nonlocal Means Applied to High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF--STEM) of the book Modeling Nanoscale Imaging in Electron Microscopy, Vogt T., Dahmen W., and Binev P., Springer Publishing.
The following diagram shows the HAADF-STEM micrograph of a bronze-type Niobium oxide (taken from http://www.microscopy.ethz.ch/BFDF-STEM.htm):
Courtesy: ETH Zurich
For pedagogical purposes, we took the following approach to solving this problem:
Segmentation of the atoms by thresholding and morphological operations.
Connected component labeling to extract each single atom for posterior examination.
Computation of the centers of mass of each label identified as an atom. This presents us with a lattice of...