The structural model of oxides

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...