Analysing atomic structure in nano-scale imagery

Abstract

This thesis presents methods for both detecting atoms and reconstructing single layer molecular geometry depicted within high resolution nanoscale imagery. Nanoscale imaging is a common method of analysing molecular structures produced through self-assembly. The second derivatives of the nanoscale images are then computed and used to aid in analysis of the depicted molecules. Peaks from the derivative images are used as the locations of the atoms and using those locations we derive the molecular geometry. In order to efficiently determine the performance of our proposed methods, a system to synthesize HRTEM imagery and ground truth data was developed. We demonstrate and compare the effectiveness of our system to other proposed systems using both experimentally produced nanoscale images and the synthetic data that has been produced.