One-click sample alignment in the transmission electron microscope: simulating and analysing Kikuchi diffraction patterns

The aim of this project is to provide tools for easy tilting of samples on to major zone-axes in the transmission electron microscope.

In order to obtain high-resolution images in the transmission electron microscope, crystalline samples have to be oriented on to a major zone-axis, i.e. with the electron beam oriented along atomic columns. This can be achieved by using Kikuchi diffraction patterns to orient the sample. Kikuchi bands are formed from diffuse inelastic scattering in thick regions of the sample, with bands connecting major zone-axes. However, Kikuchi patterns vary for different crystal systems and finding the correct zone-axis at the microscope can be difficult without a map to guide the operator.

In this project, tools will be developed to simulate and analyse Kikuchi diffraction patterns so that the orientation of samples in the microscope can be determined. A simple tool to generate Kikuchi bands will be added to the diffsims python package (https://github.com/pyxem/diffsims), using the diffraction tools already developed in the package. The maps generated will then be used to automatically assign the current sample orientation in the microscope, using a pattern matching algorithm. If the pattern matching algorithm is unsuccessful, the generated maps will be used to manually determine the current orientation. This project will also include coding of a program to tilt the microscope stage to the correct orientation, once the current orientation is determined.

These procedures are currently performed manually, resulting in a slow process that is dependent on the expertise of the microscope operator. Successful completion of this project will allow rapid tilting to correct sample orientations, which will not only save time, but will reduce electron dose for beam sensitive samples.