DrCBrennan-Rich/Pyxem_Electron_Microscopy: CBR_Pyxem_v1.0.1

A bundle of notebooks for the processing of 4D-scanning transmission electron microscopy data in Pyxem. Each notebook is well commented, though referencing the websites:

https://www.pyxem.org/en/stable/ https://hyperspy.org/

is recommended if deeper understanding of the data structures or of the mathematical processes underlying the operations are desired.

Features available in this release are: Cropping and initial processing of the STEM image High-angle annular dark field (HAADF) imaging; Fourier transform and power spectrum production; Simulation of electron spot diffraction patterns from CIF files; Fast template matching for crystallographic assignment.

To get started:

1. Use the Pyxem.yml file to construct a suitable environment.
2. Run jupyter notebooks and start analysing.
3. Generally CroppingAndProcessing.ipynb should be the first port of call.

The typical 4D-STEM file is massive (>1GB) and so binning and cropping should be used liberally to reduce the file size as required (256x256 pixels is often perfectly sufficient for the diffraction axes, for instance).