EASY-STEM is a simple self-developed free MATLAB app with a graphical user interface (GUI). The GUI can assist in the analysis of STEM images without the need for writing dedicated analysis code or software. The app includes:

  • tips for acquiring high-quality STEM images
  • denoising and drift-correction for enhancing measurement accuracy
  • obtaining initial atomic positions
  • indexing the atoms based on unit cell vectors
  • quantifying the atom column positions with either 2D-Gaussian single peak fitting
  • multi-peak fitting routines for slightly overlapping atomic columns
  • quantification of lattice distortion/strain within the crystal structures or at the defects/interfaces where the lattice periodicity is disrupted
  • some common methods to visualize and present the analysis

You can find EASY-STEM here: https://www.jove.com/fr/t/62164/picometer-precision-atomic-position-tracking-through-electron

The associated paper: Miao, L., Chmielewski, A., Mukherjee, D., & Alem, N. (2021). Picometer-Precision Atomic Position Tracking through Electron Microscopy. Journal of visualized experiments : JoVE, (173), 10.3791/62164. https://doi.org/10.3791/62164

An easy interface:

Multi-gaussian fitting of atomic columns positions:

Polarization map example:

NBA Data Analysis & Visualization « MSPY »

This GUI app is related to the NBA shot analysis project, made in the framework of Datascientest.com. It is yet to be deployed. For more details, click here.

This app includes many features such as Data exploration..

Statistics comparison..

Shot analysis..

Predictive models..

And many more..

AbStrain: Quantitative mapping of strain and displacement fields over HR-TEM and HR-STEM images of crystals with reference to a virtual lattice

A method for the reciprocal space treatment of high-resolution transmission electron microscopy (HR-TEM) and high-resolution scanning transmission electron microscopy (HR-STEM) images has been developed. Named « Absolute strain » (AbStrain), it allows for quantification and mapping of interplanar distances and angles, displacement fields and strain tensor components with reference to a user-defined Bravais lattice and with their corrections from the image distortions specific to HR-TEM and HR-STEM imaging.

The associated paper: Cherkashin, N., Louiset, A., Chmielewski, A., Kim, D. J., Dubourdieu, C., & Schamm-Chardon, S. (2023). Quantitative mapping of strain and displacement fields over HR-TEM and HR-STEM images of crystals with reference to a virtual lattice. Ultramicroscopy253, 113778. Advance online publication. https://doi.org/10.1016/j.ultramic.2023.113778

This software was developed as a plugin for DigitalMicrograph, also known as Gatan Microscopy Suite. More info here.

A software based on the reciprocal lattice of the HRSTEM image:

Atomic columns can be isolated with multiple masks:

Polarization and vector map example:

And many more..