kemstem

kemstem is a python package for quantification and visualization of atomic resolution STEM data developed in the Kourkoutis Electron Microscopy group at Cornell University. It includes algorithms for:

• Mapping translational symmetry breaking distortions, such as picometer scale atomic displacements associated with charge order as well as chemical and vacancy orderings, with Fourier space damping of superlattice peaks. See: B. H. Savitzky, I. El Baggari, A.S. Admasu, J. Kim, S.W. Cheong, R. Hovden & L.F. Kourkoutis (2017). Nature communications, 8(1), 1883.
• Mapping the amplitude and phase of periodic features to identify local orderings, defects, strains, and other nanoscale inhomogeneity with Fourier filtering and phase-lock in analysis. See: B.H. Goodge, I. El Baggari, S.S. Hong, Z. Wang, D.G. Schlom, H.Y. Hwang & L. F. Kourkoutis (2022). Microscopy and Microanalysis, 28(2), 404-411.
• Measuring inter-planar spacings and orientations with high real-space resolution and precision, as well as quantified uncertainty, with local wave fitting. See: M. A. Smeaton, I. El Baggari, D. M. Balazs, T. Hanrath & L. F. Kourkoutis (2021). ACS nano, 15(1), 719-726.

Detailed descriptions, example applications and validation of these techniques are provided in our preprint: N. Schnitzer, L. Bhatt, I. El Baggari, R. Hovden, B.H. Savitzky, M.A. Smeaton, B.H. Goodge (2025). arXiv:2504.01159.

Installation

kemstem releases can be installed from PyPI with pip:

pip install kemstem

Or to install the development version, clone from github and install with pip:

git clone https://github.com/noahschnitzer/kemstem.git
cd kemstem
pip install -e . 

Examples

Example jupyter notebooks with demonstration workflows can be found along with sample data under example_notebooks.

Documentation

Package documentation is available at https://kemstem.readthedocs.io/en/latest/.