TopoTEM: A Python Package for Quantifying and Visualizing Scanning Transmission Electron Microscopy Data of Polar Topologies

Abstract

The exotic internal structure of polar topologies in multiferroic materials offers a rich landscape for materials science research. As the spatial scale of these entities is often subatomic in nature, aberration-corrected transmission electron microscopy (TEM) is the ideal characterization technique. Software to quantify and visualize the slight shifts in atomic placement within unit cells is of paramount importance due to the now routine acquisition of images at such resolution. In the previous ~decade since the commercialization of aberration-corrected TEM, many research groups have written their own code to visualize these polar entities. More recently, open-access Python packages have been developed for the purpose of TEM atomic position quantification. Building on these packages, we introduce the TEMUL Toolkit: a Python package for analysis and visualization of atomic resolution images. Here, we focus specifically on the TopoTEM module of the toolkit where we show an easy to follow, streamlined version of calculating the atomic displacements relative to the surrounding lattice and thus plotting polarization. We hope this toolkit will benefit the rapidly expanding field of topology-based nano-electronic and quantum materials research, and we invite the electron microscopy community to contribute to this open-access project.

Emergent Ferroelectric Switching Behavior from Polar Vortex Lattice

“…The data processing was performed using the “finding polarization vector” in TopoTEM. [ 37 ] In summary, all the A sites were found using atom detection. Afterward, all the detected atoms were divided in the zone vector planes.…”

Charged Domain Wall and Polar Vortex Topologies in a Room-Temperature Magnetoelectric Multiferroic Thin Film

“…Atom position finding and 2D Gaussian refinement were completed with the Atomap Python package . Image analysis and mapping, as well as polarization vector analysis, were completed using the TopoTEM module of the TEMUL Toolkit Python package. Strain analysis was carried out by geometric phase analysis using Stem Cell …”

Tuning the 1T′/2H phases in WxMo1−xSe2 nanosheets

“…Atomically resolved high-angle annular dark-field STEM (HAADF STEM) imaging was carried on a probe corrected Nion UltraSTEM microscope at 60 kV accelerating voltage with the beam convergence semi-angle of 30 mrad. The statistical analysis on the HAADF STEM images was carried using the Atomap 36 and the TEMUL Toolkit 37 Python packages. The HAADF STEM image simulations were done with the Dr Probe software.…”