Py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Savitzky BH, Zeltmann SE, Hughes LA, Brown HG, Zhao S, Pelz PM, Pekin TC, Barnard ES, Donohue J, Dacosta LR, Kennedy E, Xie Y, Janish MT, Schneider MM, Herring P, Gopal C, Anapolsky A, Dhall R, Bustillo KC, Ercius P, Scott MC, Ciston J, Minor AM, Ophus C (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Microscopy and Microanalysis Cambridge University Press (CUP)

Book Volume: 27

Pages Range: 712-743

Journal Issue: 4

DOI: 10.1017/S1431927621000477

Abstract

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

Authors with CRIS profile

Philipp Pelz

Involved external institutions

Lawrence Berkeley National Laboratory (LBNL) US United States (USA) (US) University of California, Berkeley US United States (USA) (US) Humboldt-Universität zu Berlin DE Germany (DE) Los Alamos National Laboratory US United States (USA) (US) Toyota US United States (USA) (US)

How to cite

APA:

Savitzky, B.H., Zeltmann, S.E., Hughes, L.A., Brown, H.G., Zhao, S., Pelz, P.M.,... Ophus, C. (2021). Py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis. Microscopy and Microanalysis, 27(4), 712-743. https://doi.org/10.1017/S1431927621000477

MLA:

Savitzky, Benjamin H., et al. "Py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis." Microscopy and Microanalysis 27.4 (2021): 712-743.

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