The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis
Open accessAbstract
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.
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Cites
The quickhull algorithm for convex hulls
Barber, C. B., Dobkin, D. P., & Huhdanpaa, H. (1996) · ACM Transactions on Mathematical Software · doi:10.1145/235815.235821 · Cited by 5,359
Efficient subpixel image registration algorithms
Guizar-Sicairos, M., Thurman, S. T., & Fienup, J. R. (2008) · Optics Letters · doi:10.1364/ol.33.000156 · Cited by 1,905
Topology of covalent non-crystalline solids I: Short-range order in chalcogenide alloys
Phillips, J. C. (1979) · Journal of Non-Crystalline Solids · doi:10.1016/0022-3093(79)90033-4 · Cited by 1,876
The scattering of electrons by atoms and crystals. I. A new theoretical approach
Cowley, J. M., & Moodie, A. F. (1957) · Acta Crystallographica · doi:10.1107/s0365110x57002194 · Cited by 1,426
Ophus, C. (2019) · Microscopy and Microanalysis · doi:10.1017/s1431927619000497 · Cited by 1,075
Self-citationAdvanced Computing in Electron Microscopy
Kirkland, E. J. (2010) · Springer eBooks · doi:10.1007/978-1-4419-6533-2 · Cited by 724
Egami, T., & Billinge, S. J. L. (2003) · Materials Today · doi:10.1016/s1369-7021(03)00635-7 · Cited by 664
Electron Vortex Beams with High Quanta of Orbital Angular Momentum
McMorran, B. J., Agrawal, A., Anderson, I. M., Herzing, A. A., Lezec, H. J., McClelland, J. J., & Unguris, J. (2011) · Science · doi:10.1126/science.1198804 · Cited by 604
High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy
Täte, M. W., Purohit, P., Chamberlain, D., Nguyen, K. X., Hovden, R., Chang, C. S., Deb, P., Turgut, E., Heron, J. T., Schlom, D. G., et al. (2016) · Microscopy and Microanalysis · doi:10.1017/s1431927615015664 · Cited by 498
Differential phase-contrast microscopy at atomic resolution
Shibata, N., Findlay, S. D., Kohno, Y., Sawada, H., Kondo, Y., & Ikuhara, Y. (2012) · Nature Physics · doi:10.1038/nphys2337 · Cited by 468
Cited by
Multimodal electron microscopy of halide perovskite interfacial dynamics
Li, X., Gu, Q., Huang, W., Fairclough, S. M., Friend, R. H., Stranks, S. D., Liu, T., & Ducati, C. (2026) · Nature · doi:10.1038/s41586-026-10238-8 · Cited by 14
“Crystal orientation mapping was performed on 4D-STEM datasets using the py4DSTEM software package 51 .”
InfluentialBridging electron microscopy and materials analysis with an autonomous agentic platform
Chen, G., Yuan, W., & You, F. (2026) · Science Advances · doi:10.1126/sciadv.aed0583 · Cited by 6
Metadata
- Authors
- Savitzky, B. H., Zeltmann, S. E., Hughes, L. A., Brown, H. G., Zhao, S., Pelz, P. M., Pekin, T. C., Barnard, E. S., Donohue, J., Rangel DaCosta, L., Kennedy, E., Xie, Y., Janish, M. T., Schneider, M. M., Herring, P., Gopal, C., Anapolsky, A., Dhall, R., Bustillo, K. C., Ercius, P., Scott, M. C., Ciston, J., Minor, A. M., & Ophus, C.
- Venue
- Microscopy and Microanalysis
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-05-21
- Volume
- 27
- Issue
- 4
- Pages
- 712-743
- ISSN
- 1431-9276 (ISSN-L)
- 1435-8115
- OpenAlex
- W3012644610
- Cited by
- 353
- References
- 38
- FWCI
- 19.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- The paper
- Savitzky, B. H., Zeltmann, S. E., Hughes, L. A., Brown, H. G., Zhao, S., Pelz, P. M., Pekin, T. C., Barnard, E. S., Donohue, J., Rangel DaCosta, L., Kennedy, E., Xie, Y., Janish, M. T., Schneider, M. M., Herring, P., Gopal, C., Anapolsky, A., Dhall, R., Bustillo, K. C., . . . Ophus, C. (2021). py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis. Microscopy and Microanalysis. https://doi.org/10.1017/s1431927621000477
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