A collected reading list for the whole workshop. Each topic page also has its own focused reference list.
Key papers & reviews¶
C. Ophus, “Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond,” Microscopy and Microanalysis 25, 563–582 (2019). Ophus (2019). The standard overview of the 4D-STEM measurement family.
B. H. Savitzky et al., “py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis,” Microscopy and Microanalysis 27, 712–743 (2021). Savitzky et al. (2021). The paper for the software used in most of the hands-on sessions.
P. A. Midgley and A. S. Eggeman, “Precession electron diffraction — a topical review,” IUCrJ 2, 126–136 (2015). Midgley & Eggeman (2015)
K. C. Bustillo, S. E. Zeltmann et al., “4D-STEM of Beam-Sensitive Materials,” Accounts of Chemical Research 54, 2543–2551 (2021). Bustillo et al. (2021)
S. V. Kalinin et al., “Machine learning in scanning transmission electron microscopy,” Nature Reviews Methods Primers 2, 11 (2022). Kalinin et al. (2022)
J. M. Rodenburg and H. M. L. Faulkner, “A phase retrieval algorithm for shifting illumination,” Applied Physics Letters 85, 4795 (2004). Rodenburg & Faulkner (2004)
Y. Jiang et al., “Electron ptychography of 2D materials to deep sub-angstrom resolution,” Nature 559, 343-349 (2018). Jiang et al. (2018)
G. Varnavides et al., “Iterative phase retrieval algorithms for scanning transmission electron microscopy.” arXiv:2309.05250
S. Nord et al. and G. W. Paterson et al., “Fast Pixelated Detectors in Scanning Transmission Electron Microscopy,” Parts I and II, Microscopy and Microanalysis 26 (2020).
Textbooks¶
D. B. Williams and C. B. Carter, Transmission Electron Microscopy: A Textbook for Materials Science, 2nd ed., Springer (2009). The standard general TEM reference; Part II covers diffraction.
J. M. Zuo and J. C. H. Spence, Advanced Transmission Electron Microscopy: Imaging and Diffraction in Nanoscience, Springer (2017). The deepest treatment of electron diffraction physics relevant to this course.
M. De Graef, Introduction to Conventional Transmission Electron Microscopy, Cambridge University Press (2003). Excellent on diffraction geometry and crystallography conventions.
E. J. Kirkland, Advanced Computing in Electron Microscopy, 3rd ed., Springer (2020). The reference for image and diffraction simulation.
Software¶
| Package | Links |
|---|---|
| py4DSTEM | GitHub · tutorials · paper |
| quantEM | docs · GitHub |
| pyxem | GitHub · docs · orientation-mapping paper |
| HyperSpy | hyperspy.org |
| Kelvin_STEM | GitHub |
| abTEM | docs · GitHub · paper |
Open datasets¶
Several of the tutorial datasets are drawn from published, openly archived measurements, for example the precession 4D-STEM titanium dataset (paper · data). Links to each tutorial’s dataset are given inside the Colab notebooks.
- Ophus, C. (2019). Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond. Microscopy and Microanalysis, 25(3), 563–582. 10.1017/s1431927619000497
- 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, 27(4), 712–743. 10.1017/s1431927621000477
- Midgley, P. A., & Eggeman, A. S. (2015). Precession electron diffraction – a topical review. IUCrJ, 2(1), 126–136. 10.1107/s2052252514022283
- Bustillo, K. C., Zeltmann, S. E., Chen, M., Donohue, J., Ciston, J., Ophus, C., & Minor, A. M. (2021). 4D-STEM of Beam-Sensitive Materials. Accounts of Chemical Research, 54(11), 2543–2551. 10.1021/acs.accounts.1c00073
- Kalinin, S. V., Ophus, C., Voyles, P. M., Erni, R., Kepaptsoglou, D., Grillo, V., Lupini, A. R., Oxley, M. P., Schwenker, E., Chan, M. K. Y., Etheridge, J., Li, X., Han, G. G. D., Ziatdinov, M., Shibata, N., & Pennycook, S. J. (2022). Machine learning in scanning transmission electron microscopy. Nature Reviews Methods Primers, 2(1). 10.1038/s43586-022-00095-w
- Rodenburg, J. M., & Faulkner, H. M. L. (2004). A phase retrieval algorithm for shifting illumination. Applied Physics Letters, 85(20), 4795–4797. 10.1063/1.1823034
- Jiang, Y., Chen, Z., Han, Y., Deb, P., Gao, H., Xie, S., Purohit, P., Tate, M. W., Park, J., Gruner, S. M., Elser, V., & Muller, D. A. (2018). Electron ptychography of 2D materials to deep sub-ångström resolution. Nature, 559(7714), 343–349. 10.1038/s41586-018-0298-5
- Nord, M., Webster, R. W. H., Paton, K. A., McVitie, S., McGrouther, D., MacLaren, I., & Paterson, G. W. (2020). Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage. Microscopy and Microanalysis, 26(4), 653–666. 10.1017/s1431927620001713
- Paterson, G. W., Webster, R. W. H., Ross, A., Paton, K. A., Macgregor, T. A., McGrouther, D., MacLaren, I., & Nord, M. (2020). Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization. Microscopy and Microanalysis, 26(5), 944–963. 10.1017/s1431927620024307
- Cautaerts, N., Crout, P., Ånes, H. W., Prestat, E., Jeong, J., Dehm, G., & Liebscher, C. H. (2022). Free, flexible and fast: Orientation mapping using the multi-core and GPU-accelerated template matching capabilities in the Python-based open source 4D-STEM analysis toolbox Pyxem. Ultramicroscopy, 237, 113517. 10.1016/j.ultramic.2022.113517
- Madsen, J., & Susi, T. (2021). The abTEM code: transmission electron microscopy from first principles. Open Research Europe, 1, 24. 10.12688/openreseurope.13015.1
- MacLaren, I., Frutos‐Myro, E., Zeltmann, S., & Ophus, C. (2024). A method for crystallographic mapping of an alpha‐beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open‐source software libraries. Journal of Microscopy, 295(2), 131–139. 10.1111/jmi.13275
- MacLaren, I., Myro, E., Zeltmann, S., & Ophus, C. (2023). A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries. University of Glasgow. 10.5525/GLA.RESEARCHDATA.1514