Cite

Citing quantEM¶

Please cite the paper describing the method you used. If the method has no paper yet, cite the software itself. Citing both is welcome when a method paper covers only part of your workflow.

Method papers¶

Cite these when your work uses the corresponding method.

Iterative ptychography with deep generative priors A. R. C. McCray, S. M. Ribet, G. Varnavides, C. Ophus, Deep generative priors for robust and efficient electron ptychography, 2025. arXiv:2511.07795

Direct ptychography G. Varnavides, J. M. Bekkevold, S. M. Ribet, M. C. Scott, L. Jones, C. Ophus, Relaxing direct ptychography sampling requirements via parallax imaging insights, Microscopy and Microanalysis 32, 2 (2026). Varnavides et al. (2026)

Tomography with implicit neural representations C. Lim, C. Casert, A. R. C. McCray, S. Lee, A. Barnum, J. Dionne, C. Ophus, Missing wedge inpainting and joint alignment in electron tomography through implicit neural representations, 2025. arXiv:2512.08113

Automated crystal orientation mapping (ACOM) C. Ophus, S. E. Zeltmann, A. Bruefach, A. Rakowski, B. H. Savitzky, A. M. Minor, M. C. Scott, Automated crystal orientation mapping in py4DSTEM using sparse correlation matching, Microscopy and Microanalysis 28, 390 (2022). Ophus et al. (2022)

For two-phase orientation and phase mapping with scanning precession electron diffraction, and for the titanium dataset used in the orientation and phase mapping examples, also cite I. MacLaren, E. Frutos-Myro, S. Zeltmann, C. Ophus, 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, 131 (2024). MacLaren et al. (2024)

Multi-angle precession electron diffraction (MAPED) S. M. Ribet, R. Dhall, C. Ophus, K. C. Bustillo, Multi-angle precession electron diffraction (MAPED): a versatile approach to 4D-STEM precession, Microscopy and Microanalysis 31, 6 (2025). Ribet et al. (2025)

Software¶

Cite the software when no method paper applies, or alongside a method paper. The concept DOI below always resolves to the latest release; use the release-specific DOI from Zenodo if you need to pin an exact version.

quantEM Authors (2026). quantEM: quantitative electron microscopy analysis toolkit. McCray et al. (2026)

@software{quantem,
  author  = {{quantEM Authors}},
  title   = {quantEM: quantitative electron
             microscopy analysis toolkit},
  year    = {2026},
  doi     = {10.5281/zenodo.18642593},
  url     = {https://github.com/electronmicroscopy/quantem},
  license = {MIT},
}

The authors, in alphabetical order, are Karen Ehrhardt, Matthew Feickert, Carter Francis, Sangjoon Bob Lee, Cedric Lim, Darshan Mali, Nicholas Marchese, Arthur R. C. McCray, Will Millsaps, Colin Ophus, Stephanie M. Ribet, and Georgios Varnavides.

The authoritative, per-release metadata lives in CITATION.cff in the repository. GitHub renders it under “Cite this repository”, and most reference managers import it directly.