CITATION.cff

# This file describes how to cite the quantem software (schema: https://citation-file-format.github.io).
# It is maintained by hand. Unlike Zenodo's auto-generated author list, this file will not
# pick up new contributors on its own: update `authors`, `version`, and `date-released`
# with each release.
message: >-
  If you use quantem in your research, please cite this software using the metadata below,
  along with any relevant method papers listed in the README.
title: "quantem: quantitative electron microscopy analysis toolkit"
abstract: >-
  quantem is a quantitative electron microscopy data analysis toolkit built on PyTorch, 
  providing tools for analyzing many kinds of transmission electron microscopy data.
type: software
authors:
  - given-names: "Arthur R. C."
    family-names: McCray
    orcid: "0000-0001-6077-4698"
    affiliation: "Stanford University"  
  - given-names: Colin
    family-names: Ophus
    orcid: "0000-0003-2348-8558"  
    affiliation: "Stanford University"  
  - given-names: "Stephanie M."
    family-names: Ribet
    orcid: "0000-0002-7117-066X"  
    affiliation: "Lawrence Berkeley National Laboratory"  
  - given-names: Georgios
    family-names: Varnavides
    orcid: "0000-0001-8338-3323"  
    affiliation: "Delft University of Technology"  
  - given-names: Cedric
    family-names: Lim
    orcid: "0009-0000-1319-5175"  
    affiliation: "Stanford University"  
  - given-names: Karen
    family-names: Ehrhardt
    # orcid: ""  
    # affiliation: ""  
  - given-names: Matthew
    family-names: Feickert
    # orcid: ""  
    # affiliation: ""  
  - given-names: Carter
    family-names: Francis
    # orcid: ""  
    # affiliation: ""  
  - given-names: "Sangjoon Bob"
    family-names: Lee
    # orcid: ""  
    # affiliation: ""  
  - given-names: Darshan
    family-names: Mali
    # orcid: ""  
    # affiliation: ""  
  - given-names: Nicholas
    family-names: Marchese
    # orcid: ""  
    # affiliation: ""  
  - given-names: Will
    family-names: Millsaps
    # orcid: ""  
    # affiliation: ""  
doi: 10.5281/zenodo.18642593  # concept DOI (always resolves to the latest release)
license: MIT
repository-code: "https://github.com/electronmicroscopy/quantem"
url: "https://github.com/electronmicroscopy/quantem"
keywords:
  - electron microscopy
  - 4D-STEM
  - ptychography
  - tomography
  - TEM
  - STEM
  - PyTorch
references:
  - type: article
    title: "Deep generative priors for robust and efficient electron ptychography"
    authors:
      - given-names: "Arthur R. C."
        family-names: McCray
      - given-names: "Stephanie M."
        family-names: Ribet
      - given-names: Georgios
        family-names: Varnavides
      - given-names: Colin
        family-names: Ophus
    year: 2025
    url: "https://arxiv.org/abs/2511.07795"
    notes: "arXiv:2511.07795"
  - type: article
    title: "Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights"
    authors:
      - given-names: Georgios
        family-names: Varnavides
      - given-names: "Julie Marie"
        family-names: Bekkevold
      - given-names: "Stephanie M."
        family-names: Ribet
      - given-names: "Mary C."
        family-names: Scott
      - given-names: Lewys
        family-names: Jones
      - given-names: Colin
        family-names: Ophus
    journal: "Microscopy and Microanalysis"
    volume: 32
    issue: 2
    year: 2026
    doi: 10.1093/mam/ozaf139
  - type: article
    title: >-
      Missing Wedge Inpainting and Joint Alignment in Electron Tomography through
      Implicit Neural Representations
    authors:
      - given-names: Cedric
        family-names: Lim
      - given-names: Corneel
        family-names: Casert
      - given-names: "Arthur R. C."
        family-names: McCray
      - given-names: Serin
        family-names: Lee
      - given-names: Andrew
        family-names: Barnum
      - given-names: Jennifer
        family-names: Dionne
      - given-names: Colin
        family-names: Ophus
    year: 2025
    url: "https://arxiv.org/abs/2512.08113"
    notes: "arXiv:2512.08113"
  - type: article
    title: >-
      Multi-angle Precession Electron Diffraction (MAPED): A Versatile Approach to
      4D-STEM Precession
    authors:
      - given-names: "Stephanie M."
        family-names: Ribet
      - given-names: Rohan
        family-names: Dhall
      - given-names: Colin
        family-names: Ophus
      - given-names: "Karen C."
        family-names: Bustillo
    journal: "Microscopy and Microanalysis"
    volume: 31
    issue: 6
    year: 2025
    doi: 10.1093/mam/ozaf103