Citation

If you use copick in your research, please cite the copick paper. Depending on the tools and data you access through copick, please also cite the relevant references below.

copick

Ermel, U. H., Schwartz, J., Zhao, Z., Ji, D., Peck, A., Yu, Y., Paraan, M., Carragher, B., Frangakis, A. S., & Harrington, K. I. S. (2026). copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography data. Protein Science, 35(5).

DOI: 10.1002/pro.70578

BibTeX

@article{ermel2026copick,
  author  = {Ermel, Utz Heinrich and Schwartz, Jonathan and Zhao, Zhuowen and Ji, Daniel
             and Peck, Ariana and Yu, Yue and Paraan, Mohammadreza and Carragher, Bridget
             and Frangakis, Achilleas S. and Harrington, Kyle I. S.},
  title   = {copick: An open dataset interface and toolkit for collaborative annotation
             and analysis of cryo-electron tomography data},
  journal = {Protein Science},
  volume  = {35},
  number  = {5},
  year    = {2026},
  doi     = {10.1002/pro.70578}
}

ArtiaX

copick's particle and orientation handling — and the ChimeraX-copick plugin — build on ArtiaX. If you use copick to visualize or curate particles in ChimeraX, please also cite:

Ermel, U. H., Arghittu, S. M., & Frangakis, A. S. (2022). ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Protein Science, 31(12).

DOI: 10.1002/pro.4472

BibTeX

@article{ermel2022artiax,
  author  = {Ermel, Utz H. and Arghittu, Serena M. and Frangakis, Achilleas S.},
  title   = {ArtiaX: An electron tomography toolbox for the interactive handling of
             sub-tomograms in UCSF ChimeraX},
  journal = {Protein Science},
  volume  = {31},
  number  = {12},
  year    = {2022},
  doi     = {10.1002/pro.4472}
}

copick integrates with several external tools and data sources. If your work relies on one of them through copick, please also cite its reference.

membrain-seg

A pretrained network for membrane segmentation, run through copick as copick inference membrain-seg (see the tutorial).

Lamm, L., Zufferey, S., Zhang, H., Righetto, R. D., Waltz, F., Wietrzynski, W., Yamauchi, K. A., Burt, A., Liu, Y., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J. A., Engel, B. D., & Peng, T. (2024). MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. bioRxiv.

DOI: 10.1101/2024.01.05.574336

easymode

Pretrained, general-purpose 3D U-Nets for segmenting common cellular features, run through copick as copick inference easymode (see the tutorial).

So-Last et al. (2026). Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging. bioRxiv.

DOI: 10.64898/2026.05.19.726344

CZ cryoET Data Portal

copick can read datasets directly from the CZ cryoET Data Portal (see the tutorial). Please cite the data portal:

Ermel, U., Cheng, A., Ni, J. X., Gadling, J., Venkatakrishnan, M., Evans, K., Asuncion, J., Sweet, A., Pourroy, J., Wang, Z. S., Khandwala, K., Nelson, B., McCarthy, D., Wang, E. M., Agarwal, R., & Carragher, B. (2024). A data portal for providing standardized annotations for cryo-electron tomography. Nature Methods, 21(12), 2200–2202.

DOI: 10.1038/s41592-024-02477-2

When you use portal data, also cite the specific dataset(s) you used — each dataset on the portal lists its own citation and DOI.