Found while auditing the documentation website.
The five *_Thev2016 modality configs imply a reference to "Thevenaz 2016", but those parameters are the NPC reference-standard modality settings from Thevathasan et al. 2019, Nuclear Pores as Versatile Reference Standards for Quantitative Superresolution Microscopy, Nature Methods 16(10):1045-1053, doi:10.1038/s41592-019-0574-9. The Thev2016 abbreviation has the wrong author spelling implication and the wrong year (2019, not 2016).
Evidence it is Thevathasan 2019: the pixel sizes in these configs (Widefield 100, Confocal 70, AiryScan 40, STED 15 nm) match the manuscript SI Methods NPC modality pixel sizes exactly, and it is the same five-modality set (Widefield/Confocal/AiryScan/STED/SMLM) used on NPCs in that paper. There is no "Thevenaz" reference in the manuscript bibliography.
Affected files
src/vlab4mic/configs/modalities/{Widefield,Confocal,AiryScan,STED,STORM}_Thev2016.yaml (filename and internal name: field)- Referenced by name in
examples/real_vs_simulation.py and examples/article_figures/figS_NPC_quantification.py
Note: this is a breaking change — the config IDs are loaded by name in the figure scripts (and possibly saved configs / notebooks), so a rename must update those references together. The documentation website citation has already been corrected (HenriquesLab/website-VLab4Mic#1); only the package-side config IDs still carry the misnomer.
Suggested fix (post-submission / non-urgent): rename the family to a Thevathasan-2019-aligned identifier (e.g. *_Thev2019 or *_NPCref) and update the two example scripts, or keep the IDs and add a comment in each YAML clarifying the source is Thevathasan et al. 2019. Deferring is reasonable given the current code freeze.
Found while auditing the documentation website.
The five
*_Thev2016modality configs imply a reference to "Thevenaz 2016", but those parameters are the NPC reference-standard modality settings from Thevathasan et al. 2019, Nuclear Pores as Versatile Reference Standards for Quantitative Superresolution Microscopy, Nature Methods 16(10):1045-1053, doi:10.1038/s41592-019-0574-9. TheThev2016abbreviation has the wrong author spelling implication and the wrong year (2019, not 2016).Evidence it is Thevathasan 2019: the pixel sizes in these configs (Widefield 100, Confocal 70, AiryScan 40, STED 15 nm) match the manuscript SI Methods NPC modality pixel sizes exactly, and it is the same five-modality set (Widefield/Confocal/AiryScan/STED/SMLM) used on NPCs in that paper. There is no "Thevenaz" reference in the manuscript bibliography.
Affected files
src/vlab4mic/configs/modalities/{Widefield,Confocal,AiryScan,STED,STORM}_Thev2016.yaml(filename and internalname:field)examples/real_vs_simulation.pyandexamples/article_figures/figS_NPC_quantification.pyNote: this is a breaking change — the config IDs are loaded by name in the figure scripts (and possibly saved configs / notebooks), so a rename must update those references together. The documentation website citation has already been corrected (HenriquesLab/website-VLab4Mic#1); only the package-side config IDs still carry the misnomer.
Suggested fix (post-submission / non-urgent): rename the family to a Thevathasan-2019-aligned identifier (e.g.
*_Thev2019or*_NPCref) and update the two example scripts, or keep the IDs and add a comment in each YAML clarifying the source is Thevathasan et al. 2019. Deferring is reasonable given the current code freeze.