Patch_analysis

Python codes related to the patch analysis for this publication:

Surface morphometrics reveals local membrane thickness variation in organellar subcompartments. Michaela Medina^†, Ya-Ting Chang^†, Hamidreza Rahmani, Daniel Fuentes, Benjamin A. Barad, Danielle A. Grotjahn BioRxiv 2025 May 1:2025.04.30.651574. doi: https://doi.org/10.1101/2025.04.30.651574

The development of the scripts was based on the Surface Morphometrics toolkit. Installing Surface Morphometrics is highly recommended.

Citation

Pycurv and Surface Morphometrics toolkits were applied to this project.

Surface morphometrics: https://github.com/GrotjahnLab/surface_morphometrics

Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline.
Benjamin A. Barad^†, Michaela Medina^†, Daniel Fuentes, R. Luke Wiseman, Danielle A. Grotjahn
J Cell Biol. 2023 Apr 3;222(4):e202204093; doi: https://doi.org/10.1083/jcb.202204093

Pycurv: https://github.com/kalemaria/pycurv

Reliable estimation of membrane curvature for cryo-electron tomography.
Maria Salfer,Javier F. Collado,Wolfgang Baumeister,Rubén Fernández-Busnadiego,Antonio Martínez-Sánchez
PLOS Comp Biol August 2020; doi: https://doi.org/10.1371/journal.pcbi.1007962