2020Martinez-Sanchez PySeg

Citation

Martinez-Sanchez, A., Kochovski, Z., Laugks, U. et al. Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods 17, 209–216 (2020). https://doi.org/10.1038/s41592-019-0675-5

Abstract

With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification (PySeg). Applications to intact cells and isolated endoplasmic reticulum (ER) allowed us to detect and classify small protein complexes. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Spatial distribution analysis showed that ER complexes have different localization patterns forming nanodomains. Therefore, this procedure allows a comprehensive detection and structural analysis of complexes in situ.

Links

https://github.com/anmartinezs/pyseg_system

Related software

You can run PySeg through Scipion.

Comments

De novo analysis for cryo-electron tomography.