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Ultramicroscopy. 2015 Aug;155:20-26. doi: 10.1016/j.ultramic.2015.03.021. Epub 2015 Mar 30.

Accurate membrane tracing in three-dimensional reconstructions from electron cryotomography data.

Author information

1
Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA.
2
Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA. Electronic address: niels@burnham.org.

Abstract

The connection between the extracellular matrix and the cell is of major importance for mechanotransduction and mechanobiology. Electron cryo-tomography, in principle, enables better than nanometer-resolution analysis of these connections, but restrictions of data collection geometry hamper the accurate extraction of the ventral membrane location from these tomograms, an essential prerequisite for the analysis. Here, we introduce a novel membrane tracing strategy that enables ventral membrane extraction at high fidelity and extraordinary accuracy. The approach is based on detecting the boundary between the inside and the outside of the cell rather than trying to explicitly trace the membrane. Simulation studies show that over 99% of the membrane can be correctly modeled using this principle and the excellent match of visually identifiable membrane stretches with the extracted boundary of experimental data indicates that the accuracy is comparable for actual data.

KEYWORDS:

Cryo; Electron tomography; Feature extraction; Image processing; Membrane detection

PMID:
25863868
PMCID:
PMC4451430
DOI:
10.1016/j.ultramic.2015.03.021
[Indexed for MEDLINE]
Free PMC Article

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