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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
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Related Experiment Video

Updated: Apr 15, 2026

Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows

Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows

Published on: September 13, 2021

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

Christopher Page¹, Dorit Hanein¹, Niels Volkmann¹

¹Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA.

Ultramicroscopy

|April 13, 2015

Summary

We developed a new method to accurately extract cell membrane locations from electron cryo-tomography data, crucial for understanding mechanobiology and mechanotransduction. This approach improves the analysis of cell-extracellular matrix connections.

Keywords:

Cryo Electron tomography Feature extraction Image processing Membrane detection

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Visualization of Organelles In Situ by Cryo-STEM Tomography

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Published on: June 23, 2023

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Last Updated: Apr 15, 2026

Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows

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Visualization of Organelles In Situ by Cryo-STEM Tomography

Visualization of Organelles In Situ by Cryo-STEM Tomography

Published on: June 23, 2023

Area of Science:

Cell biology
Biophysics
Microscopy

Background:

Cell-extracellular matrix connections are vital for mechanotransduction and mechanobiology.
Electron cryo-tomography (ECT) offers high-resolution analysis of these structures.
Accurate extraction of the ventral cell membrane location from ECT data is challenging due to geometric limitations.

Purpose of the Study:

To introduce a novel strategy for high-fidelity ventral membrane extraction from ECT data.
To enable accurate analysis of cell-matrix interactions in mechanobiology.

Main Methods:

A new membrane tracing strategy based on detecting the cell's interior-exterior boundary.
Utilizing simulation studies to validate the method's accuracy.
Comparing extracted boundaries with visually identified membrane features in experimental data.

Main Results:

The novel strategy accurately models over 99% of the membrane in simulations.
Experimental data showed excellent agreement between visually identified membrane stretches and the extracted boundary.
The method achieves high fidelity and extraordinary accuracy in ventral membrane extraction.

Conclusions:

The developed membrane tracing strategy overcomes limitations in ECT data analysis.
This technique provides a robust tool for high-resolution studies of mechanobiology.
Accurate ventral membrane localization is now feasible for detailed cell-matrix interaction analysis.