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Isotropic 3D electron microscopy reference data of wild-type, THP-1 macrophage (jrc_macrophage-2)

posted on 12.11.2020, 23:32 by C. Shan Xu, Gleb Shtengel, Davis Bennett, Huxley Hoffman, Schuyler van Engelenburg, Harald Hess

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.

Sample: Wild-type THP-1 macrophage

Protocol: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.

Contributions: Sample provided by Huxley K. Hoffman and Schuyler B. van Engelenburg (U. Denver), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).

Dataset ID: jrc_macrophage-1

Final voxel size (nm): 4.0 x 4.0 x 3.36 (X, Y, Z)

Dimensions (µm): 40 x 8 x 37 (X, Y, Z)

Acquisition date: 2018-11-11

Dataset URL:

Visualization Website:

Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu, et al. (in preparation)




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