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Isotropic 3D electron microscopy reference data of wild-type, immortalized breast cancer cell, SUM159 (jrc_sum159-1)
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 SUM-159 cell
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 Jeeyun Chung, Tobias Walther and Bob Farese (Harvard U.), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).
Dataset ID: jrc_sum159-1
Final voxel size (nm): 4.00 x 4.00 x 4.56 (X, Y, Z)
Dimensions (µm): 64 x 11 x 35 (X, Y, Z)
Acquisition date: 2017-11-21
Dataset URL: https://data.janelia.org/8eTqV
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_sum159-1
Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu, et al. (in preparation)