Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-4)

dataset

posted on 2024-10-17, 21:53 authored by FIB-SEM Technology GroupFIB-SEM Technology Group, CellMap Project TeamCellMap Project Team, Jeeyun Chung, Robert V. Farese Jr, Gleb Shtengel, Tobias C. Walther, C. Shan Xu

This acquisition is part of the CellMap 2024 Segmentation Challenge

Challenge DOI: https://doi.org/10.25378/janelia.c.7456966
Challenge Website: https://cellmapchallenge.janelia.org/

Sample: Wild-type SUM-159 cell

Sample Description: 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.

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).

Acquisition ID: jrc_sum159-4

Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)

Dimensions (µm): 95 x 8.5 x 47.8 (X, Y, Z)

Imaging start date: 1/19/2018

Imaging duration (days): 6

Primary energy (eV): 1200

Imaging current (nA): 2

Scanning speed (MHz): .5

Dataset URL: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/em/

Visualization Website: https://openorganelle.janelia.org/datasets/jrc_sum159-4

Publication: Xu, et al., 2017