Isotropic 3D electron microscopy reference data of wild-type, immortalized T-Cells (jrc_jurkat-1)

This acquisition is part of the CellMap 2024 Segmentation Challenge
Challenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type Jurkats
Sampe 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 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)
Acquisition ID: jrc_jurkat-1
Final voxel size (nm): 4.0 x 4.0 x 3.44 (X, Y, Z)
Dimensions (µm): 40 x 12 x 29 (X, Y, Z)
Imaging start date: 2018-08-10
Imaging duration (days): 3
Landing energy (eV): 1000
Imaging current (nA): .25
Scanning speed (MHz): .2
Dataset URL: s3://janelia-cosem-datasets/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/em/
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_jurkat-1

Publication: Xu et al., 2021, Heinrich et al., 2021