Isotropic 3D electron microscopy reference data of wild-type, immortalized breast cancer cell, SUM159 (jrc_sum159-1)

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type SUM-159 cell<b>Sample description</b>: 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.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in Acetone, resin embedding in Eponate 12.<b>Contributions</b>: 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).<b>Acquisition ID</b>: jrc_sum159-1<b>Final voxel size (nm)</b>: 4.00 x 4.00 x 4.56 (X, Y, Z)<b>Dimensions (µm)</b>: 64 x 11 x 35 (X, Y, Z)<b>Imaging start date:</b> 2017-11-21<b>Imaging duration (days)</b>: 17<b>Primary energy (eV)</b>: 1200<b>Imaging current (nA)</b>: .25<b>Scanning speed (MHz)</b>: .2<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<br><b>Publication:</b> Xu et al., 2021