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

<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 THP-1 macrophage<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.<br><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 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).<b>Acquisition ID</b>: jrc_macrophage-1<b>Final voxel size (nm)</b>: 4.0 x 4.0 x 3.36 (X, Y, Z)<b>Dimensions (µm)</b>: 40 x 8 x 37 (X, Y, Z)<b>Imaging start date</b>: 2018-11-11<b>Imaging duration (days)</b>: 19<b>Landing energy (eV)</b>: 1200<b>Imaging current (nA)</b>: 0.25<b>Scanning speed (MHz)</b>: 0.2<b>Dataset URL:</b> s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/<b>Visualization Website:</b> https://openorganelle.janelia.org/datasets/jrc_macrophage-2<br><br><b>Publication</b>: Xu et al., 2021; Heinrich et al., 2021<br>