This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type JurkatsSampe 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-1Final 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: 2018-08-10Imaging duration (days): 3Landing energy (eV): 1000Imaging current (nA): .25Scanning speed (MHz): .2Dataset 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

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type THP-1 macrophageSample 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_macrophage-1Final voxel size (nm): 4.0 x 4.0 x 3.36 (X, Y, Z)Dimensions (µm): 40 x 8 x 37 (X, Y, Z)Imaging start date: 2018-11-11Imaging duration (days): 19Landing energy (eV): 1200Imaging current (nA): 0.25Scanning speed (MHz): 0.2Dataset URL: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/Visualization Website: https://openorganelle.janelia.org/datasets/jrc_macrophage-2

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

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type THP-1 macrophageSample 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_macrophage-1Final voxel size (nm): 4.0 x 4.0 x 3.36 (X, Y, Z)Dimensions (µm): 40 x 8 x 37 (X, Y, Z)Imaging start date: 2018-11-11Imaging duration (days): 19Landing energy (eV): 1200Imaging current (nA): 0.25Scanning speed (MHz): 0.2Dataset URL: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/Visualization Website: https://openorganelle.janelia.org/datasets/jrc_macrophage-2

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

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type JurkatsSampe 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-1Final 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: 2018-08-10Imaging duration (days): 3Landing energy (eV): 1000Imaging current (nA): .25Scanning speed (MHz): .2Dataset 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

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 JurkatsProtocol: 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)Dataset ID: jrc_jurkat-1Final voxel size (nm): 4.0 x 4.0 x 3.44 (X, Y, Z)Dimensions (µm): 40 x 12 x 29 (X, Y, Z)Acquisition date: 2018-08-10Dataset URL: https://data.janelia.org/XJem8Visualization Website: https://openorganelle.janelia.org/datasets/jrc_jurkat-1
Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu, et al. (in preparation)

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 THP-1 macrophageProtocol: 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).Dataset ID: jrc_macrophage-1Final voxel size (nm): 4.0 x 4.0 x 3.36 (X, Y, Z)Dimensions (µm): 40 x 8 x 37 (X, Y, Z)Acquisition date: 2018-11-11Dataset URL: https://data.janelia.org/PzMhfVisualization Website: https://openorganelle.janelia.org/datasets/jrc_macrophage-2
Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu, et al. (in preparation)