Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila ventral nerve cord (jrc_fly-vnc-1)

Sample: A subset sample of the VNC of the adult male Drosophila melanogaster (Genome type: iso Canton S G1 x w1118)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: Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.Contributions: Sample provided by David Stern (HHMI/Janelia), prepared by Zhiyuan Lu (HHMI/Janelia), imaged by Wei Qiu (HHMI/Janelia), with post-processing by Eric Trautman (HHMI/Janelia) and Stephan Preibisch (HHMI/Janelia).Acquisition ID: jrc_fly-vnc-1Voxel size (nm): 4 x 4 x 4 (x, y, z)Data dimensions (µm): 37.6 x 10 x 8 (x, y, z)Imaging start date: 2018-12-05Imaging duration (days): 12Landing energy (eV): 900Imaging current (nA): 0.25Scanning speed (MHz): 0.200Dataset URL: s3://janelia-cosem-datasets/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-2/em/Visualization Website: https://openorganelle.janelia.org/datasets/jrc_fly-vnc-1Publication: Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021