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Isotropic 3D electron microscopy reference data of fan-shaped body of a 5 day-old male Drosophila (jrc_fly-fsb-1)

posted on 12.11.2020, 23:43 by C. Shan Xu, Song Pang, Davis Bennett, Zhiyuan Lu, Shin-ya Takemura, Harald Hess

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.

Fan-shaped body, the largest substructure of the central complex controls various behaviors of insects. To understand brain functions, knowing neuron connectivity at synapse level is critical. High-resolution FIB-SEM images with large volume provide significant values in both identifying synaptic structures and tracing fine neuronal profiles. The detailed examination of synapses and unique intracellular features could add important insights to the understanding of the types of synaptic vesicles, synaptic polarity and neuron’s property.

Sample: Fan-shaped body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118 iso 5905).

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 Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (HHMI/Janelia), with post-processing by C. Shan Xu (HHMI/Janelia).

Dataset ID: jrc_fly-fsb-1

Final voxel size (nm): 4.00 x 4.00 x 4.00 (X, Y, Z)

Dimensions (µm): 45 x 56 x 45 (X, Y, Z)

Acquisition date: 2019-09-14

Dataset URL:

Visualization Website:

Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu et al. (in preparation)