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Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: ellipsoid body (jrc_fly-ellipsoid-body)

dataset
posted on 2024-03-01, 15:22 authored by CellMap Project TeamCellMap Project Team, Harald HessHarald Hess, Zhiyuan Lu, Song Pang, C. Shan XuC. Shan Xu

Sample: Ellipsoid body of a 5 day-old adult male Drosophila (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 Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).

Acquisition ID: jrc_fly-ellipsoid-body

Voxel size (nm): 4 x 4 x 4 (X, Y, Z)

Data dimensions (µm): 7.6 x 7.3 x 9.4 (X, Y, Z)

Imaging start date: 2016-06-08

Imaging duration (days): 6

Landing energy (eV): 200

Imaging current (nA): 0.22

Scanning speed (MHz): 0.200

Dataset URL (Redirect): https://data.janelia.org/Oz2Rq

Visualization Website: https://openorganelle.janelia.org/datasets/jrc_fly-ellipsoid-body

Publication: Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021


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