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Reference isotropic 3D electron microscopy data of mushroom body (entire alpha and alpha’ lobes) of a 5 day-old female Drosophila (jrc_fly-mb-Z0419-20)

posted on 08.12.2021, 21:14 authored by Song Pang, Zhiyuan Lu, Davis Bennett, Yoshinori Aso, Harald HessHarald Hess, Gerald M. Rubin, C. Shan XuC. Shan Xu

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 imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform at 4-nm voxels with month-long acquisition. We use this approach to generate diverse reference 3D image datasets and hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents. These open-access data represent a foundation to nucleate a new field of high-resolution whole-cell volume EM and subsequent analyses, and invite biologists to explore this new paradigm and pose fundamentally new questions.

In Drosophila, the mushroom body (MB) is the major site of associative learning. Sensory information enters the MB via the calyx, where the dendritic claws of Kenyon cells (KCs) receive synaptic inputs from projection neurons of olfactory and other modalities including visual, gustatory and thermal. This dataset provides synapse level anatomical information on neuronal circuits involved in learning and memory in Drosophila at the finest isotropic resolution.

Sample: Mushroom body (entire alpha and alpha’ lobes) of a 5 day-old adult female Drosophila (Genome type: iso Canton S G1 x w1118 iso 5905). The largest tissue sample imaged at 4-nm voxels to date (2021).

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 for imaging by Song Pang (HHMI/Janelia), with imaging by Song Pang (HHMI/Janelia) and C. Shan Xu (HHMI/Janelia), and post-processing by C. Shan Xu (HHMI/Janelia).

Dataset ID: jrc_fly-mb-Z0419-20

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

Dimensions (µm): 120 x 72 x 105 (X, Y, Z)

Acquisition date: 2020-05-12

Dataset URL:

Visualization Website:


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