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Isotropic 3D electron microscopy reference data of accessory calyx of a 5 day-old male Drosophila (jrc_fly-acc-calyx-1)

posted on 12.11.2020, 23:41 by C. Shan Xu, Song Pang, Davis Bennett, Shin-ya Takemura, Zhiyuan Lu, 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.

Accessory calyx is the input region of the mushroom body, a center of associative learning in insect brain. In Drosophila, the calyx has three small subregions called accessory calyces. As well studied for its role in olfactory associative learning, the mushroom body also receives inputs from several other sensory modalities. While the main calyx receives olfactory input as a main, accessory calyces are largely sites of non-olfactory input. The unique ability of enhanced FIB-SEM to image tissues at 4-nm isotropic voxels encompassing particular region of interests enables us to examine the fine structures in great detail, which allows for new biological insights.

Sample: Accessory calyx 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), and prepared, imaged and post-processed by Song Pang (HHMI/Janelia).

Dataset ID: jrc_fly-acc-calyx-1

Final voxel size (nm): 4.00 x 4.00 x 3.72 (X, Y, Z)

Dimensions (µm): 50 x 40 x 81 (X, Y, Z)

Acquisition date: 2019-12-06

Dataset URL:

Visualization Website:

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