Reference isotropic 3D electron microscopy data of mouse liver tissue (jrc_mus-liver)
This acquisition is part of the CellMap 2024 Segmentation Challenge
- Challenge DOI: https://doi.org/10.25378/janelia.c.7456966
- Challenge Website: https://cellmapchallenge.janelia.org/
Sample: Wild-type, 8 week old mouse, strain: C57BL/6 from Jackson Lab
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 because they only visualize a single slice or a relatively small volume of the cell, respectively. We overcame these limitations by imaging whole cells and tissues via the enhanced focused ion beam scanning EM (FIB-SEM) platform at 8-nm voxels with week-long acquisition or 4-nm voxels with month-long acquisition. We used 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 offer a foundation upon which to nucleate a new volume of high-resolution whole-cell EM images and subsequent analyses, a new paradigm that invites biologists to explore and pose questions with a fresh perspective.
This dataset captures a region within the mouse liver that includes several structures of metabolic significance. The data set contains profiles of many complete hepatocytes and their surrounding sinusoids and bile ductules. Some hepatocytes show two nuclei due to their enormous metabolic activity. Perforated endothelial cells and Kupffer cells form the lining of sinusoids. Inside each hepatocyte, many metabolic relevant organelles such as ER, mitochondria, lipid droplets and their structural relationship can be visualized in their entirety.
Protocol: Perfusion fixation with glutaraldehyde and vibratome section followed by room temperature reducing OTO staining. After dehydration and infiltration with graded ethanol and Durcupan resin, polymerize the sample in 60°C oven.
Contributions: Sample provided by Wei-Ping Li (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 Eric Trautman and Stephan Preibisch (HHMI/Janelia).
Acquisition ID: jrc_mus-liver
Final voxel size (nm): 8.00 x 8.00 x 8.00 (X, Y, Z)
Dimensions (µm): 102.0 x 101.8 x 71.5 (X, Y, Z)
Imaging start date: 2021-03-19
Imaging duration (days): 8
Landing energy (eV): 1200
Imaging current (nA): 3
Scanning speed (MHz): 3
Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/em/
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-liver
Publication: Conrad and Nayaran, 2023; Xu et al., 2017
