Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of human renal carcinoma cell (jrc_ut21-1413-003)

This acquisition is part of the CellMap 2024 Segmentation Challenge
Challenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Human Renal Cell Carcinoma sample with healthy, marginal and cancerous tissue.
Sample Description: This dataset features isotropic 3D electron microscopy data of tumor tissue from patients with renal cell carcinoma (RCC) following NCI protocol NCI-97-C-0147. Tumor and related normal tissues were immersion-fixed in glutaraldehyde and sectioned using a vibratome. After reducing OTO staining at room temperature, the sample was dehydrated in graded ethanol, infiltrated with Durcupan resin, and polymerized in a 60°C oven. The sample was provided by Dan Crooks and W. Marston Linehan (NIH), stained and resin-embedded by Wei-Ping Li (HHMI/Janelia), prepared for FIB-SEM imaging by Zhiyuan Lu (HHMI/Janelia), imaged by Wei Qiu (HHMI/Janelia), and post-processed by Eric Trautman and Stephan Preibisch (HHMI/Janelia).
Protocol: Tumor and related normal tissues were collected from renal cancer patients following NCI protocol NCI-97-C-0147. The tissues were immersion-fixed in glutaraldehyde and sectioned using a vibratome. After room temperature reducing OTO staining, the sample was dehydrated in graded ethanol, infiltrated with Durcupan resin, and polymerized in a 60°C oven.
Contributions: Sample provided by Dan Crooks (NIH) and W. Marston Linehan (NIH), stained and resin embedded by Wei-Ping Li (HHMI/Janelia), prepared for FIB-SEM imaging by Zhiyuan Lu (HHMI/Janelia), imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).

Acquisition ID: jrc_ut21-1413-003
Voxel size (nm): 8 x 8 x 8 (x, y, z)
Data dimensions (µm): 130.42 x 91.22 x 121.19 (x, y, z)
Imaging start date: 2022-07-03
Imaging duration (days): 10
Primary energy (eV): 1200
Imaging current (nA): 3
Scanning speed (MHz): 6
Dataset URL: s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/em/
EM DOI: https://doi.org/10.25378/janelia.27075529
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003
Publication: Xu et al., 2017