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

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Human Renal Cell Carcinoma sample with healthy, marginal and cancerous tissue.<b>Sample Description</b>: 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).<b>Protocol</b>: 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.<b>Contributions</b>: 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).<br><br><b>Acquisition ID</b>: jrc_ut21-1413-003<b>Voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Data dimensions (µm)</b>: 130.42 x 91.22 x 121.19 (x, y, z)<b>Imaging start date</b>: 2022-07-03<b>Imaging duration (days)</b>: 10<b>Primary energy (eV)</b>: 1200<b>Imaging current (nA)</b>: 3<b>Scanning speed (MHz)</b>: 6<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.27075529<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003<b>Publication</b>: Xu et al., 2017