Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver-2)

<b>Sample: </b>Wild-type, 8 week old mouse, strain: C57BL/6 from Jackson Lab<b>Sample Description: </b>This dataset features isotropic 3D electron microscopy data of the mouse liver (jrc_mus-liver-2). The sample was obtained from an 8-week-old wild-type C57BL/6 mouse strain, sourced from Jackson Laboratory. Euthanasia was performed in accordance with IACUC guidelines, with perfusion conducted by Shu-Hsien Shu.The sample preparation involved cutting 1.5 mm punches from 100 µm-thick vibratome slices. High-pressure freezing (HPF) was performed using the Wohlwend HPF. Freeze substitution (FS) was carried out with 0.5% OsO₄, 0.1% uranyl acetate, and 20 mM 1,2,4 triazole in acetone, followed by acetone rinses. The sample was infiltrated with increasing concentrations of Durcupan in acetone, followed by three exchanges with 100% Durcupan. The embedding was completed in 100% Durcupan and cured at 60°C for 48 hours.Shu-Hsien Shu was responsible for the perfusion, while Nirmala Iyer (HHMI/Janelia) handled HPF, freeze substitution, and resin embedding. Zhiyuan Lu (HHMI/Janelia) trimmed the sample for FIBSEM, and Wei Qiu (HHMI/Janelia) performed the imaging. Post-processing was completed by Eric Trautman and Stephan Preibisch (HHMI/Janelia).This dataset provides a detailed view of the cellular architecture of a young mouse liver, contributing valuable data for research in hepatology and related areas.<b>Protocol: </b>Mouse euthanasia was performed as IACUC guidelines. Perfusion by Shu-Hsien.1.5 mm punches were cut out of 100µm thick vibratome slices and HPF using the Wohlwend HPF. FS using 0.5% OsO4, 0.1% UA,20mM 1,2,4 triazole in acetone. Acetone rinses followed by infiltration with increasing concentrations of Durcupan in Acetone and 3 exchanges of 100% Durcupan. Embedding in 100% Durcupan and curing at 60 degrees for 48 hours.<b>Contributions:</b> Sample preparation by Shu-Hsien Shu (perfusion) and Nirmala Iyer (HHMI/ Janelia) - HPF FS and resin embedding. Trimmed for FIBSEM by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID:</b> jrc_mus-liver-2<b>Voxel size (nm):</b> 8.0 x 8.0 x 8.0 (X, Y, Z)<b>Data dimensions (µm): </b>82.208, 92.088, 101.704 (X, Y, Z)<b>Imaging start date:</b> 2022-10-20<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_mus-liver-2/jrc_mus-liver-2.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-2<b>Imaging duration (days): </b>9<b>Scanning speed (MHz):</b> 3.000