Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse liver (jrc_mus-liver-3)

dataset

posted on 2023-09-11, 18:17 authored by CellMap Project TeamCellMap Project Team, Wei-Ping Li, Zhiyuan Lu, Stephan PreibischStephan Preibisch, Wei Qiu, Eric T. Trautman

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: Liver tissue from a wild-type, postnatal day 7 mouse, strain: C57BL/6J from Jackson Lab

Sample Description: A dataset featuring isotropic 3D electron microscopy data of the mouse liver (jrc_mus-liver-3). The sample was obtained from a 7-day-old, wild-type C57BL/6 mouse strain sourced from Jackson Laboratory. Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven. The sample was provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia). Post-processing was conducted by Eric Trautman and Stephan Preibisch (HHMI/Janelia).

Protocol: Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven.

Contributions: Sample provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).

Acquisition ID: jrc_mus-liver-3

Voxel size (nm): 8 x 8 x 8 (x, y, z)

Data dimensions (µm): 145.32 x 114.98 x 114.26 (x, y, z)

Imaging start date: 2023-05-03

Imaging duration (days): 31

Scanning speed (MHz): 3

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver-3/jrc_mus-liver-3.zarr/recon-1/em/

Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-liver-3

Publication: Xu et al., 2017; Ackerman et al., 2024