Near-isotropic, aligned volume electron microscopy (eFIB-SEM) of Mouse cerebral cortex (jrc_mus-cortex-3)
Sample: Wild-type, 8 month old mouse, strain: C57BL6/129 from Gene Targeting & Transgenic Facility of HHMI Janelia Research Campus
Sample Description: The mouse cerebral cortex is a highly organized and complex structure that plays a central role in sensory processing, motor control, and cognition. Its modular organization, plasticity, and functional specialization make it a critical region for understanding brain function and neurological disorders. The mouse model provides valuable insights into cortical development, plasticity, and disease, advancing our understanding of both basic neuroscience and neurodegenerative conditions. Electron microscopy has provided essential insights into the ultrastructure of the mouse cerebral cortex, allowing for a deeper understanding of synaptic organization, neuronal connectivity, and synaptic plasticity, which are advancing our knowledge of normal brain function and how abnormalities in cortical circuits contribute to disease. By revealing the fine details of neurons, synapses, and cellular structures, EM continues to be a powerful tool for studying the mouse cerebral cortex in both healthy and diseased states.
Protocol: 8-month-old female C57BL6/129 mice were anesthetized with a ketamine/xylazine anesthetic mixture before perfusion with 2% depolymerized paraformaldehyde and 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer. Samples were postfixed in 2% OsO₄, 1.5% K₄Fe(CN)₆, and 0.1 M sodium cacodylate buffer for 1 hour. Subsequently, specimens were stained en bloc with 2% aqueous uranyl acetate (1 hour), dehydrated in increasing concentrations of ethanol and propylene oxide, embedded in Epon, and then re-embedded in Durcupan.
Contributions: Sample provided by Yumei Wu, Christina Whites, and Pietro De Camilli (Yale), prepared for imaging by Yumei Wu and Christina Whites (Yale), with imaging and post-processing by Wei Qui, Gleb Shtengel, and Harald Hess(HHMI/Janelia).
Acquisition ID: jrc_mus-cortex-3
Voxel size (nm): 4 x 4 x 4 (x, y, z)
Data dimensions (µm): 25.4 x 25.58 x 23.64 (x, y, z)
Imaging start date: 2023-09-03
Imaging duration (days): 31
Primary energy (eV): 900
Imaging current (nA): 0.25
Scanning speed (MHz): 0.100
Dataset URL: s3://janelia-cosem-datasets/jrc_mus-cortex-3/jrc_mus-cortex-3.zarr/recon-1/em/
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-cortex-3
Publication: Xu et al, 2020; Xu et al, 2021
