Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Zebrafish cardiac tisue (jrc_zf-cardiac-1)

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: 7 day post fertilization larval zebrafishSample Description: The study utilized 7-day post-fertilization larval zebrafish from the Casper strain provided by Virginia Ruetten and Misha Ahrens (HHMI/Janelia). The heads of the larvae were carefully peeled to enhance fixative penetration, after which the tissue was fixed in a mixture of glutaraldehyde and paraformaldehyde. Staining was conducted using low-temperature reduced osmium for contrast, followed by en bloc staining with lead and uranyl acetate for detailed ultrastructural visualization. The samples underwent dehydration through graded acetone solutions and were then infiltrated with Durcupan resin in propylene oxide. Finally, the specimens were embedded in Durcupan and polymerized at 60°C for 72 hours. Dissection, staining, and resin embedding were performed by Nirmala Iyer (HHMI/Janelia), imaging was conducted by Wei Qiu (HHMI/Janelia), and post-processing was completed by Eric Trautman and Stephan Preibisch (HHMI/Janelia).Protocol: The head of a zebrafish larvae at 7 days post-fertilization (dpf) was carefully peeled to enhance fixative penetration. The tissue was then fixed in a mixture of glutaraldehyde and paraformaldehyde. Staining was performed using low-temperature reduced osmium for contrast, followed by en bloc staining with lead and uranyl acetate for detailed ultrastructural visualization. The samples were dehydrated through graded acetone solutions and infiltrated with Durcupan resin in propylene oxide. Finally, the specimens were embedded in Durcupan and polymerized at 60°C for 72 hours.Contributions: Sample provided by Virginia Ruetten and Misha Ahrens (HHMI/Janelia), dissection, staining and resin embedding by Nirmala Iyer, (HHMI/Janelia), prepared for imaging by Nirmala Iyer HHMI/Janelia), with imaging by Wei Qiu (HHMI/Janlia), and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).Acquisition ID: jrc_zf-cardiac-1Voxel size (nm): 8 x 8 x 8 (x, y, z)Data dimensions (µm):165.03 x 158.51 x 321.22 (x, y, z)Imaging start date: 2022-07-06Imaging duration (days): 69Primary energy (eV): 1200Imaging current (nA): 3Scanning speed (MHz): 3Dataset URL: s3://janelia-cosem-datasets/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/em/EM DOI: https://doi.org/10.25378/janelia.22630519Visualization Website: https://openorganelle.janelia.org/datasets/jrc_zf-cardiac-1Publication: Xu et al., 2017