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本数据集隶属于CellMap 2024分割挑战赛（CellMap 2024 Segmentation Challenge），挑战赛DOI：https://doi.org/10.25378/janelia.c.7456966，挑战赛官网：https://cellmapchallenge.janelia.org/。 样本：受精后7天的斑马鱼幼体 样本描述：本研究使用由Virginia Ruetten与Misha Ahrens（HHMI/Janelia）提供的Casper品系斑马鱼幼体。研究人员小心剥离幼体头部以增强固定液渗透效率，随后将组织置于戊二醛与多聚甲醛混合固定液中进行固定。采用低温还原锇染色以提升对比度，随后使用铅盐与醋酸铀进行块染，以实现精细超微结构的可视化。样本经梯度丙酮溶液脱水后，使用环氧丙烷中的Durcupan树脂（Durcupan）进行渗透浸润。最终将标本包埋于Durcupan树脂中，并于60℃下聚合72小时。剥离操作、染色与树脂包埋由Nirmala Iyer（HHMI/Janelia）完成，成像工作由Wei Qiu（HHMI/Janelia）执行，后处理流程由Eric Trautman与Stephan Preibisch（HHMI/Janelia）完成。 实验方案：小心剥离受精后7天（days post fertilization, dpf）的斑马鱼幼体头部以增强固定液渗透能力。随后将组织置于戊二醛与多聚甲醛混合液中固定。采用低温还原锇染色以增强对比度，接着使用铅盐与醋酸铀进行块染，实现精细超微结构的可视化。样本经梯度丙酮溶液脱水后，使用环氧丙烷中的Durcupan树脂进行渗透浸润。最终将标本包埋于Durcupan树脂中，并于60℃下聚合72小时。 贡献说明：样本由Virginia Ruetten与Misha Ahrens（HHMI/Janelia）提供；剥离、染色与树脂包埋由Nirmala Iyer（HHMI/Janelia）完成；成像准备由Nirmala Iyer（HHMI/Janelia）执行，成像由Wei Qiu（HHMI/Janelia）完成；后处理由Eric Trautman与Stephan Preibisch（HHMI/Janelia）完成。 采集ID：jrc_zf-cardiac-1 体素尺寸（nm）：8 × 8 × 8（x、y、z轴） 数据尺寸（µm）：165.03 × 158.51 × 321.22（x、y、z轴） 成像起始日期：2022-07-06 成像时长（天）：69 加速电压（eV）：1200 成像电流（nA）：3 扫描速度（MHz）：3 数据集URL：s3://janelia-cosem-datasets/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/em/ 电子显微镜DOI：https://doi.org/10.25378/janelia.22630519 可视化官网：https://openorganelle.janelia.org/datasets/jrc_zf-cardiac-1 相关文献：Xu等，2017年