Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-4)

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type SUM-159 cell<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in Acetone, resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by Jeeyun Chung, Tobias Walther and Bob Farese (Harvard U.), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).<b>Acquisition ID</b>: jrc_sum159-4<b>Final voxel size (nm)</b>: 8.0 x 8.0 x 8.0 (X, Y, Z)<b>Dimensions (µm)</b>: 95 x 8.5 x 47.8 (X, Y, Z)<b>Imaging start date</b>: 1/19/2018<b>Imaging duration (days):</b> 6<b>Primary energy (eV)</b>: 1200<b>Imaging current (nA)</b>: 2<b>Scanning speed (MHz)</b>: .5<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<b>Publication</b>: Xu, et al., 2017

本数据集属于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：野生型SUM-159细胞
样本说明：解析细胞架构是理解生命科学的核心基础。电子显微镜（Electron Microscopy, EM）可凭借纳米级分辨率独特可视化细胞结构，但传统方法如超薄切片电子显微镜或电子断层成像术存在局限：前者仅能呈现单张切片的视野，后者则仅能覆盖细胞内相对狭小的体积范围。本研究通过增强型聚焦离子束扫描电子显微镜（Focus Ion Beam Scanning Electron Microscopy, FIB-SEM）平台的高分辨率模式，以长达一月的采集时长对完整细胞与组织进行长期成像，从而突破上述限制。我们依托该方法生成了各向同性体素尺寸为4纳米的三维参考图像数据集。结合后续的图像分割工作，本研究旨在构建一套参考文库，以实现对完整细胞及其所有组成成分的全面定量分析，进而解答与细胞身份、细胞形态、细胞间相互作用，以及细胞内细胞器组织与结构相关的科学问题。
实验方案：采用高压冷冻、冷冻替代树脂包埋工艺：以丙酮为溶剂，配制含2%四氧化锇（OsO4）、0.1%乙酸铀（UA）、3%水的包埋液，最终使用Eponate 12树脂完成包埋。
贡献者：样本由Jeeyun Chung、Tobias Walther与Bob Farese（哈佛大学，Harvard University）提供，成像前样品制备由Gleb Shtengel（HHMI/简维亚研究所，HHMI/Janelia）完成，成像与后处理工作由C. Shan Xu（HHMI/简维亚研究所）执行。
采集编号：jrc_sum159-4
最终体素尺寸（纳米）：8.0 × 8.0 × 8.0（X、Y、Z轴）
数据集维度（微米）：95 × 8.5 × 47.8（X、Y、Z轴）
成像开始日期：2018年1月19日
成像时长（天）：6
加速电压（电子伏特）：1200
成像电流（纳安）：2
扫描速度（兆赫兹）：0.5
数据集链接：s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/em/
可视化网站：https://openorganelle.janelia.org/datasets/jrc_sum159-4
相关文献：Xu等人，2017年