Isotropic 3D electron microscopy reference data of wild-type, immortalized breast cancer cell, SUM159 (jrc_sum159-1)

<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_sum159-1<b>Final voxel size (nm)</b>: 4.00 x 4.00 x 4.56 (X, Y, Z)<b>Dimensions (µm)</b>: 64 x 11 x 35 (X, Y, Z)<b>Imaging start date:</b> 2017-11-21<b>Imaging duration (days)</b>: 17<b>Primary energy (eV)</b>: 1200<b>Imaging current (nA)</b>: .25<b>Scanning speed (MHz)</b>: .2<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<br><b>Publication:</b> Xu et al., 2021

本数据集隶属于CellMap 2024图像分割挑战赛。
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：解析细胞结构是阐释生命活动的核心前提。电子显微镜（Electron Microscopy, EM）可凭借纳米级分辨率独特地可视化细胞内部结构。然而传统电子显微技术，如超薄切片电子显微镜技术与电子断层扫描技术，均存在固有局限：前者仅能呈现单切片视野，后者则仅可覆盖细胞内相对有限的三维体积范围。本研究通过搭载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，采用高分辨率模式开展长达月余的全细胞与全组织长期成像，攻克了上述技术瓶颈。我们依托该方案，生成了体素尺寸为4nm的各向同性三维参考图像数据集。结合后续图像分割工作，我们旨在构建一套标准化参考数据库，以实现对完整细胞及其所有组成成分的全面量化分析，进而解答与细胞身份、细胞形态、细胞间相互作用，以及胞内细胞器组织与结构相关的一系列科学问题。
实验方案：采用高压冷冻技术，以含2%四氧化锇（OsO₄）、0.1%醋酸铀（UA）及3%去离子水的丙酮混合液进行冷冻替代树脂包埋，最终使用Eponate 12树脂完成包埋。
贡献说明：样本由Jeeyun Chung、Tobias Walther与Bob Farese（哈佛大学）提供；成像样本制备由Gleb Shtengel（HHMI/简维亚研究所）完成；成像与后处理工作由C. Shan Xu（HHMI/简维亚研究所）负责。
采集编号：jrc_sum159-1
最终体素尺寸（纳米）：4.00 × 4.00 × 4.56（X、Y、Z轴）
数据集三维尺寸（微米）：64 × 11 × 35（X、Y、Z轴）
成像起始日期：2017-11-21
成像总时长（天）：17
加速电压（电子伏特）：1200
成像束流（纳安）：0.25
扫描速率（兆赫兹）：0.2
数据集存储路径：s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/em/
可视化浏览平台：https://openorganelle.janelia.org/datasets/jrc_sum159-1
相关发表文献：Xu等，2021