Isotropic 3D electron microscopy reference data of wild-type, THP-1 macrophage (jrc_macrophage-2)

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: Wild-type THP-1 macrophageSample description: 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.Protocol: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Huxley K. Hoffman and Schuyler B. van Engelenburg (U. Denver), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Acquisition ID: jrc_macrophage-1Final voxel size (nm): 4.0 x 4.0 x 3.36 (X, Y, Z)Dimensions (µm): 40 x 8 x 37 (X, Y, Z)Imaging start date: 2018-11-11Imaging duration (days): 19Landing energy (eV): 1200Imaging current (nA): 0.25Scanning speed (MHz): 0.2Dataset URL: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/Visualization Website: https://openorganelle.janelia.org/datasets/jrc_macrophage-2Publication: Xu et al., 2021; Heinrich et al., 2021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**：野生型THP-1巨噬细胞（Wild-type THP-1 macrophage） **样本说明**：解析细胞架构是理解生命科学的核心前提。电子显微镜（Electron Microscopy, EM）可实现纳米级分辨率下的细胞结构可视化，具备独特技术优势。但传统成像方法，如超薄切片电子显微镜或电子断层扫描技术，分别仅能获取单切片图像或仅覆盖较小体积的细胞区域，存在固有局限性。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，以高分辨率模式开展长达一月的全细胞与全组织长期成像，克服了上述技术瓶颈。我们采用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，本研究期望构建一套标准化参考数据集库，以实现对全细胞及其所有组成成分的全面定量分析，进而解决与细胞身份、细胞形态、细胞间相互作用，以及细胞内细胞器的组织与结构相关的科学问题。 **实验方案**：高压冷冻、基于丙酮体系（含2%四氧化锇、0.1%醋酸铀、3%去离子水）的冷冻替代树脂包埋，随后采用Eponate 12树脂进行包埋。 **贡献说明**：样本由丹佛大学的Huxley K. Hoffman与Schuyler B. van Engelenburg提供，由HHMI/贾内利亚研究所的Gleb Shtengel完成成像前样本制备，成像与后处理工作由HHMI/贾内利亚研究所的C. Shan Xu完成。 **采集编号**：jrc_macrophage-1 **最终体素尺寸（纳米）**：4.0 × 4.0 × 3.36（X、Y、Z轴） **数据集维度（微米）**：40 × 8 × 37（X、Y、Z轴） **成像起始日期**：2018-11-11 **成像时长（天）**：19 **着陆能量（电子伏特）**：1200 **成像束流（纳安）**：0.25 **扫描速率（兆赫兹）**：0.2 **数据集存储地址**：s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/ **可视化官网**：https://openorganelle.janelia.org/datasets/jrc_macrophage-2 **相关发表文献**：Xu等人，2021年；Heinrich等人，2021年