Manual organelle segmentations (crop73) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of macrophage cell (jrc_macrophage-2)

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of extracellular space in jrc_macrophage-2 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br><br><b>Annotation ID</b>: crop73<br><br><b>Primary Annotator</b>: COSEM Project Team<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 6115 x 5387 x 20279 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop73<br><b>Source (EM) dataset ID</b>: jrc_macrophage-2<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 40 x 8 x 44.35 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114343<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_macrophage-2<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.

<b>本数据集隶属于CellMap 2024图像分割挑战赛（CellMap 2024 Segmentation Challenge）</b><br><br>- <b>挑战赛数字对象标识符（DOI）</b>：https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>挑战赛官方网站</b>：https://cellmapchallenge.janelia.org/<br><br><b>标注说明</b>：针对jrc_macrophage-2样本中的细胞外间隙开展稠密分割工作，所用工具包括Amira 3D 2021.1、Classic Segmentation Workroom，以及《用于机器学习的体积电子显微镜样品中细胞器手动分割（V.3版）》标注规程。<br><br><b>标注ID</b>：crop73<br><br><b>主要标注团队</b>：COSEM项目团队<br><br><b>标注规程</b>：《用于机器学习的体积电子显微镜样品中细胞器手动分割（V.3版）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）<br><br><b>所用软件</b>：Amira 3D 2021.1、Classic Segmentation Workroom<br><br><b>标注体素尺寸（纳米）</b>：2 × 2 × 2（x、y、z轴）<br><br><b>标注数据维度（微米）</b>：0.8 × 0.8 × 0.8（x、y、z轴）<br><br><b>标注数据偏移量（纳米）</b>：6115 × 5387 × 20279（x、y、z轴）<br><br><b>标注类别</b>：细胞外间隙<br><br><b>数据集地址</b>：s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop73<br><br><b>源电子显微镜（EM）数据集ID</b>：jrc_macrophage-2<br><br><b>源电子显微镜体素尺寸（纳米）</b>：4 × 4 × 4（x、y、z轴）<br><br><b>源电子显微镜数据维度（微米）</b>：40 × 8 × 44.35（x、y、z轴）<br><br><b>源电子显微镜数据集数字对象标识符（DOI）</b>：https://doi.org/10.25378/janelia.13114343<br><br><b>可视化网站</b>：https://openorganelle.janelia.org/datasets/jrc_macrophage-2<br><br><b>相关出版物</b>：<i>CellMap Segmentation Challenge</i>, 2024.<br><br><b>本项目当期参与团队成员</b>：David Ackerman、Davis Bennett、Marley Bryant、Hannah Nguyen、Grace Park、Alyson Petruncio、Alannah Post、Jacquelyn Price、Diana Ramirez、Jeff Rhoades、Rebecca Vorimo、Aubrey Weigel、Marwan Zouinkhi、Yurii Zubov。<br><br><b>本项目当期指导委员会成员</b>：Misha Ahrens、Christopher Beck、Teng-Leong Chew、Daniel Feliciano、Jan Funke、Harald Hess、Wyatt Korff、Jennifer Lippincott-Schwartz、Zhe J. Liu、Kayvon Pedram、Stephan Preibisch、Stephan Saalfeld、Ronald Vale、Aubrey Weigel。