Manual organelle segmentations (crop88) 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 nucleus 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>: crop88<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>: 13639 x 2159 x 21359 (x, y, z)<br><br><b>Classes annotated</b>: nucleus<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop88<br><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.

**本次采集数据属于CellMap 2024图像分割挑战赛（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/

**标注说明**：针对jrc_macrophage-2样本中的细胞核开展密集分割，所用工具包括Amira 3D 2021.1、Classic Segmentation Workroom，以及标注协议《使用Amira手动分割体积电子显微镜（volume electron microscopy，vEM）中细胞器以适配机器学习V.3》。

**标注ID**：crop88

**主要标注者**：COSEM项目团队（COSEM Project Team）

**标注协议**：《使用Amira手动分割体积电子显微镜（vEM）中细胞器以适配机器学习V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）

**所用软件**：Amira 3D 2021.1、Classic Segmentation Workroom

**标注体素尺寸（nm）**：2 × 2 × 2（x、y、z轴）

**标注数据维度（µm）**：0.8 × 0.8 × 0.8（x、y、z轴）

**标注数据偏移量（nm）**：13639 × 2159 × 21359（x、y、z轴）

**标注类别**：细胞核

**数据集URL**：s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop88

**原始电子显微镜数据集ID**：jrc_macrophage-2

**原始电子显微镜体素尺寸（nm）**：4 × 4 × 4（x、y、z轴）

**原始电子显微镜数据维度（µm）**：40 × 8 × 44.35（x、y、z轴）

**原始电子显微镜DOI**：https://doi.org/10.25378/janelia.13114343

**可视化网站**：https://openorganelle.janelia.org/datasets/jrc_macrophage-2

**发表文献**：《CellMap Segmentation Challenge》，2024年。

**本阶段CellMap项目团队成员包括**：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。

**本阶段CellMap项目团队指导委员会成员包括**：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。