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.

**本数据集属于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/

**注释说明**：使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《用于机器学习的体积电子显微镜（vEM）样本中细胞器手动分割（V.3）》注释协议，对jrc_macrophage-2样本的细胞外间隙进行密集分割。

**注释ID**：crop73

**主要注释团队**：COSEM项目团队（COSEM Project Team）

**注释协议**：《用于机器学习的体积电子显微镜（vEM）样本中细胞器手动分割（V.3）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）

**所用软件**：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）

**注释体素（voxel）尺寸（纳米）**：2 × 2 × 2（x、y、z轴）

**注释数据尺寸（微米）**：0.8 × 0.8 × 0.8（x、y、z轴）

**注释数据偏移量（纳米）**：6115 × 5387 × 20279（x、y、z轴）

**注释类别**：细胞外间隙

**数据集存储地址**：s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop73

**源电子显微镜数据集ID**：jrc_macrophage-2

**源电子显微镜体素（voxel）尺寸（纳米）**：4 × 4 × 4（x、y、z轴）

**源电子显微镜数据尺寸（微米）**：40 × 8 × 44.35（x、y、z轴）

**源电子显微镜数据集DOI**：https://doi.org/10.25378/janelia.13114343

**可视化官网**：https://openorganelle.janelia.org/datasets/jrc_macrophage-2

**相关出版物**：*《CellMap图像分割挑战赛》，2024*

**本项目期间的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。

**本项目期间的CellMap项目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以及Aubrey Weigel。