Manual organelle segmentations (crop18) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-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 vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_hela-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>: crop18<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 0.44 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 7639 x 799 x 14919 (x, y, z)<br><br><b>Classes annotated</b>: vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop18<br><br><b>Source (EM) dataset ID</b>: jrc_hela-2<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 5.2 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 48 x 6.4 x 33.11 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114211<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_hela-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/

**标注说明**：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（volume EM，简称vEM）样本中细胞器手动分割（V.3）》标注协议，在jrc_hela-2样本中对囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、胞质溶胶、内体、囊泡、内质网、微管、细胞、内质网膜集合体进行密集三维分割。

**标注ID**：crop18

**主要标注团队**：COSEM项目组

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

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

**标注体素尺寸（纳米）**：2×2×2（x、y、z轴）

**标注数据尺寸（微米）**：0.8×0.8×0.44（x、y、z轴）

**标注数据偏移量（纳米）**：7639×799×14919（x、y、z轴）

**标注类别**：囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、胞质溶胶、内体、囊泡、内质网、微管、细胞、内质网膜集合体

**数据集地址**：s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop18

**源电子显微镜数据集ID**：jrc_hela-2

**源电子显微镜体素尺寸（纳米）**：4×4×5.2（x、y、z轴）

**源电子显微镜数据尺寸（微米）**：48×6.4×33.11（x、y、z轴）

**源电子显微镜数据集DOI**：https://doi.org/10.25378/janelia.13114211

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

**相关出版物**：《CellMap图像分割挑战赛》，2024年。

**本阶段CellMap项目组成员**：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项目指导委员会成员**：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。