Manual organelle segmentations (crop51) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-3)

<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, plasma membrane, 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-3 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>: crop51<br><br><b>Primary Annotator</b>: Woohyun Park<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>: 1.02 x 1.02 x 1.02 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 10735 x 331 x 29455 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, 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-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop51<br><br><b>Source (EM) dataset ID</b>: jrc_hela-3<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 3.24 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 49.6 x 4 x 38.88 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114244<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_hela-3<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.

**本数据集隶属于CellMap 2024图像分割挑战赛（CellMap 2024 Segmentation Challenge）**

- **挑战赛数字对象标识符（DOI, Digital Object Identifier）**: https://doi.org/10.25378/janelia.c.7456966

- **挑战赛官网**: https://cellmapchallenge.janelia.org/

**标注说明**: 针对jrc_hela-3样本中的细胞外间隙、质膜、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、细胞质基质、内体、囊泡、内质网、微管、细胞、内质网膜集合（endoplasmic reticulum membrane collective），使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《利用Amira手动对体积电子显微镜（vEM, volume electron microscopy）图像中的细胞器进行分割以用于机器学习 V.3》标注协议完成密集型三维分割。

**标注ID**: crop51

**主要标注者**: 朴宇炫（Woohyun Park）

**标注协议**: 《利用Amira手动对体积电子显微镜图像中的细胞器进行分割以用于机器学习 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（nm）**: 2 × 2 × 2（x、y、z轴）

**标注数据尺寸（µm）**: 1.02 × 1.02 × 1.02（x、y、z轴）

**标注数据偏移量（nm）**: 10735 × 331 × 29455（x、y、z轴）

**标注类别**: 细胞外间隙、质膜、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、细胞质基质、内体、囊泡、内质网、微管、细胞、内质网膜集合（endoplasmic reticulum membrane collective）

**数据集访问地址**: s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop51

**原始电子显微镜（EM, Electron Microscopy）数据集ID**: jrc_hela-3

**原始电子显微镜体素尺寸（nm）**: 4 × 4 × 3.24（x、y、z轴）

**原始电子显微镜数据尺寸（µm）**: 49.6 × 4 × 38.88（x、y、z轴）

**原始电子显微镜数据集数字对象标识符（DOI）**: https://doi.org/10.25378/janelia.13114244

**可视化官网**: https://openorganelle.janelia.org/datasets/jrc_hela-3

**相关出版物**: 《CellMap图像分割挑战赛》，2024年。

**此阶段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。

**此阶段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、Aubrey Weigel。