Manual organelle segmentations (crop6) 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 mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, 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>: crop6<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>: 1 x 1 x 1 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 12079 x 1599 x 11995 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, 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/crop6<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.

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

- **挑战赛DOI（数字对象唯一标识符，Digital Object Identifier）**：https://doi.org/10.25378/janelia.c.7456966

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

**标注描述**：在jrc_hela-2样本中，使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《用于机器学习的体视电子显微镜（volume EM, vEM）图像中细胞器手动分割方法V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3）标注协议，完成了以下结构的密集分割：线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网出口位点腔、内质网出口位点膜、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、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体。

**标注ID**：crop6

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

**标注协议**：《用于机器学习的体视电子显微镜图像中细胞器手动分割方法V.3》（Using Amira to manually segment organelles in vEM for machine learning 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（voxel）尺寸（纳米）**：2×2×2（x、y、z轴）

**标注数据维度（微米）**：1×1×1（x、y、z轴）

**标注数据偏移量（纳米）**：12079×1599×11995（x、y、z轴）

**标注类别**：线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网出口位点腔、内质网出口位点膜、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、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体

**数据集访问地址**：s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop6

**源电子显微镜（Electron Microscopy, EM）数据集ID**：jrc_hela-2

**源电子显微镜数据体素尺寸（纳米）**：4×4×5.2（x、y、z轴）

**源电子显微镜数据维度（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

**发表文献**：《CellMap分割挑战赛（CellMap Segmentation Challenge）》，2024年。

**本项目期间的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。

**本项目期间的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。