Manual organelle segmentations (crop292) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase COS-7 cell (jrc_cos7-1a)

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, endosome membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, endosome, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective in jrc_cos7-1a 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.<b>Annotation ID</b>: crop292<b>Primary Annotator</b>: Woohyun Park<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<b>Annotated data offset (nm)</b>: 6702 x 5282 x 862 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, endosome membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, endosome, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop292<b>Source (EM) dataset ID</b>: jrc_cos7-1a<b>Source (EM) voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 41.22 x 8.74 x 3.63 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24943716<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_cos7-1a<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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DOI：** https://doi.org/10.25378/janelia.c.7456966
**挑战赛官网：** https://cellmapchallenge.janelia.org/
**注释描述：** 采用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样品中细胞器手动分割V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3）注释协议，对jrc_cos7-1a样本中的以下结构开展密集分割：线粒体膜、线粒体腔、内体膜、内质网腔、内质网膜、内体腔、异染色质、核孔内侧、核孔外侧、核被膜腔、核被膜、核质、细胞质基质、细胞核、内体、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合体、核被膜集合体
**注释ID：** crop292
**主要注释者：** Woohyun Park
**注释协议：** 《用于机器学习的体视电子显微镜样品中细胞器手动分割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）
**所用软件：** Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）
**注释体素尺寸（nm）：** 2 × 2 × 2（x、y、z轴）
**注释数据尺寸（µm）：** 0.8 × 0.8 × 0.8（x、y、z轴）
**注释数据偏移量（nm）：** 6702 × 5282 × 862（x、y、z轴）
**注释类别：** 线粒体膜、线粒体腔、内体膜、内质网腔、内质网膜、内体腔、异染色质、核孔内侧、核孔外侧、核被膜腔、核被膜、核质、细胞质基质、细胞核、内体、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合体、核被膜集合体
**数据集URL：** s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop292
**源（电子显微镜）数据集ID：** jrc_cos7-1a
**源（电子显微镜）体素尺寸（nm）：** 2 × 2 × 2（x、y、z轴）
**源（电子显微镜）数据尺寸（µm）：** 41.22 × 8.74 × 3.63（x、y、z轴）
**源（电子显微镜）DOI：** https://doi.org/10.25378/janelia.24943716
**可视化网站：** https://openorganelle.janelia.org/datasets/jrc_cos7-1a
**发表文献：** *CellMap 2024图像分割挑战赛*，2024年
**该时期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
**该时期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