Manual organelle segmentations (crop252) 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 extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum 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>: crop252<b>Primary Annotator</b>: Nora Forknall<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>: 9600 x 5000 x 240 (x, y, z)<b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop252<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.

本数据集隶属于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/
注释描述：使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《面向机器学习的体电子显微镜（vEM）中细胞器手动分割方案V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3），对jrc_cos7-1a样本完成以下类别的全密实例分割：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、线粒体核糖体、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、胞质溶胶、溶酶体、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。
注释ID：crop252
主要注释者：Nora Forknall
注释方案：《面向机器学习的体电子显微镜中细胞器手动分割方案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）
注释体素尺寸（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）：9600 × 5000 × 240（x、y、z轴）
注释类别：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、线粒体核糖体、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、胞质溶胶、溶酶体、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
数据集地址：s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop252
原始电子显微镜数据集ID：jrc_cos7-1a
原始电子显微镜体素尺寸（纳米）：2 × 2 × 2（x、y、z轴）
原始电子显微镜数据尺寸（微米）：41.22 × 8.74 × 3.63（x、y、z轴）
原始电子显微镜数据集DOI：https://doi.org/10.25378/janelia.24943716
可视化官网：https://openorganelle.janelia.org/datasets/jrc_cos7-1a
发表文献：《CellMap Segmentation Challenge》，2024年。
本项目实施期间的CellMap项目组成员包括：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。
本项目实施期间的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及Aubrey Weigel。