Manual organelle segmentations (crop81) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-1)

<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 in jrc_sum159-1 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>: crop81<br><br><b>Primary Annotator</b>: Aubrey Weigel<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 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 4371 x 8839 x 16947 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop81<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-1<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 4.56 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 64 x 11.2 x 34.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114352<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<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.

<b>本数据集隶属于CellMap 2024分割挑战赛（CellMap 2024 Segmentation Challenge）</b>

- <b>挑战赛DOI：</b> https://doi.org/10.25378/janelia.c.7456966

- <b>挑战赛官网：</b> https://cellmapchallenge.janelia.org/

<b>注释说明</b>：使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《使用Amira对体积电子显微镜（vEM）样本中的细胞器进行手动分割以适配机器学习 V.3》注释规程，对jrc_sum159-1样本的细胞外间隙开展密集分割标注。

<b>标注ID</b>：crop81

<b>主标注员</b>：Aubrey Weigel

<b>标注规程</b>：《使用Amira对体积电子显微镜（vEM）样本中的细胞器进行手动分割以适配机器学习 V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）

<b>所用软件</b>：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）

<b>标注体素尺寸（nm）</b>：2 × 2 × 2（x、y、z轴）

<b>标注数据尺寸（µm）</b>：0.8 × 0.8 × 0.8（x、y、z轴）

<b>标注数据偏移量（nm）</b>：4371 × 8839 × 16947（x、y、z轴）

<b>标注类别</b>：细胞外间隙

<b>数据集URL</b>：s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop81

<b>源电子显微镜（EM）数据集ID</b>：jrc_sum159-1

<b>源电子显微镜（EM）体素尺寸（nm）</b>：4 × 4 × 4.56（x、y、z轴）

<b>源电子显微镜（EM）数据尺寸（µm）</b>：64 × 11.2 × 34.8（x、y、z轴）

<b>源电子显微镜（EM）DOI</b>：https://doi.org/10.25378/janelia.13114352

<b>可视化网站</b>：https://openorganelle.janelia.org/datasets/jrc_sum159-1

<b>关联出版物</b>：<i>《CellMap分割挑战赛》</i>，2024年。

<b>本阶段CellMap项目团队成员如下：</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>本阶段CellMap项目指导委员会成员如下：</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及Aubrey Weigel。