Manual organelle segmentations (crop82) 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>: crop82<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>: 19587 x 243 x 16919 (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/crop82<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>本数据集采集属于CellMap 2024分割挑战赛的一部分</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>标注描述</b>：使用Amira 3D 2021.1、经典分割工作室及‘Using Amira to manually segment organelles in vEM for machine learning V.3’标注协议对jrc_sum159-1中的细胞外空间进行密集分割。

<b>标注ID</b>：crop82

<b>主要标注者</b>：Aubrey Weigel

<b>标注协议</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>软件</b>：Amira 3D 2021.1、经典分割工作室

<b>标注体素大小（纳米）</b>：2×2×2（x、y、z）

<b>标注数据维度（微米）</b>：0.8×0.8×0.8（x、y、z）

<b>标注数据偏移量（纳米）</b>：19587×243×16919（x、y、z）

<b>标注类别</b>：细胞外空间

<b>数据集URL</b>：s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop82

<b>源（电子显微镜（EM））数据集ID</b>：jrc_sum159-1

<b>源（电子显微镜（EM））体素大小（纳米）</b>：4×4×4.56（x、y、z）

<b>源（电子显微镜（EM））数据维度（微米）</b>：64×11.2×34.8（x、y、z）

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

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

<b>出版物</b>：《CellMap Segmentation Challenge》，2024年。

<b>此期间CellMap项目团队成员包括</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>此期间CellMap项目团队指导委员会成员包括</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。