Manual organelle segmentations (crop149) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney)

<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, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endosome lumen, cytosol, endosome, vesicle, cell in jrc_mus-kidney 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>: crop149<br><br><b>Primary Annotator</b>: Woohyun Park<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>: 4 x 4 x 4 (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>: 11174 x 22006 x 96598 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endosome lumen, cytosol, endosome, vesicle, cell<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop149<br><br><b>Source (EM) dataset ID</b>: jrc_mus-kidney<br><br><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 98.3 x 63.81 x 177.59 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913035<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-kidney<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>该采集属于CellMap 2024分割挑战赛的一部分</b><br><br>- <b>挑战赛DOI：</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>挑战赛官网：</b> https://cellmapchallenge.janelia.org/<br><br><b>标注描述</b>：使用Amira 3D 2021.1、Classic Segmentation Workroom及《使用Amira手动分割vEM中的细胞器以用于机器学习V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3）标注协议，对jrc_mus-kidney数据集中的细胞外空间、质膜、囊泡膜、内体膜、囊泡腔、内体腔、细胞质、内体、囊泡和细胞进行了密集分割。<br><br><b>标注ID</b>：crop149<br><br><b>主要标注者</b>：Woohyun Park<br><br><b>标注协议</b>：《使用Amira手动分割vEM中的细胞器以用于机器学习V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）<br><br><b>软件</b>：Amira 3D 2021.1、Classic Segmentation Workroom<br><br><b>标注体素大小（纳米）</b>：4 x 4 x 4（x, y, z）<br><br><b>标注数据维度（微米）</b>：0.8 x 0.8 x 0.8（x, y, z）<br><br><b>标注数据偏移量（纳米）</b>：11174 x 22006 x 96598（x, y, z）<br><br><b>标注类别</b>：细胞外空间、质膜、囊泡膜、内体膜、囊泡腔、内体腔、细胞质、内体、囊泡、细胞<br><br><b>数据集URL</b>：s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop149<br><br><b>源（电镜）数据集ID</b>：jrc_mus-kidney<br><br><b>源（电镜）体素大小（纳米）</b>：8 x 8 x 8（x, y, z）<br><br><b>源（电镜）数据维度（微米）</b>：98.3 x 63.81 x 177.59（x, y, z）<br><br><b>源（电镜）DOI</b>：https://doi.org/10.25378/janelia.16913035<br><br><b>可视化网站</b>：https://openorganelle.janelia.org/datasets/jrc_mus-kidney<br><br><b>出版物：</b> <i>CellMap分割挑战赛</i>，2024年。<br><br><b>在此期间，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。<br><br><b>在此期间，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和Aubrey Weigel。