Manual organelle segmentations (crop226) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_ut21-1413-003)

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Annotation description: Dense segmentations of extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, endoplasmic reticulum, cell, basement membrane, endoplasmic reticulum membrane collective in jrc_ut21-1413-003 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.Annotation ID: crop226Primary Annotator: Woohyun ParkAnnotation protocol: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)Software: Amira 3D 2021.1, Classic Segmentation WorkroomAnnotated voxel size (nm): 4 x 4 x 4 (x, y, z)Annotated data dimensions (µm): 1.6 x 1.6 x 1.6 (x, y, z)Annotated data offset (nm): 36398 x 25758 x 60998 (x, y, z)Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, endoplasmic reticulum, cell, basement membrane, endoplasmic reticulum membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop226Source (EM) dataset ID: jrc_ut21-1413-003Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)Source (EM) data dimensions (µm): 130.42 x 91.22 x 121.19 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.27075529Visualization website: https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003Publication: CellMap Segmentation Challenge, 2024.The CellMap Project Team during this time consisted of: 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.The CellMap Project Team Steering Committee during this time consisted of: 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分割挑战赛（CellMap 2024 Segmentation Challenge），其DOI为：https://doi.org/10.25378/janelia.c.7456966，挑战赛官网地址为：https://cellmapchallenge.janelia.org/ ### 注释说明 本注释通过Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《使用Amira手动分割体电子显微镜（vEM）中适配机器学习的细胞器 V.3》注释规程，对样本jrc_ut21-1413-003中的目标类别进行密集分割：细胞外间隙、质膜、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、胞质溶胶、内体、囊泡、内质网、细胞、基底膜、内质网膜集合体。 注释ID：crop226 主要注释者：Woohyun Park 注释规程：《使用Amira手动分割体电子显微镜中适配机器学习的细胞器 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 注释体素尺寸（纳米）：4 × 4 × 4（x、y、z轴） 注释数据维度（微米）：1.6 × 1.6 × 1.6（x、y、z轴） 注释数据偏移量（纳米）：36398 × 25758 × 60998（x、y、z轴） 注释类别：细胞外间隙、质膜、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、胞质溶胶、内体、囊泡、内质网、细胞、基底膜、内质网膜集合体 数据集URL：s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop226 源电子显微镜（EM）数据集ID：jrc_ut21-1413-003 源电子显微镜体素尺寸（纳米）：8 × 8 × 8（x、y、z轴） 源电子显微镜数据维度（微米）：130.42 × 91.22 × 121.19（x、y、z轴） 源电子显微镜DOI：https://doi.org/10.25378/janelia.27075529 可视化网站：https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003 相关出版物：2024年CellMap分割挑战赛 同期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。 同期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及Aubrey Weigel。