Manual organelle segmentations (crop101) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-3)

This acquisition is part of the CellMap 2024 Segmentation Challenge- Challenge DOI: https://doi.org/10.25378/janelia.c.7456966- Challenge Website: https://cellmapchallenge.janelia.org/Annotation description: Dense segmentations of extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_hela-3 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: crop101Primary Annotator: Alyson PetruncioAnnotation 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): 2 x 2 x 2 (x, y, z)Annotated data dimensions (µm): 0.8 x 0.8 x 0.8 (x, y, z)Annotated data offset (nm): 40931 x 467 x 24083 (x, y, z)Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop101Source (EM) dataset ID: jrc_hela-3Source (EM) voxel size (nm): 4 x 4 x 3.24 (x, y, z)Source (EM) data dimensions (µm): 49.6 x 4 x 38.88 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.13114244Visualization website: https://openorganelle.janelia.org/datasets/jrc_hela-3Publication: 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——挑战赛DOI：https://doi.org/10.25378/janelia.c.7456966，挑战赛官网：https://cellmapchallenge.janelia.org/ 标注说明：使用Amira 3D 2021.1、经典分割工作间（Classic Segmentation Workroom）以及《用于机器学习的体积电子显微镜细胞器手动标注V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3）标注协议，对jrc_hela-3样本中的细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、胞质溶胶、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体进行密集分割。 标注ID：crop101 主要标注员：Alyson Petruncio 标注协议：《用于机器学习的体积电子显微镜细胞器手动标注V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） 使用软件：Amira 3D 2021.1、经典分割工作间（Classic Segmentation Workroom） 标注体素尺寸（nm）：2×2×2（x、y、z轴） 标注数据维度（µm）：0.8×0.8×0.8（x、y、z轴） 标注数据偏移量（nm）：40931×467×24083（x、y、z轴） 标注类别：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、胞质溶胶、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体 数据集URL：s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop101 源电子显微镜数据集ID：jrc_hela-3 源电子显微镜体素尺寸（nm）：4×4×3.24（x、y、z轴） 源电子显微镜数据维度（µm）：49.6×4×38.88（x、y、z轴） 源电子显微镜DOI：https://doi.org/10.25378/janelia.13114244 可视化网站：https://openorganelle.janelia.org/datasets/jrc_hela-3 相关发表：《2024年CellMap分割挑战赛》（CellMap Segmentation Challenge, 2024） 本次研究期间的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。 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以及Aubrey Weigel。