Manual organelle segmentations (crop54) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-2)

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 in jrc_hela-2 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: crop54Primary Annotator: COSEM Project TeamAnnotation 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): 41332 x 3912 x 10160 (x, y, z)Classes annotated: extracellular spaceDataset URL: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop54Source (EM) dataset ID: jrc_hela-2Source (EM) voxel size (nm): 4 x 4 x 5.2 (x, y, z)Source (EM) data dimensions (µm): 48 x 6.4 x 33.11 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.13114211Visualization website: https://openorganelle.janelia.org/datasets/jrc_hela-2Publication: 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.

本数据集属于CellMap 2024分割挑战赛（CellMap 2024 Segmentation Challenge），挑战赛DOI：https://doi.org/10.25378/janelia.c.7456966，挑战赛官网：https://cellmapchallenge.janelia.org/。标注描述：使用Amira 3D 2021.1、经典分割工作间（Classic Segmentation Workroom）以及《使用Amira手动分割体积电子显微镜（volume electron microscopy, vEM）中细胞器以支持机器学习 V.3》标注规程，对jrc_hela-2样本中的细胞外间隙进行密集分割。标注ID：crop54；主要标注者：COSEM项目团队；标注规程：《使用Amira手动分割体积电子显微镜中细胞器以支持机器学习 V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）；所用软件：Amira 3D 2021.1、经典分割工作间。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）：41332×3912×10160（x、y、z轴）。标注类别：细胞外间隙。数据集URL：s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop54。原始电子显微镜（electron microscopy, EM）数据集ID：jrc_hela-2；原始电子显微镜体素尺寸（nm）：4×4×5.2（x、y、z轴）；原始电子显微镜数据维度（µm）：48×6.4×33.11（x、y、z轴）；原始电子显微镜数据集DOI：https://doi.org/10.25378/janelia.13114211。可视化官网：https://openorganelle.janelia.org/datasets/jrc_hela-2。相关出版物：CellMap Segmentation Challenge, 2024，即《2024年CellMap分割挑战赛》。在此期间的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。同期CellMap项目团队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。