Manual organelle segmentations (crop65) 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 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: crop65Primary 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): 4183 x 2491 x 19359 (x, y, z)Classes annotated: extracellular spaceDataset URL: s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop65Source (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/）。 注释说明：采用Amira 3D 2021.1、Classic Segmentation Workroom及《用于机器学习的体积电子显微镜细胞器手动分割（V.3版）》（Using Amira to manually segment organelles in vEM for machine learning V.3）注释协议，对jrc_hela-3样本中的细胞外间隙进行全密度分割。 注释ID：crop65 主要注释团队：COSEM项目团队 注释协议：《用于机器学习的体积电子显微镜细胞器手动分割（V.3版）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） 使用软件：Amira 3D 2021.1、Classic Segmentation Workroom 标注体素尺寸（纳米）：2×2×2（x、y、z轴） 标注数据维度（微米）：0.8×0.8×0.8（x、y、z轴） 标注数据偏移量（纳米）：4183×2491×19359（x、y、z轴） 标注类别：细胞外间隙 数据集URL：s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop65 原始电子显微镜（Electron Microscopy, EM）数据集ID：jrc_hela-3 原始电子显微镜体素尺寸（纳米）：4×4×3.24（x、y、z轴） 原始电子显微镜数据维度（微米）：49.6×4×38.88（x、y、z轴） 原始电子显微镜数据集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：《CellMap Segmentation Challenge, 2024》 本研究期间的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。 本研究期间的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。