Manual organelle segmentations (crop94) 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 nucleus 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: crop94Primary Annotator: Aubrey WeigelAnnotation 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): 22911 x 2567 x 11935 (x, y, z)Classes annotated: nucleusDataset URL: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop94Source (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/
注释描述：使用Amira 3D 2021.1、经典分割工作间（Classic Segmentation Workroom）及《用于机器学习的体积电子显微镜（volume electron microscopy, vEM）样品中细胞器手动分割 V.3》注释规程，对jrc_hela-2样本中的细胞核开展密集分割。
注释ID：crop94
主注释员：Aubrey Weigel
注释规程：《用于机器学习的体积电子显微镜样品中细胞器手动分割 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（Classic Segmentation Workroom）
注释体素尺寸（纳米）：2×2×2（x、y、z轴）
注释数据维度（微米）：0.8×0.8×0.8（x、y、z轴）
注释数据偏移量（纳米）：22911×2567×11935（x、y、z轴）
注释类别：细胞核
数据集URL：s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop94
原始电子显微镜（EM）数据集ID：jrc_hela-2
原始电子显微镜体素尺寸（纳米）：4×4×5.2（x、y、z轴）
原始电子显微镜数据维度（微米）：48×6.4×33.11（x、y、z轴）
原始电子显微镜DOI：https://doi.org/10.25378/janelia.13114211
可视化网站：https://openorganelle.janelia.org/datasets/jrc_hela-2
相关出版物：《CellMap 2024分割挑战赛》，2024年。
本项目彼时团队成员包括：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项目指导委员会彼时成员包括：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。