Manual organelle segmentations (crop212) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

Name: Manual organelle segmentations (crop212) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)
Creator: Janelia Research Campus
Published: 2024-12-17 17:11:35
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DataCite Commons2024-12-17 更新2025-04-16 收录

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https://janelia.figshare.com/articles/dataset/Manual_organelle_segmentations_crop212_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_jrc_sum159-4_/24256027/1

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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, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_sum159-4 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: crop212 Primary Annotator: Alyson Petruncio Annotation 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 Workroom Annotated 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): 45246 x 4270 x 27398 (x, y, z) Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop212 Source (EM) dataset ID: jrc_sum159-4 Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z) Source (EM) data dimensions (µm): 95 x 8.5 x 47.8 (x, y, z) Source (EM) DOI: https://doi.org/10.25378/janelia.20134103 Visualization website: https://openorganelle.janelia.org/datasets/jrc_sum159-4 Publication: 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图像分割挑战赛（CellMap 2024 Segmentation Challenge） - 挑战赛数字对象标识符（Challenge 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样本中细胞器手动分割方案 V.3》标注协议，对jrc_sum159-4样本中的细胞外间隙、质膜、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、胞质溶胶、溶酶体、内体、囊泡、内质网、细胞、内质网膜集合体进行了密集分割。 标注编号（Annotation ID）：crop212 主要标注人员：Alyson Petruncio 标注方案：《用于机器学习的体积电子显微镜样本中细胞器手动分割方案 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）：4 × 4 × 4（x、y、z轴） 标注数据尺寸（µm）：1.6 × 1.6 × 1.6（x、y、z轴） 标注数据偏移量（nm）：45246 × 4270 × 27398（x、y、z轴） 标注类别：细胞外间隙、质膜、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、胞质溶胶、溶酶体、内体、囊泡、内质网、细胞、内质网膜集合体 数据集地址：s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop212 源电子显微镜数据集编号：jrc_sum159-4 源电子显微镜体素尺寸（nm）：8 × 8 × 8（x、y、z轴） 源电子显微镜数据尺寸（µm）：95 × 8.5 × 47.8（x、y、z轴） 源电子显微镜数据集数字对象标识符：https://doi.org/10.25378/janelia.20134103 可视化官网：https://openorganelle.janelia.org/datasets/jrc_sum159-4 相关出版物：CellMap图像分割挑战赛，2024年。 本阶段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。 本阶段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和Aubrey Weigel。

提供机构：

Janelia Research Campus

创建时间：

2024-12-13