Manual organelle segmentations (crop187) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

Name: Manual organelle segmentations (crop187) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)
Creator: Janelia Research Campus
Published: 2024-12-17 19:24:00
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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_crop187_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_jrc_sum159-4_/24255778/1

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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, lipid droplet lumen, lipid droplet membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, lipid droplet, 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: crop187 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): 42982 x 3750 x 29046 (x, y, z) Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lipid droplet lumen, lipid droplet membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, lipid droplet, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop187 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DOI：https://doi.org/10.25378/janelia.c.7456966 - 挑战赛官网：https://cellmapchallenge.janelia.org/ 标注说明：针对jrc_sum159-4样本，使用Amira 3D 2021.1、Classic Segmentation Workroom以及标注协议《利用Amira对体积电子显微镜（volume EM, vEM）中的细胞器进行手动分割以用于机器学习 V.3》完成了以下类别的密集分割：细胞外间隙、质膜、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、脂滴腔、脂滴膜、溶酶体腔、溶酶体膜、内体腔、细胞质基质、溶酶体、内体、囊泡、脂滴、内质网、细胞以及内质网膜集合。 标注ID：crop187 主要标注人员：Alyson Petruncio 标注协议：《利用Amira对体积电子显微镜图像中的细胞器进行手动分割以用于机器学习 V.3》（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）：4×4×4（x、y、z轴） 标注数据维度（微米）：1.6×1.6×1.6（x、y、z轴） 标注数据偏移量（纳米）：42982×3750×29046（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、脂滴腔、脂滴膜、溶酶体腔、溶酶体膜、内体腔、细胞质基质、溶酶体、内体、囊泡、脂滴、内质网、细胞以及内质网膜集合 数据集URL：s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop187 源电子显微镜数据集ID：jrc_sum159-4 源电子显微镜体素尺寸（纳米）：8×8×8（x、y、z轴） 源电子显微镜数据维度（微米）：95×8.5×47.8（x、y、z轴） 源电子显微镜数据集DOI：https://doi.org/10.25378/janelia.20134103 可视化官网：https://openorganelle.janelia.org/datasets/jrc_sum159-4 发表文献：《CellMap图像分割挑战赛》，2024年。 本项目期间的CellMap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。 本项目期间的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、Aubrey Weigel。

提供机构：

Janelia Research Campus

创建时间：

2024-12-13