Manual organelle segmentations (crop80) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-1)

Name: Manual organelle segmentations (crop80) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-1)
Creator: Janelia Research Campus
Published: 2024-12-17 19:21:17
License: 暂无描述

DataCite Commons2024-12-17 更新2025-04-16 收录

下载链接：

https://janelia.figshare.com/articles/dataset/Manual_organelle_segmentations_crop80_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_immortalized_breast_cancer_cell_jrc_sum159-1_/24246532

下载链接

链接失效反馈

官方服务：

资源简介：

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 mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, Golgi lumen, Golgi membrane, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, Golgi, lysosome, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_sum159-1 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: crop80 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): 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): 35439 x 2543 x 19595 (x, y, z) Classes annotated: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, Golgi lumen, Golgi membrane, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, Golgi, lysosome, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop80 Source (EM) dataset ID: jrc_sum159-1 Source (EM) voxel size (nm): 4 x 4 x 4.56 (x, y, z) Source (EM) data dimensions (µm): 64 x 11.2 x 34.8 (x, y, z) Source (EM) DOI: https://doi.org/10.25378/janelia.13114352 Visualization website: https://openorganelle.janelia.org/datasets/jrc_sum159-1 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 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、经典分割工作室（Classic Segmentation Workroom）以及《用于机器学习的体积电子显微镜（vEM）样本中细胞器手动分割 V.3》标注规范，对jrc_sum159-1中的以下对象开展稠密分割：线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、高尔基体腔、高尔基体膜、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、胞质溶胶、高尔基体、溶酶体、内体、囊泡、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体。 **标注ID**：crop80 **主要标注员**：Alyson Petruncio **标注规范**：《用于机器学习的体积电子显微镜（vEM）样本中细胞器手动分割 V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） **所用软件**：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom） **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）**：35439 × 2543 × 19595（x、y、z轴） **标注类别**：线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、高尔基体腔、高尔基体膜、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、胞质溶胶、高尔基体、溶酶体、内体、囊泡、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体 **数据集URL**：s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop80 **源电子显微镜数据集ID**：jrc_sum159-1 **源电子显微镜体素尺寸（nm）**：4 × 4 × 4.56（x、y、z轴） **源电子显微镜数据维度（µm）**：64 × 11.2 × 34.8（x、y、z轴） **源电子显微镜DOI**：https://doi.org/10.25378/janelia.13114352 **可视化网站**：https://openorganelle.janelia.org/datasets/jrc_sum159-1 **出版物**：CellMap 分割挑战赛，2024年。 **当期CellMap项目团队成员**：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。 **当期CellMap项目指导委员会成员**：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：

2023-10-04