Manual organelle segmentations (crop160) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney)

Name: Manual organelle segmentations (crop160) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney)
Creator: Janelia Research Campus
Published: 2024-12-18 18:42:40
License: 暂无描述

DataCite Commons2024-12-18 更新2025-04-16 收录

下载链接：

https://janelia.figshare.com/articles/dataset/Manual_organelle_segmentations_crop160_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_mouse_kidney_jrc_mus-kidney_/24247252/1

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 extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, mitochondria, endoplasmic reticulum, cell, basement membrane, endoplasmic reticulum membrane collective in jrc_mus-kidney 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: crop160 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): 0.8 x 0.8 x 0.8 (x, y, z) Annotated data offset (nm): 73798 x 47158 x 81294 (x, y, z) Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, mitochondria, endoplasmic reticulum, cell, basement membrane, endoplasmic reticulum membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop160 Source (EM) dataset ID: jrc_mus-kidney Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z) Source (EM) data dimensions (µm): 98.3 x 63.81 x 177.59 (x, y, z) Source (EM) DOI: https://doi.org/10.25378/janelia.16913035 Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-kidney 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分割挑战赛的一部分 - 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：在jrc_mus-kidney数据集中，使用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）及'Using Amira to manually segment organelles in vEM for machine learning V.3'标注协议，对细胞外空间（extracellular space）、质膜（plasma membrane）、线粒体膜（mitochondrial membrane）、线粒体腔（mitochondrial lumen）、内体膜（endosome membrane）、线粒体核糖体（mitochondrial ribosome）、内质网腔（endoplasmic reticulum lumen）、内质网膜（endoplasmic reticulum membrane）、内体腔（endosome lumen）、胞质溶胶（cytosol）、内体（endosome）、线粒体（mitochondria）、内质网（endoplasmic reticulum）、细胞（cell）、基底膜（basement membrane）及内质网膜集合体（endoplasmic reticulum membrane collective）进行了密集分割。 标注ID：crop160 主要标注者：Alyson Petruncio 标注协议：Using Amira to manually segment organelles in vEM for machine learning V.3（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） 软件：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom） 标注体素大小（nm）：4 x 4 x 4（x, y, z） 标注数据维度（µm）：0.8 x 0.8 x 0.8（x, y, z） 标注数据偏移量（nm）：73798 x 47158 x 81294（x, y, z） 标注类别：细胞外空间、质膜、线粒体膜、线粒体腔、内体膜、线粒体核糖体、内质网腔、内质网膜、内体腔、胞质溶胶、内体、线粒体、内质网、细胞、基底膜、内质网膜集合体 数据集URL：s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop160 源（电镜）数据集ID：jrc_mus-kidney 源（电镜）体素大小（nm）：8 x 8 x 8（x, y, z） 源（电镜）数据维度（µm）：98.3 x 63.81 x 177.59（x, y, z） 源（电镜）DOI：https://doi.org/10.25378/janelia.16913035 可视化网站：https://openorganelle.janelia.org/datasets/jrc_mus-kidney 出版物：CellMap Segmentation Challenge,2024. 此期间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 此期间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、Aubrey Weigel

提供机构：

Janelia Research Campus

创建时间：

2024-12-13