Manual organelle segmentations (crop120) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_fly-mb-1a)

Name: Manual organelle segmentations (crop120) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_fly-mb-1a)
Creator: Janelia Research Campus
Published: 2024-12-19 18:13:00
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DataCite Commons2024-12-19 更新2025-04-16 收录

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https://janelia.figshare.com/articles/dataset/Manual_organelle_segmentations_crop120_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_jrc_fly-mb-1a_/24246763

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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, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_fly-mb-1a 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: crop120 Primary Annotator: Woohyun Park 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): 25971 x 19807 x 19043 (x, y, z) Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop120 Source (EM) dataset ID: jrc_fly-mb-1a Source (EM) voxel size (nm): 4 x 4 x 4 (x, y, z) Source (EM) data dimensions (µm): 44.02 x 37.14 x 38.02 (x, y, z) Source (EM) DOI: https://doi.org/10.25378/janelia.27075448 Visualization website: https://openorganelle.janelia.org/datasets/jrc_fly-mb-1a 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.

本采集数据集隶属于CellMap 2024分割挑战赛（CellMap 2024 Segmentation Challenge） - 挑战赛DOI： https://doi.org/10.25378/janelia.c.7456966 - 挑战赛官方网站： https://cellmapchallenge.janelia.org/ 标注描述：在jrc_fly-mb-1a样本中，使用Amira 3D 2021.1、Classic Segmentation Workroom以及《面向机器学习的体视电子显微镜细胞器手动标注（V.3版）》标注协议，对细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、线粒体核糖体、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、细胞质基质、溶酶体、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体进行密集分割。 标注ID：crop120 主要标注者：Woohyun Park 标注协议：《面向机器学习的体视电子显微镜细胞器手动标注（V.3版）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） 所用软件：Amira 3D 2021.1、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）：25971 × 19807 × 19043（x、y、z轴） 标注类别：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、线粒体核糖体、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、细胞质基质、溶酶体、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体 数据集存储链接：s3://janelia-cosem-datasets/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop120 源电子显微镜数据集ID：jrc_fly-mb-1a 源电子显微镜体素尺寸（nm）：4 × 4 × 4（x、y、z轴） 源电子显微镜数据维度（µm）：44.02 × 37.14 × 38.02（x、y、z轴） 源电子显微镜数据集DOI：https://doi.org/10.25378/janelia.27075448 可视化网站：https://openorganelle.janelia.org/datasets/jrc_fly-mb-1a 发表信息：CellMap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、Aubrey Weigel。

提供机构：

Janelia Research Campus

创建时间：

2023-10-04