Manual organelle segmentations (crop116) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of killer T-cell attacking cancer cell (jrc_ctl-id8-1)

Name: Manual organelle segmentations (crop116) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of killer T-cell attacking cancer cell (jrc_ctl-id8-1)
Creator: Janelia Research Campus
Published: 2024-12-19 18:12:40
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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_crop116_in_near-isotropic_reconstructed_volume_electron_microscopy_FIB-SEM_of_killer_T-cell_attacking_cancer_cell_jrc_ctl-id8-1_/24246676/1

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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, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, endosome, vesicle, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective in jrc_ctl-id8-1 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: crop116 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): 35703 x 7903 x 23595 (x, y, z) Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, endosome, vesicle, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective Dataset URL: s3://janelia-cosem-datasets/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop116 Source (EM) dataset ID: jrc_ctl-id8-1 Source (EM) voxel size (nm): 4 x 4 x 4 (x, y, z) Source (EM) data dimensions (µm): 74 x 12.8 x 47.99 (x, y, z) Source (EM) DOI: https://doi.org/10.25378/janelia.13114454 Visualization website: https://openorganelle.janelia.org/datasets/jrc_ctl-id8-1 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.

本次采集数据属于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/ 注释描述：使用Amira 3D 2021.1、Classic Segmentation Workroom及《Using Amira to manually segment organelles in 体积电子显微镜（volume Electron Microscopy，vEM）for machine learning V.3》注释协议，对jrc_ctl-id8-1数据集中的细胞外空间、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、异染色质、核孔内侧、核孔外侧、核膜腔、核膜、核质、胞质、细胞核、内体、囊泡、线粒体、内质网、核膜、核孔、染色质、细胞、内质网膜集合体、核膜集合体进行密集分割。 注释ID：crop116 主要注释者：Woohyun Park 注释协议：《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、Classic Segmentation Workroom 注释体素大小（纳米）：2×2×2（x、y、z） 注释数据维度（微米）：0.8×0.8×0.8（x、y、z） 注释数据偏移量（纳米）：35703×7903×23595（x、y、z） 注释类别：细胞外空间、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、异染色质、核孔内侧、核孔外侧、核膜腔、核膜、核质、胞质、细胞核、内体、囊泡、线粒体、内质网、核膜、核孔、染色质、细胞、内质网膜集合体、核膜集合体 数据集URL：s3://janelia-cosem-datasets/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop116 源（电子显微镜，Electron Microscopy，EM）数据集ID：jrc_ctl-id8-1 源（电子显微镜）体素大小（纳米）：4×4×4（x、y、z） 源（电子显微镜）数据维度（微米）：74×12.8×47.99（x、y、z） 源（电子显微镜）DOI：https://doi.org/10.25378/janelia.13114454 可视化网站：https://openorganelle.janelia.org/datasets/jrc_ctl-id8-1 出版物：CellMap Segmentation Challenge, 2024. 在此期间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 在此期间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