Manual organelle segmentations (crop197) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_ut21-1413-003)

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, euchromatin, 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_ut21-1413-003 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: crop197Primary Annotator: Alyson PetruncioAnnotation 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 WorkroomAnnotated 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): 80526 x 53294 x 82998 (x, y, z)Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, euchromatin, 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 collectiveDataset URL: s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop197Source (EM) dataset ID: jrc_ut21-1413-003Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)Source (EM) data dimensions (µm): 130.42 x 91.22 x 121.19 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.27075529Visualization website: https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003Publication: 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《用于机器学习的体电子显微镜（volume electron microscopy，vEM）图像中细胞器手动分割方案V.3》标注协议，对样本jrc_ut21-1413-003中的以下对象执行稠密分割：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、常染色质、内质网腔、内质网膜、内体腔、异染色质、核孔内、核孔外、核被膜腔、核被膜、核质、胞质溶胶、细胞核、内体、囊泡、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合体、核被膜集合体。 标注ID：crop197 主要标注员：Alyson Petruncio 标注协议：《用于机器学习的体电子显微镜（volume electron microscopy，vEM）图像中细胞器手动分割方案V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3，http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3） 标注所用软件：Amira 3D 2021.1、经典分割工作室（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）：80526×53294×82998（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、常染色质、内质网腔、内质网膜、内体腔、异染色质、核孔内、核孔外、核被膜腔、核被膜、核质、胞质溶胶、细胞核、内体、囊泡、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合体、核被膜集合体 数据集访问地址：s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop197 源电子显微镜数据集ID：jrc_ut21-1413-003 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）：130.42×91.22×121.19（x、y、z轴） 源电子显微镜数据集DOI：https://doi.org/10.25378/janelia.27075529 可视化网站：https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003 相关发表文献：《CellMap Segmentation Challenge, 2024》 当期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。 当期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及Aubrey Weigel。