Manual organelle segmentations (crop132) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective, endosome in jrc_mus-liver 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: crop132Primary Annotator: Woohyun ParkAnnotation 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): 8 x 8 x 8 (x, y, z)Annotated data dimensions (µm): 1.6 x 1.6 x 1.6 (x, y, z)Annotated data offset (nm): 26576 x 45728 x 35544 (x, y, z)Classes annotated: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective, endosomeDataset URL: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop132Source (EM) dataset ID: jrc_mus-liverSource (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)Source (EM) data dimensions (µm): 101.98 x 101.82 x 71.46 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.16913047Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liverPublication: 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/ 标注说明：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（volume electron microscopy，vEM）中细胞器手动分割 V.3》标注协议，对jrc_mus-liver数据集内的如下结构完成了密集分割：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、异染色质、核孔内区、核孔外区、核被膜腔、核被膜、核质、胞质溶胶、细胞核、囊泡、过氧化物酶体膜、过氧化物酶体、过氧化物酶体腔、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合、核被膜集合、内体。 标注ID：crop132 主要标注者：Woohyun Park 标注协议：《用于机器学习的体积电子显微镜中细胞器手动分割 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（纳米）：8×8×8（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）：26576×45728×35544（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、线粒体核糖体、常染色质、内质网腔、内质网膜、异染色质、核孔内区、核孔外区、核被膜腔、核被膜、核质、胞质溶胶、细胞核、囊泡、过氧化物酶体膜、过氧化物酶体、过氧化物酶体腔、线粒体、内质网、核被膜、核孔、染色质、细胞、内质网膜集合、核被膜集合、内体 数据集URL：s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop132 源电子显微镜数据集ID：jrc_mus-liver 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）：101.98×101.82×71.46（x、y、z轴） 源电子显微镜DOI：https://doi.org/10.25378/janelia.16913047 可视化官网：https://openorganelle.janelia.org/datasets/jrc_mus-liver 相关出版物：2024年CellMap分割挑战赛 本次项目期间的CellMap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。 同期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、Aubrey Weigel。