Manual organelle segmentations (crop150) 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, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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: crop150Primary 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): 0.8 x 0.8 x 0.8 (x, y, z)Annotated data offset (nm): 72998 x 16198 x 34790 (x, y, z)Classes annotated: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop150Source (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——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、Classic Segmentation Workroom及《面向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》标注规程，对jrc_mus-liver样本中的线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网腔、内质网膜、内体腔、胞质、内体、囊泡、线粒体、内质网、细胞、内质网膜集合体进行稠密分割。标注ID：crop150；主要标注者：Alyson Petruncio；标注规程：《面向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、Classic Segmentation Workroom；标注体素尺寸（nm）：4×4×4（x、y、z轴）；标注数据尺寸（µm）：0.8×0.8×0.8（x、y、z轴）；标注数据偏移量（nm）：72998×16198×34790（x、y、z轴）；标注类别涵盖：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、胞质、内体、囊泡、线粒体、内质网、细胞、内质网膜集合体。数据集URL：s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop150；源电子显微镜数据集ID：jrc_mus-liver；源电子显微镜体素尺寸（nm）：8×8×8（x、y、z轴）；源电子显微镜数据尺寸（µm）：101.98×101.82×71.46（x、y、z轴）；源电子显微镜DOI：https://doi.org/10.25378/janelia.16913047；可视化网站：https://openorganelle.janelia.org/datasets/jrc_mus-liver；相关出版物：《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、Aubrey Weigel。