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

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: crop120Primary 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): 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 collectiveDataset URL: s3://janelia-cosem-datasets/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop120Source (EM) dataset ID: jrc_fly-mb-1aSource (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.27075448Visualization website: https://openorganelle.janelia.org/datasets/jrc_fly-mb-1aPublication: 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.7456966-1，挑战赛官网：https://cellmapchallenge.janelia.org/。 注释说明：针对jrc_fly-mb-1a样本，使用Amira 3D 2021.1、Classic Segmentation Workroom以及《用于机器学习的体积电子显微镜中细胞器手动分割V.3》（Using Amira to manually segment organelles in vEM for machine learning V.3）注释协议，完成了细胞外间隙、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、胞质溶胶、溶酶体、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体的密集三维分割。 注释ID：crop120；主要注释者：Woohyun Park；注释协议：《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、Classic Segmentation Workroom；注释体素尺寸（nm）：2×2×2（x、y、z轴）；注释数据维度（µm）：0.8×0.8×0.8（x、y、z轴）；注释数据偏移量（nm）：25971×19807×19043（x、y、z轴）。 注释类别：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、胞质溶胶、溶酶体、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体。 数据集访问URL：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DOI：https://doi.org/10.25378/janelia.27075448；可视化网站：https://openorganelle.janelia.org/datasets/jrc_fly-mb-1a；相关出版物：2024年CellMap分割挑战赛。 同期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。 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。