Manual organelle segmentations (crop23) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-2)

his 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 exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_hela-2 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: crop23Primary 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): 1 x 1 x 1 (x, y, z)Annotated data offset (nm): 10999 x 1119 x 8119 (x, y, z)Classes annotated: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop23Source (EM) dataset ID: jrc_hela-2Source (EM) voxel size (nm): 4 x 4 x 5.2 (x, y, z)Source (EM) data dimensions (µm): 48 x 6.4 x 33.11 (x, y, z)Source (EM) DOI: https://doi.org/10.25378/janelia.13114211Visualization website: https://openorganelle.janelia.org/datasets/jrc_hela-2Publication: 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图像分割挑战赛（CellMap 2024 Segmentation Challenge）——挑战赛DOI：https://doi.org/10.25378/janelia.c.7456966-1，挑战赛官网：https://cellmapchallenge.janelia.org/。标注说明：使用Amira 3D 2021.1、Classic Segmentation Workroom及《Using Amira to manually segment organelles in vEM for machine learning V.3》标注规程，对jrc_hela-2样本中的如下结构进行密集分割：线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、细胞质、内体、囊泡、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体。标注ID：crop23；主要标注人员：Woohyun Park；标注规程：《Using Amira to manually segment organelles in vEM for machine learning 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）：2×2×2（x、y、z轴）；标注数据维度（µm）：1×1×1（x、y、z轴）；标注数据偏移量（nm）：10999×1119×8119（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、内质网出口位点腔、内质网出口位点膜、内质网腔、内质网膜、内体腔、微管外侧、微管内侧、细胞质、内体、囊泡、内质网出口位点、线粒体、内质网、微管、细胞、内质网膜集合体。数据集URL：s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop23；原始电子显微镜数据集ID：jrc_hela-2；原始电子显微镜体素尺寸（nm）：4×4×5.2（x、y、z轴）；原始电子显微镜数据维度（µm）：48×6.4×33.11（x、y、z轴）；原始电子显微镜DOI：https://doi.org/10.25378/janelia.13114211；可视化网站：https://openorganelle.janelia.org/datasets/jrc_hela-2；相关出版物：CellMap Segmentation Challenge, 2024。本阶段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。本阶段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。