Manual organelle segmentations (crop200) 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, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum 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: crop200Primary 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): 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): 52438 x 57998 x 45006 (x, y, z)Classes annotated: extracellular space, plasma membrane, 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, cytosol, endosome, vesicle, endoplasmic reticulum exit site, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop200Source (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（挑战赛DOI：https://doi.org/10.25378/janelia.c.7456966-1，挑战赛官方网站：https://cellmapchallenge.janelia.org/）。

### 注释详情
针对样本jrc_ut21-1413-003完成了以下对象的密集分割：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、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、胞质溶胶、内体、囊泡、内质网出口位点、线粒体、内质网、细胞、内质网膜集合体。本次分割工作采用Amira 3D 2021.1、Classic Segmentation Workroom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》注释方案。

注释ID：crop200；主要注释人员：Woohyun Park；注释方案：《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）：4×4×4（x、y、z轴）；注释数据维度（µm）：1.6×1.6×1.6（x、y、z轴）；注释数据偏移量（nm）：52438×57998×45006（x、y、z轴）。

数据集访问地址：s3://janelia-cosem-datasets/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop200；源电子显微镜数据集ID：jrc_ut21-1413-003；源电子显微镜体素尺寸（nm）：8×8×8（x、y、z轴）；源电子显微镜数据维度（µm）：130.42×91.22×121.19（x、y、z轴）；源电子显微镜DOI：https://doi.org/10.25378/janelia.27075529；可视化平台网址：https://openorganelle.janelia.org/datasets/jrc_ut21-1413-003；相关出版物：《CellMap Segmentation Challenge, 2024》。

本项目执行期间的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。

本项目执行期间的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。