Manual organelle segmentations (crop248) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Interphase COS-7 cell (jrc_cos7-1a)

This acquisition is part of the CellMap 2024 Segmentation Challenge
Challenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge 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, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_cos7-1a 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: crop248
Primary Annotator: Woohyun Park
Annotation 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 Workroom
Annotated 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): 7922 x 4300 x 90 (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, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective
Dataset URL: s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop248
Source (EM) dataset ID: jrc_cos7-1a
Source (EM) voxel size (nm): 2 x 2 x 2 (x, y, z)
Source (EM) data dimensions (µm): 41.22 x 8.74 x 3.63 (x, y, z)
Source (EM) DOI: https://doi.org/10.25378/janelia.24943716
Visualization website: https://openorganelle.janelia.org/datasets/jrc_cos7-1a
Publication: 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
挑战赛官网：https://cellmapchallenge.janelia.org/
标注说明：使用Amira 3D 2021.1、Classic Segmentation Workroom及《使用Amira手动分割体积电子显微镜（volume electron microscopy, vEM）中的细胞器以用于机器学习 V.3》标注协议，对jrc_cos7-1a样本进行密集分割。
标注ID：crop248
主要标注者：Woohyun Park
标注协议：《使用Amira手动分割体积电子显微镜（vEM）中的细胞器以用于机器学习 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（纳米）：2×2×2（x、y、z轴）
标注数据尺寸（微米）：0.8×0.8×0.8（x、y、z轴）
标注数据偏移量（纳米）：7922×4300×90（x、y、z轴）
标注类别：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、内体腔、微管外侧、微管内侧、细胞质基质、内体、囊泡、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_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop248
源电子显微镜（electron microscopy, EM）数据集ID：jrc_cos7-1a
源电子显微镜体素尺寸（纳米）：2×2×2（x、y、z轴）
源电子显微镜数据尺寸（微米）：41.22×8.74×3.63（x、y、z轴）
源电子显微镜数据集DOI：https://doi.org/10.25378/janelia.24943716
可视化官网：https://openorganelle.janelia.org/datasets/jrc_cos7-1a
相关出版物：CellMap图像分割挑战赛（CellMap Segmentation Challenge, 2024）。
本项目期间的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。
本项目期间的CellMap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。