Manual organelle segmentations (crop150) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

<b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: 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.<br><br><b>Annotation ID</b>: crop150<br><br><b>Primary Annotator</b>: Alyson Petruncio<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 72998 x 16198 x 34790 (x, y, z)<br><br><b>Classes annotated</b>: 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<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop150<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<br><br><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> 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.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> 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.

本次采集数据隶属于CellMap 2024图像分割挑战赛（CellMap 2024 Segmentation Challenge）

- 挑战赛数字对象标识符：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、经典分割工作室（Classic Segmentation Workroom）以及《基于机器学习的体积电子显微镜样本中细胞器手动分割方法V.3》标注协议，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密集分割。

标注ID：crop150

主要标注人员：Alyson Petruncio

标注协议：《基于机器学习的体积电子显微镜样本中细胞器手动分割方法V.3》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）

使用软件：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）

标注体素尺寸（纳米）：4×4×4（x、y、z轴）

标注数据维度（微米）：0.8×0.8×0.8（x、y、z轴）

标注数据偏移量（纳米）：72998×16198×34790（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

数据集存储地址：s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop150

原始电子显微镜数据集ID：jrc_mus-liver

原始电子显微镜体素尺寸（纳米）：8×8×8（x、y、z轴）

原始电子显微镜数据维度（微米）：101.98×101.82×71.46（x、y、z轴）

原始电子显微镜数据集数字对象标识符：https://doi.org/10.25378/janelia.16913047

可视化官网：https://openorganelle.janelia.org/datasets/jrc_mus-liver

发表文献：《CellMap Segmentation Challenge》，2024年。

此阶段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。

此阶段CellMap项目团队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。