Manual organelle segmentations (crop145) 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 extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, microtubule out, nucleoplasm, microtubule in, cytosol, nucleus, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, microtubule, cell, endoplasmic reticulum membrane collective, nuclear envelope 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>: crop145<br><br><b>Primary Annotator</b>: nan<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>: 3 x 3 x 1.44 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 46350 x 61750 x 17558 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, microtubule out, nucleoplasm, microtubule in, cytosol, nucleus, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, microtubule, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop145<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：** 针对jrc_mus-liver样本，采用Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）以及《用于机器学习的体积电子显微镜（vEM）样本中细胞器手动分割方法V.3》标注协议，对以下类别进行密集分割：细胞外间隙、质膜、线粒体膜、线粒体腔、囊泡膜、内体膜、囊泡腔、线粒体核糖体、内质网腔、内质网膜、内体腔、异染色质、核孔内、核孔外、核被膜腔、核被膜膜、微管外侧、核质、微管内侧、胞质溶胶、细胞核、内体、囊泡、过氧化物酶体膜、过氧化物酶体、过氧化物酶体腔、线粒体、内质网、核被膜、核孔、染色质、微管、细胞、内质网膜集合体、核被膜膜集合体。

**标注ID：** crop145

**主要标注者：** 无

**标注协议：** 《用于机器学习的体积电子显微镜（vEM）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）：** 3×3×1.44（x、y、z轴）

**标注数据偏移量（纳米）：** 46350×61750×17558（x、y、z轴）

**已标注类别：** 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、异染色质、核孔内、核孔外、核被膜腔、核被膜膜、微管外侧、核质、微管内侧、胞质溶胶、细胞核、内体、囊泡、过氧化物酶体膜、过氧化物酶体、过氧化物酶体腔、线粒体、内质网、核被膜、核孔、染色质、微管、细胞、内质网膜集合体、核被膜膜集合体

**数据集URL：** s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop145

**源电子显微镜（EM）数据集ID：** jrc_mus-liver

**源电子显微镜体素尺寸（纳米）：** 8×8×8（x、y、z轴）

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

**源电子显微镜数据集DOI：** https://doi.org/10.25378/janelia.16913047

**可视化网站：** https://openorganelle.janelia.org/datasets/jrc_mus-liver

**发表信息：** *《CellMap图像分割挑战赛》*，2024年。

**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。