Manual organelle segmentations (crop38) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized T-cells (jrc_jurkat-1)

<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, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_jurkat-1 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>: crop38<br><br><b>Primary Annotator</b>: COSEM Project Team<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>: 2 x 2 x 2 (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>: 28507 x 5119 x 22031 (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, lysosome lumen, lysosome membrane, endosome lumen, microtubule out, microtubule in, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop38<br><br><b>Source (EM) dataset ID</b>: jrc_jurkat-1<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 3.44 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 40 x 12 x 29.45 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114259<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_jurkat-1<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

- **挑战赛官网：** https://cellmapchallenge.janelia.org/

**注释说明**：使用Amira 3D 2021.1、Classic Segmentation Workroom软件，以及《用于机器学习的体视电子显微镜（volume electron microscopy, vEM）细胞器手动分割（V.3）》注释流程，对jrc_jurkat-1样本中的以下结构进行全致密分割：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、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、细胞质基质、溶酶体、内体、囊泡、线粒体、内质网、微管、细胞、内质网膜集合体。

**注释ID：** crop38

**主要注释团队：** COSEM项目团队（COSEM Project Team）

**注释流程：** 《用于机器学习的体视电子显微镜细胞器手动分割（V.3）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）

**使用软件：** Amira 3D 2021.1、Classic Segmentation Workroom

**注释体素尺寸（纳米）：** 2 × 2 × 2（x、y、z轴）

**注释数据维度（微米）：** 0.8 × 0.8 × 0.8（x、y、z轴）

**注释数据偏移量（纳米）：** 28507 × 5119 × 22031（x、y、z轴）

**注释类别：** 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、溶酶体腔、溶酶体膜、内体腔、微管外侧、微管内侧、细胞质基质、溶酶体、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_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop38

**原始电子显微镜数据集ID：** jrc_jurkat-1

**原始电子显微镜体素尺寸（纳米）：** 4 × 4 × 3.44（x、y、z轴）

**原始电子显微镜数据维度（微米）：** 40 × 12 × 29.45（x、y、z轴）

**原始电子显微镜数据集DOI：** https://doi.org/10.25378/janelia.13114259

**可视化网站：** https://openorganelle.janelia.org/datasets/jrc_jurkat-1

**相关出版物：** *CellMap图像分割挑战赛*，2024年。

**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。