Manual organelle segmentations (crop89) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of macrophage cell (jrc_macrophage-2)

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 nucleus in jrc_macrophage-2 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: crop89

Primary Annotator: COSEM Project Team

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): 12559 x 2519 x 18999 (x, y, z)

Classes annotated: nucleus

Dataset URL: s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop89

Source (EM) dataset ID: jrc_macrophage-2

Source (EM) voxel size (nm): 4 x 4 x 4 (x, y, z)

Source (EM) data dimensions (µm): 40 x 8 x 44.35 (x, y, z)

Source (EM) DOI: https://doi.org/10.25378/janelia.13114343

Visualization website: https://openorganelle.janelia.org/datasets/jrc_macrophage-2

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.

本次数据集采集属于CellMap 2024分割挑战赛（CellMap 2024 Segmentation Challenge）
- 挑战赛数字对象标识符（DOI）：https://doi.org/10.25378/janelia.c.7456966
- 挑战赛官方网站：https://cellmapchallenge.janelia.org/
- 注释说明：使用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）细胞器手动分割（V.3版）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）注释规程，对jrc_macrophage-2样本中的细胞核进行密集分割
- 注释ID：crop89
- 主要注释者：COSEM项目团队（COSEM Project Team）
- 注释规程：《用于机器学习的体积电子显微镜（vEM）细胞器手动分割（V.3版）》（http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3）
- 所用软件：Amira 3D 2021.1、经典分割工作室（Classic Segmentation Workroom）
- 注释体素尺寸（纳米）：2 × 2 × 2（x、y、z轴）
- 注释数据尺寸（微米）：0.8 × 0.8 × 0.8（x、y、z轴）
- 注释数据偏移量（纳米）：12559 × 2519 × 18999（x、y、z轴）
- 注释类别：细胞核
- 数据集URL：s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop89
- 源电子显微镜（electron microscopy, EM）数据集ID：jrc_macrophage-2
- 源电子显微镜（electron microscopy, EM）体素尺寸（纳米）：4 × 4 × 4（x、y、z轴）
- 源电子显微镜（electron microscopy, EM）数据尺寸（微米）：40 × 8 × 44.35（x、y、z轴）
- 源电子显微镜（electron microscopy, EM）数字对象标识符（DOI）：https://doi.org/10.25378/janelia.13114343
- 可视化网站：https://openorganelle.janelia.org/datasets/jrc_macrophage-2
- 相关出版物：《CellMap 2024分割挑战赛》（CellMap Segmentation Challenge, 2024）
- 本项目实施期间的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
- 本项目实施期间的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。