Manual organelle segmentations (crop369) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-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 mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, endoplasmic reticulum exit site, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-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: crop369
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): 4 x 4 x 4 (x, y, z)
Annotated data dimensions (µm): 1.6 x 1.6 x 1.6 (x, y, z)
Annotated data offset (nm): 40798 x 66478 x 336798 (x, y, z)
Classes annotated: mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, endoplasmic reticulum exit site, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective
Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop369
Source (EM) dataset ID: jrc_mus-liver-zon-2
Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)
Source (EM) data dimensions (µm): 210 x 155.73 x 426.69 (x, y, z)
Source (EM) DOI: https://doi.org/10.25378/janelia.24135486
Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-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.
