Manual organelle segmentations (crop417) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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 extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum exit site, 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.

Annotation ID: crop417

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 2 x 2 (x, y, z)

Annotated data offset (nm): 33254 x 57430 x 16310 (x, y, z)

Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum exit site lumen, endoplasmic reticulum exit site membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, endoplasmic reticulum exit site, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop417

Source (EM) dataset ID: jrc_mus-liver

Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)

Source (EM) data dimensions (µm): 101.98 x 101.82 x 71.46 (x, y, z)

Source (EM) DOI: https://doi.org/10.25378/janelia.16913047

Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liver

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.