Manual organelle segmentations (crop278) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

dataset

posted on 2024-12-13, 19:13 authored by CellMap Project TeamCellMap Project Team, Rebecca Arruda, Davis BennettDavis Bennett, Nora Forknall, Woohyun Park, Alyson Petruncio, Jacquelyn Price, Diana RamirezDiana Ramirez, Thomson Rymer, Alia Suleiman, Rebecca VorimoRebecca Vorimo, Aubrey WeigelAubrey Weigel, Yurii Zubov

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, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, lysosome, endosome, vesicle, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective in jrc_mus-liver-zon-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.

Annotation ID: crop278

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): 129062 x 56798 x 114478 (x, y, z)

Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, nucleoplasm, cytosol, nucleus, lysosome, endosome, vesicle, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop278

Source (EM) dataset ID: jrc_mus-liver-zon-1

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

Source (EM) data dimensions (µm): 397.16 x 171.61 x 188.81 (x, y, z)

Source (EM) DOI: https://doi.org/10.25378/janelia.24128700

Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1

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.