Manual organelle segmentations (crop298) 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, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lipid droplet lumen, lipid droplet membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, lipid droplet, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum 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: crop298

Primary Annotator: Rebecca Vorimo

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): 101958 x 83774 x 116758 (x, y, z)

Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lipid droplet lumen, lipid droplet membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, lipid droplet, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop298

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.