Manual organelle segmentations (crop50) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase HeLa cell (jrc_hela-3)

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 lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_hela-3 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: crop50

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): 2 x 2 x 2 (x, y, z)

Annotated data dimensions (µm): 1.02 x 1.02 x 1.02 (x, y, z)

Annotated data offset (nm): 37091 x 327 x 26427 (x, y, z)

Classes annotated: extracellular space, plasma membrane, vesicle membrane, endosome membrane, vesicle lumen, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective

Dataset URL: s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop50

Source (EM) dataset ID: jrc_hela-3

Source (EM) voxel size (nm): 4 x 4 x 3.24 (x, y, z)

Source (EM) data dimensions (µm): 49.6 x 4 x 38.88 (x, y, z)

Source (EM) DOI: https://doi.org/10.25378/janelia.13114244

Visualization website: https://openorganelle.janelia.org/datasets/jrc_hela-3

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.