Manual organelle segmentations (crop277) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge 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, 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, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, 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: crop277Primary Annotator: Diana RamirezAnnotation 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 WorkroomAnnotated 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): 124566 x 61502 x 118502 (x, y, z)Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, 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, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collectiveDataset URL: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop277Source (EM) dataset ID: jrc_mus-liver-zon-1Source (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.24128700Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1Publication: 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.