Manual nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse nucleus accumbens (jrc_mus-nacc-2)

dataset

posted on 2025-02-13, 19:23 authored by CellMap Project TeamCellMap Project Team, David Ackerman, Emma Avetissian, Alyson Petruncio, Rebecca VorimoRebecca Vorimo, Yurii Zubov

Annotation description: Dense segmentations of nuclei in jrc_mus-nacc-2 using Amira-Avizo (Thermo Fisher Scientific) and "Using Amira to manually segment organelles in vEM for machine learning V.3" protocol.

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

Classes annotated: Nuclei

Source (EM) dataset ID: jrc_mus-nacc-2

Source (EM) voxel size (nm): 4 x 4 x 4 (X, Y, Z)

Source (EM) data dimensions (µm): 10.4 x 10.0 x 2.3 (X, Y, Z)

Source (EM) DOI: https://doi.org/10.25378/janelia.24222898

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-nacc-2/jrc_mus-nacc-2.zarr/recon-2/labels/inference/segmentations/nuc/

Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-nacc-2