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Refined, automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse epididymis (jrc_mus-epididymis-2)

posted on 2024-03-12, 20:14 authored by CellMap Project TeamCellMap Project Team, David Ackerman, Jeff Rhoades, Aubrey WeigelAubrey Weigel, Yurii Zubov

Segmentation description: Nuclei segmentations in jrc_mus-epididymis-2 using Cellpose 2.0 with minimal manual corrections.

Software: Cellpose 2.0

Software DOI: https://doi.org/10.1038/s41592-022-01663-4

GPU: RTX A6000

RAM: 256.0 GiB

Label voxel size (nm): 64 x 64 x 64 (x, y, z)

Reconstructed data dimensions (µm): 20.9 x 20.5 x 7.0 (x, y, z)

Classes annotated: Nucleus

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

Source dataset (EM) voxel size (nm): 4.0 x 4.0 x 4.0 (X, Y, Z)

Source dataset (EM) data dimensions (µm): 20.9 x 20.5 x 7.0 (X, Y, Z)

Source dataset (EM) DOI: https://doi.org/10.25378/janelia.23407907

Dataset URL (redirect): https://data.janelia.org/ipPBc

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