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Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse kidney (jrc_mus-kidney-3) model

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posted on 2024-03-12, 20:22 authored by CellMap Project TeamCellMap Project Team, Aubrey WeigelAubrey Weigel

Model description: Cellpose 2.0 was trained on nuclei from 22 2D slices from jrc_mus-kidney-3.

Architecture: Cellpose 2.0

Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)

Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)

Classes trained on: Nucleus

GPU: NVIDIA TITAN RTX

RAM: 768.0 GiB

Wall time (sec): 2198.31

Software: Cellpose 2.0

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

Source dataset (EM) ID: jrc_mus-kidney-3

Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24020799

Generated dataset DOI: https://doi.org/10.25378/janelia.25352215

Model URL (redirect): https://data.janelia.org/NXtm9

Github repo: https://github.com/janelia-cellmap/cellmap-models

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


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