Refined, automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse heart (jrc_mus-heart-1)

Segmentation description: Nuclei segmentations in jrc_mus-heart-1 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): 128 x 128 x 128 (x, y, z)

Reconstructed data dimensions (µm): 163.2 x 151.7 x 135.4 (x, y, z)

Classes annotated: Nucleus

Source dataset (EM) ID: jrc_mus-heart-1

Source dataset (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)

Source dataset (EM) data dimensions (µm): 163.23 x 151.69 x 135.87 (x, y, z)

Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24020919

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/inference/segmentations/nuc/

Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-heart-1