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

Segmentation description: Nuclei segmentations in jrc_mus-kidney using Cellpose 3.0.9 with cursory manual corrections.

Software: Cellpose 3.0.9

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

Prediction Duration (seconds): 542.62

GPU: NVIDIA TITAN RTX

RAM: 251.0 GiB

Label voxel size (nm): 128 x 128 x 128 (x, y, z)

Reconstructed data dimensions (µm): 98.3 x 63.6 x 177.6 (X, Y, Z)

Classes annotated: Nucleus

Source dataset (EM) ID: jrc_mus-kidney

Source dataset (EM) voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)

Source dataset (EM) data dimensions (µm): 98.3 x 63.6 x 177.6 (X, Y, Z)

Source dataset (EM) DOI: https://doi.org/10.25378/janelia.16913035

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

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