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

<p><br></p><p dir="ltr"><b>Model description</b>: Cellpose 3.0.9 was trained on nuclei from 28 2D slices from jrc_mus-kidney.</p><p dir="ltr"><b>Architecture</b>: Cellpose 3.0.9</p><p dir="ltr"><b>Number of parameters</b>: 6600845</p><p dir="ltr"><b>Input voxel size (nm)</b>: 128 x 128 x 128 (X, Y, Z)</p><p dir="ltr"><b>Output voxel size (nm)</b>: 128 x 128 x 128 (X, Y, Z)</p><p dir="ltr"><b>Classes trained on</b>: Nucleus</p><p dir="ltr"><b>Training steps</b>: 28000</p><p dir="ltr"><b>Epochs</b>: 1000</p><p dir="ltr"><b>GPU</b>: NVIDIA TITAN RTX</p><p dir="ltr"><b>RAM</b>: 251.0 GiB</p><p dir="ltr"><b>Model wall time (sec)</b>: 542.62</p><p dir="ltr"><b>Software</b>: Cellpose 3.0.9</p><p dir="ltr"><b>Software DOI</b>: <a href="https://doi.org/10.1038/s41592-022-01663-4" target="_blank">https://doi.org/10.1038/s41592-022-01663-4</a></p><p dir="ltr"><b>Source dataset (EM) ID</b>: jrc_mus-kidney</p><p dir="ltr"><b>Source dataset (EM) DOI</b>: <a href="https://doi.org/10.25378/janelia.16913035" rel="noreferrer noopener" target="_blank">https://doi.org/10.25378/janelia.16913035</a></p><p dir="ltr"><b>Generated dataset DOI</b>: <a href=" https://doi.org/10.25378/janelia.26506522" rel="noreferrer" target="_blank">https://doi.org/10.25378/janelia.26506522</a></p><p dir="ltr"><b>Model URL</b>: <a href="https://data.janelia.org/6d93n7" rel="noreferrer" target="_blank">https://data.janelia.org/6d93n7</a></p><p dir="ltr"><b>Github repo</b>: <a href="https://github.com/janelia-cellmap/cellmap-models" target="_blank">https://github.com/janelia-cellmap/cellmap-models</a></p><p dir="ltr"><b>Visualization website</b>: <a href="https://openorganelle.janelia.org/datasets/jrc_mus-kidney" rel="noreferrer" target="_blank">https://openorganelle.janelia.org/datasets/jrc_mus-kidney</a></p>