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Model Information
Description: A 3D U-Net trained to predict the nuclei and their boundaries in fixed confocal images of developing mouse embryo.Voxel size: (0.2×0.2×1 µm^3) (XYZ).
Task: 3D nucleus segmentation
Licence: MIT
Tags: 3D, nuclei, mouse embryo, fixed tissue, confocal microscopy, semantic segmentation, torchscript, ilastik, U-Net, plantseg, deepimagej, pytorch
Benchmarking
| Study | Dataset | Precision | Recall | IoU | Dice | Analysis parameters |
|---|---|---|---|---|---|---|
| S-BIAD1518 | Scale-cleared rat kidney | 0.751 | 0.024 | 0.023 | 0.046 | z_slices_analysed: 1,11 |
| S-BIAD1492 | Simulated fluorescence images | 1 | 0.376 | 0.376 | 0.546 | z_slices_analysed: 58,68 |
| S-BIAD1518 | Human kidney cortex | 0.778 | 0.171 | 0.163 | 0.281 | z_slices_analysed: 3,13 |
| S-BIAD1518 | Human kidney nephrectomy | 0.743 | 0.001 | 0.001 | 0.001 | z_slices_analysed: 11,21 |
| S-BIAD1518 | Cleared mouse intestine | 0.775 | 0.256 | 0.239 | 0.385 | z_slices_analysed: 14,24 |
| S-BIAD1518 | Synthetic cell nuclei | 0.973 | 0.151 | 0.15 | 0.261 | z_slices_analysed: 58,68 |
| S-BIAD1196 | brain cell nucleus patches | 0.32 | 0.155 | 0.117 | 0.209 | z_slices_analysed: 94,104 |
| S-BIAD1026 | Go-Nuclear image dataset | 0.999 | 0.33 | 0.329 | 0.496 | z_slices_analysed: 126,136 |
| S-BIAD1518 | BABB-cleared kidney | 1 | 0.139 | 0.139 | 0.244 | z_slices_analysed: 58,68 |
| S-BIAD1518 | Biopsy of diabetic human kidney | 0.927 | 0.177 | 0.175 | 0.298 | z_slices_analysed: 11,21 |
Model predictions
| Study | Dataset | Original image | Reference annotation | Prediction | Analysis parameters |
|---|---|---|---|---|---|
| S-BIAD1518 | Scale-cleared rat kidney | 
Download | 
Download | 
Download | z_slices_analysed: 1,11 |
| S-BIAD1492 | Simulated fluorescence images | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |
| S-BIAD1518 | Human kidney cortex | 
Download | 
Download | 
Download | z_slices_analysed: 3,13 |
| S-BIAD1518 | Human kidney nephrectomy | 
Download | 
Download | 
Download | z_slices_analysed: 11,21 |
| S-BIAD1518 | Cleared mouse intestine | 
Download | 
Download | 
Download | z_slices_analysed: 14,24 |
| S-BIAD1518 | Synthetic cell nuclei | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |
| S-BIAD1196 | brain cell nucleus patches | 
Download | 
Download | 
Download | z_slices_analysed: 94,104 |
| S-BIAD1026 | Go-Nuclear image dataset | 
Download | 
Download | 
Download | z_slices_analysed: 126,136 |
| S-BIAD1518 | BABB-cleared kidney | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |
| S-BIAD1518 | Biopsy of diabetic human kidney | 
Download | 
Download | 
Download | z_slices_analysed: 11,21 |