noisy-fish alpha
3D UNet Arabidopsis Ovules Nuclei
Qin Yu, Adrian Wolny
10.5281/zenodo.7772662/7781091
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Model Information
Description: Unet trained on confocal images of Arabidopsis Ovules nuclei.
Task: 3D nucleus segmentation
Licence: MIT
Tags: 3D, nuclei, arabidopsis ovule, confocal microscopy, semantic segmentation, plantseg, U-Net, pytorch
Benchmarking
| Study | Dataset | Precision | Recall | IoU | Dice | Analysis parameters |
|---|---|---|---|---|---|---|
| S-BIAD1518 | Biopsy of diabetic human kidney | 0.747 | 0.68 | 0.552 | 0.711 | z_slices_analysed: 11,21 |
| S-BIAD1518 | Cleared mouse intestine | 0.522 | 0.955 | 0.51 | 0.675 | z_slices_analysed: 14,24 |
| S-BIAD1518 | Human kidney nephrectomy | 0.606 | 0.193 | 0.172 | 0.293 | z_slices_analysed: 11,21 |
| S-BIAD1196 | brain cell nucleus patches | 0.163 | 0.488 | 0.139 | 0.245 | z_slices_analysed: 94,104 |
| S-BIAD1518 | Scale-cleared rat kidney | 0.431 | 0.852 | 0.401 | 0.573 | z_slices_analysed: 1,11 |
| S-BIAD1026 | Go-Nuclear image dataset | 0.877 | 0.793 | 0.714 | 0.833 | z_slices_analysed: 126,136 |
| S-BIAD1518 | Human kidney cortex | 0.635 | 0.695 | 0.496 | 0.663 | z_slices_analysed: 3,13 |
| S-BIAD1518 | BABB-cleared kidney | 0.693 | 0.723 | 0.547 | 0.707 | z_slices_analysed: 58,68 |
| S-BIAD1518 | Synthetic cell nuclei | 0.754 | 0.82 | 0.647 | 0.785 | z_slices_analysed: 58,68 |
| S-BIAD1492 | Simulated fluorescence images | 0.985 | 0.543 | 0.538 | 0.7 | z_slices_analysed: 58,68 |
Model predictions
| Study | Dataset | Original image | Reference annotation | Prediction | Analysis parameters |
|---|---|---|---|---|---|
| S-BIAD1518 | Biopsy of diabetic human kidney | 
Download | 
Download | 
Download | z_slices_analysed: 11,21 |
| S-BIAD1518 | Cleared mouse intestine | 
Download | 
Download | 
Download | z_slices_analysed: 14,24 |
| S-BIAD1518 | Human kidney nephrectomy | 
Download | 
Download | 
Download | z_slices_analysed: 11,21 |
| S-BIAD1196 | brain cell nucleus patches | 
Download | 
Download | 
Download | z_slices_analysed: 94,104 |
| S-BIAD1518 | Scale-cleared rat kidney | 
Download | 
Download | 
Download | z_slices_analysed: 1,11 |
| S-BIAD1026 | Go-Nuclear image dataset | 
Download | 
Download | 
Download | z_slices_analysed: 126,136 |
| S-BIAD1518 | Human kidney cortex | 
Download | 
Download | 
Download | z_slices_analysed: 3,13 |
| S-BIAD1518 | BABB-cleared kidney | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |
| S-BIAD1518 | Synthetic cell nuclei | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |
| S-BIAD1492 | Simulated fluorescence images | 
Download | 
Download | 
Download | z_slices_analysed: 58,68 |