powerful-fish alpha
3D UNet Mouse Embryo Live
A. Wolny, V. Bondarenko
10.5281/zenodo.6384845/7774490
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Model Information
Description: A 3D U-Net trained to predict the cell boundaries in live light sheet images of developing mouse embryo. Voxel size: 0.2×0.2×1.0 µm^3
Task: 3D cell segmentation
Licence: MIT
Tags: 3D, cell membrane, mouse embryo, live tissue, light sheet microscopy, semantic segmentation, torchscript, ilastik, U-Net, plantseg, deepimagej, pytorch, animal
Benchmarking
This model was not tested on datasets with reference annotations, so we cannot produce benchmarking metrics.
Model predictions
| Study | Dataset | Original image | Prediction | Analysis parameters |
|---|---|---|---|---|
| S-BIAD1490 | Source data | 
Download | 
Download | z_slices_analysed: 6,22 xy_image_crop_size: 512,512 t_slices_analysed: 0,1 |
| S-BIAD915 | Microscopy data | 
Download | 
Download | z_slices_analysed: 53,69 xy_image_crop_size: 1024,1024 input_channel_analysed: 1 |
| S-BIAD827 | Experiment A | 
Download | 
Download | z_slices_analysed: 24,40 input_channel_analysed: 0 |
| S-BIAD1241 | Colocalization N. benthamiana | 
Download | 
Download | z_slices_analysed: 9,25 input_channel_analysed: 0 |