Add weights for 16 3D cloud instance-segmentation models (8 architectures x 2 conditions)
Browse files- README.md +114 -0
- attentionunet/real_only/config.json +85 -0
- attentionunet/real_only/model.safetensors +3 -0
- attentionunet/real_plus_synth/config.json +90 -0
- attentionunet/real_plus_synth/model.safetensors +3 -0
- resattnunet3d/real_only/config.json +74 -0
- resattnunet3d/real_only/model.safetensors +3 -0
- resattnunet3d/real_plus_synth/config.json +79 -0
- resattnunet3d/real_plus_synth/model.safetensors +3 -0
- resunet3d/real_only/config.json +74 -0
- resunet3d/real_only/model.safetensors +3 -0
- resunet3d/real_plus_synth/config.json +79 -0
- resunet3d/real_plus_synth/model.safetensors +3 -0
- segformer3d/real_only/config.json +73 -0
- segformer3d/real_only/model.safetensors +3 -0
- segformer3d/real_plus_synth/config.json +78 -0
- segformer3d/real_plus_synth/model.safetensors +3 -0
- segresnet/real_only/config.json +74 -0
- segresnet/real_only/model.safetensors +3 -0
- segresnet/real_plus_synth/config.json +79 -0
- segresnet/real_plus_synth/model.safetensors +3 -0
- swinunetr/real_only/config.json +74 -0
- swinunetr/real_only/model.safetensors +3 -0
- swinunetr/real_plus_synth/config.json +79 -0
- swinunetr/real_plus_synth/model.safetensors +3 -0
- umamba/real_only/config.json +75 -0
- umamba/real_only/model.safetensors +3 -0
- umamba/real_plus_synth/config.json +80 -0
- umamba/real_plus_synth/model.safetensors +3 -0
- unet/real_only/config.json +86 -0
- unet/real_only/model.safetensors +3 -0
- unet/real_plus_synth/config.json +91 -0
- unet/real_plus_synth/model.safetensors +3 -0
README.md
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---
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license: cc-by-nc-4.0
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tags:
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- segmentation
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- instance-segmentation
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- 3d
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- volumetric
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- monai
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- atmospheric-science
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---
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# 3D Convective-Cloud Instance Segmentation — 8 Architectures
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Weights for **16 volumetric segmentation networks** that separate individual
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convective clouds in 3D atmospheric-simulation volumes. Eight architectures,
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each trained under two data conditions: real volumes only, and real volumes
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plus synthetic volumes from the companion
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[3D convective-cloud DDPM](https://huggingface.co/HoqueMahmudul/convective-cloud-denoising-diffusion-probabilistic-model-3d).
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**Project:** [3D Convective-Cloud Generation collection](https://huggingface.co/collections/HoqueMahmudul/3d-convective-cloud-generation-ddpm-190m-params-6a6ba230c89356ff617d481a)
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> **Status:** research artifact from work with an associated manuscript **in
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> preparation**. This repository contains **weights only**. Training code,
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> methodology and evaluation are not included here and will appear in the
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> publication.
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## Contents
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```
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<architecture>/<condition>/model.safetensors # weights
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<architecture>/<condition>/config.json # constructor args, normalization, inference + post-processing settings
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```
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`condition` is `real_only` or `real_plus_synth`. All runs use seed 42; the
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saved weights are the checkpoint with the best validation panoptic quality.
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| Architecture | Folder | Implementation | Parameters | Loadable from this repo alone |
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|---|---|---|---|---|
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| 3D U-Net | `unet` | `monai.networks.nets.UNet` | 4.81M | Yes |
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| Attention U-Net 3D | `attentionunet` | `monai.networks.nets.AttentionUnet` | 5.91M | Yes |
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| SegResNet | `segresnet` | `monai.networks.nets.SegResNet` | 4.70M | Yes |
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| SwinUNETR | `swinunetr` | `monai.networks.nets.SwinUNETR` | 15.70M | Yes |
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| ResUNet3D | `resunet3d` | custom | 5.91M | No: definition not released |
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| Residual Attention U-Net 3D | `resattnunet3d` | custom | 5.93M | No: definition not released |
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| SegFormer3D | `segformer3d` | custom (not Perera et al. 2024) | 2.64M | No: definition not released |
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| U-Mamba | `umamba` | custom, built on `mamba_ssm` kernels (not Ma et al. 2024) | 6.50M | No: definition not released |
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The four MONAI models can be rebuilt from `config.json` and used directly. The
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four custom models are published for archival and reproducibility; their
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architecture definitions will be released with the publication.
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## Model contract
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| | |
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|---|---|
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| Input | `(B, 1, D, H, W)`, single-channel volume, 0.5 km isotropic voxels |
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| Normalization | `x = clip((v - 302) / (1921 - 302), 0, 1)` (background maps to 0) |
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| Output | `(B, 3, D, H, W)` **logits**: channel 0 = foreground, 1 = seeds, 2 = boundary |
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| Training patch | `(32, 160, 160)` (D, H, W) |
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| Full-volume inference | MONAI `sliding_window_inference`, `roi_size=(32,160,160)`, `overlap=0.5`, `mode="gaussian"` blending on logits, then sigmoid |
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Instances are obtained by thresholding foreground and seeds, then running a
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marker-controlled watershed. `config.json` lists two threshold sets:
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`global_operating_point` (shared by all models) and
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`calibrated_operating_point` (tuned per model on the validation volume).
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## Usage (MONAI architectures)
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```bash
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pip install monai==1.5.2 torch safetensors huggingface_hub
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```
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```python
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import json, torch
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from huggingface_hub import hf_hub_download
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from safetensors.torch import load_file
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from monai.networks.nets import SegResNet # or UNet, AttentionUnet, SwinUNETR
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from monai.inferers import sliding_window_inference
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repo, sub = "HoqueMahmudul/convective-cloud-3d-instance-segmentation", "segresnet/real_only"
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cfg = json.load(open(hf_hub_download(repo, f"{sub}/config.json")))
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weights = load_file(hf_hub_download(repo, f"{sub}/model.safetensors"))
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# Weights were saved from a thin wrapper, so keys carry a "network." prefix.
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weights = {k.removeprefix("network."): v for k, v in weights.items()}
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model = SegResNet(spatial_dims=3, in_channels=1, out_channels=3, **cfg["model_kwargs"])
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model.load_state_dict(weights, strict=True)
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model.eval()
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lo, hi = cfg["input_normalization"]["lo"], cfg["input_normalization"]["hi"]
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volume = torch.from_numpy(raw).float() # raw: (D, H, W) numpy array
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x = ((volume - lo) / (hi - lo)).clamp(0, 1)[None, None]
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with torch.no_grad():
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logits = sliding_window_inference(x, roi_size=(32, 160, 160), sw_batch_size=1,
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predictor=model, overlap=0.5, mode="gaussian")
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probs = torch.sigmoid(logits)[0] # (3, D, H, W): foreground, seeds, boundary
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```
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This loading recipe was verified with MONAI 1.5.2 and PyTorch 2.5.1 for all
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four MONAI architectures (`strict=True`).
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## Limitations
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- Trained on a small number of real simulation volumes from a single
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simulation setup; not validated on other models, resolutions or observational
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data.
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- One training seed per configuration.
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- Not a weather-forecasting or nowcasting tool.
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## License
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CC BY-NC 4.0, same as the companion DDPM.
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attentionunet/real_only/config.json
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{
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"architecture": "attentionunet",
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"implementation": "monai.networks.nets.AttentionUnet",
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| 4 |
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"spatial_dims": 3,
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| 5 |
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"in_channels": 1,
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| 6 |
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"out_channels": 3,
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"model_kwargs": {
|
| 8 |
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"channels": [
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| 9 |
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16,
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+
32,
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| 11 |
+
64,
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| 12 |
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128,
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+
256
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+
],
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"strides": [
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2,
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+
2,
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| 18 |
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2,
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| 19 |
+
2
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+
]
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},
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| 22 |
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"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 23 |
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"output_channels": [
|
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"foreground",
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| 25 |
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"seeds",
|
| 26 |
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"boundary"
|
| 27 |
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],
|
| 28 |
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"output_activation": "logits (apply sigmoid)",
|
| 29 |
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"condition": "real_only",
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| 30 |
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"condition_label": "Real only volumes",
|
| 31 |
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"seed": 42,
|
| 32 |
+
"train_volumes": [
|
| 33 |
+
"real_253",
|
| 34 |
+
"real_255",
|
| 35 |
+
"real_257",
|
| 36 |
+
"real_259",
|
| 37 |
+
"real_261"
|
| 38 |
+
],
|
| 39 |
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"validation_volume": "real_263",
|
| 40 |
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"selected_step": 8000,
|
| 41 |
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"selection": "best validation panoptic quality on real_263",
|
| 42 |
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"best_val_pq": 0.6819144096495348,
|
| 43 |
+
"parameter_count": 5909147,
|
| 44 |
+
"input_normalization": {
|
| 45 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 46 |
+
"lo": 302.0,
|
| 47 |
+
"hi": 1921.0
|
| 48 |
+
},
|
| 49 |
+
"voxel_spacing_km": 0.5,
|
| 50 |
+
"patch_size_dhw": [
|
| 51 |
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32,
|
| 52 |
+
160,
|
| 53 |
+
160
|
| 54 |
+
],
|
| 55 |
+
"sliding_window": {
|
| 56 |
+
"roi_size": [
|
| 57 |
+
32,
|
| 58 |
+
160,
|
| 59 |
+
160
|
| 60 |
+
],
|
| 61 |
+
"overlap": 0.5,
|
| 62 |
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"mode": "gaussian",
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| 63 |
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"blend": "logits, then sigmoid"
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| 64 |
+
},
|
| 65 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 66 |
+
"global_operating_point": {
|
| 67 |
+
"foreground_threshold": 0.4,
|
| 68 |
+
"seed_threshold": 0.7,
|
| 69 |
+
"boundary_threshold": 0.5,
|
| 70 |
+
"min_seed_size": 3,
|
| 71 |
+
"min_instance_size": 6,
|
| 72 |
+
"foreground_closing_iterations": 1,
|
| 73 |
+
"seed_opening_iterations": 0
|
| 74 |
+
},
|
| 75 |
+
"calibrated_operating_point": {
|
| 76 |
+
"foreground_threshold": 0.3,
|
| 77 |
+
"seed_threshold": 0.5,
|
| 78 |
+
"boundary_threshold": 0.5,
|
| 79 |
+
"min_seed_size": 5,
|
| 80 |
+
"min_instance_size": 12,
|
| 81 |
+
"foreground_closing_iterations": 1,
|
| 82 |
+
"seed_opening_iterations": 0
|
| 83 |
+
},
|
| 84 |
+
"source_checkpoint_sha256": "91700d9947d23bc3f89c630f56f5c3886dab9f70e8f836c44c509aa7c233d3df"
|
| 85 |
+
}
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attentionunet/real_only/model.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:949c326197ef969eff430be9c42690075a84fdba98c96e51fe95da194af5f6e3
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size 23672820
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attentionunet/real_plus_synth/config.json
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "attentionunet",
|
| 3 |
+
"implementation": "monai.networks.nets.AttentionUnet",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"channels": [
|
| 9 |
+
16,
|
| 10 |
+
32,
|
| 11 |
+
64,
|
| 12 |
+
128,
|
| 13 |
+
256
|
| 14 |
+
],
|
| 15 |
+
"strides": [
|
| 16 |
+
2,
|
| 17 |
+
2,
|
| 18 |
+
2,
|
| 19 |
+
2
|
| 20 |
+
]
|
| 21 |
+
},
|
| 22 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 23 |
+
"output_channels": [
|
| 24 |
+
"foreground",
|
| 25 |
+
"seeds",
|
| 26 |
+
"boundary"
|
| 27 |
+
],
|
| 28 |
+
"output_activation": "logits (apply sigmoid)",
|
| 29 |
+
"condition": "real_plus_synth",
|
| 30 |
+
"condition_label": "Real + synthetic volumes",
|
| 31 |
+
"seed": 42,
|
| 32 |
+
"train_volumes": [
|
| 33 |
+
"real_253",
|
| 34 |
+
"real_255",
|
| 35 |
+
"real_257",
|
| 36 |
+
"real_259",
|
| 37 |
+
"real_261",
|
| 38 |
+
"synthetic_901",
|
| 39 |
+
"synthetic_902",
|
| 40 |
+
"synthetic_903",
|
| 41 |
+
"synthetic_904",
|
| 42 |
+
"synthetic_908"
|
| 43 |
+
],
|
| 44 |
+
"validation_volume": "real_263",
|
| 45 |
+
"selected_step": 51000,
|
| 46 |
+
"selection": "best validation panoptic quality on real_263",
|
| 47 |
+
"best_val_pq": 0.656567639274456,
|
| 48 |
+
"parameter_count": 5909147,
|
| 49 |
+
"input_normalization": {
|
| 50 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 51 |
+
"lo": 302.0,
|
| 52 |
+
"hi": 1921.0
|
| 53 |
+
},
|
| 54 |
+
"voxel_spacing_km": 0.5,
|
| 55 |
+
"patch_size_dhw": [
|
| 56 |
+
32,
|
| 57 |
+
160,
|
| 58 |
+
160
|
| 59 |
+
],
|
| 60 |
+
"sliding_window": {
|
| 61 |
+
"roi_size": [
|
| 62 |
+
32,
|
| 63 |
+
160,
|
| 64 |
+
160
|
| 65 |
+
],
|
| 66 |
+
"overlap": 0.5,
|
| 67 |
+
"mode": "gaussian",
|
| 68 |
+
"blend": "logits, then sigmoid"
|
| 69 |
+
},
|
| 70 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 71 |
+
"global_operating_point": {
|
| 72 |
+
"foreground_threshold": 0.4,
|
| 73 |
+
"seed_threshold": 0.7,
|
| 74 |
+
"boundary_threshold": 0.5,
|
| 75 |
+
"min_seed_size": 3,
|
| 76 |
+
"min_instance_size": 6,
|
| 77 |
+
"foreground_closing_iterations": 1,
|
| 78 |
+
"seed_opening_iterations": 0
|
| 79 |
+
},
|
| 80 |
+
"calibrated_operating_point": {
|
| 81 |
+
"foreground_threshold": 0.5,
|
| 82 |
+
"seed_threshold": 0.7,
|
| 83 |
+
"boundary_threshold": 0.5,
|
| 84 |
+
"min_seed_size": 5,
|
| 85 |
+
"min_instance_size": 12,
|
| 86 |
+
"foreground_closing_iterations": 1,
|
| 87 |
+
"seed_opening_iterations": 0
|
| 88 |
+
},
|
| 89 |
+
"source_checkpoint_sha256": "ae78a1d30f1944c02adb64d83b58c6575032165bec783ec740dbdc851be9edca"
|
| 90 |
+
}
|
attentionunet/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:72dd84ae4898701799c1e5df615b62979ecd1293a2fa22d4c2d97bea35ae9fba
|
| 3 |
+
size 23672820
|
resattnunet3d/real_only/config.json
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "resattnunet3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_only",
|
| 19 |
+
"condition_label": "Real only volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261"
|
| 27 |
+
],
|
| 28 |
+
"validation_volume": "real_263",
|
| 29 |
+
"selected_step": 4000,
|
| 30 |
+
"selection": "best validation panoptic quality on real_263",
|
| 31 |
+
"best_val_pq": 0.6610435600235838,
|
| 32 |
+
"parameter_count": 5929559,
|
| 33 |
+
"input_normalization": {
|
| 34 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 35 |
+
"lo": 302.0,
|
| 36 |
+
"hi": 1921.0
|
| 37 |
+
},
|
| 38 |
+
"voxel_spacing_km": 0.5,
|
| 39 |
+
"patch_size_dhw": [
|
| 40 |
+
32,
|
| 41 |
+
160,
|
| 42 |
+
160
|
| 43 |
+
],
|
| 44 |
+
"sliding_window": {
|
| 45 |
+
"roi_size": [
|
| 46 |
+
32,
|
| 47 |
+
160,
|
| 48 |
+
160
|
| 49 |
+
],
|
| 50 |
+
"overlap": 0.5,
|
| 51 |
+
"mode": "gaussian",
|
| 52 |
+
"blend": "logits, then sigmoid"
|
| 53 |
+
},
|
| 54 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 55 |
+
"global_operating_point": {
|
| 56 |
+
"foreground_threshold": 0.4,
|
| 57 |
+
"seed_threshold": 0.7,
|
| 58 |
+
"boundary_threshold": 0.5,
|
| 59 |
+
"min_seed_size": 3,
|
| 60 |
+
"min_instance_size": 6,
|
| 61 |
+
"foreground_closing_iterations": 1,
|
| 62 |
+
"seed_opening_iterations": 0
|
| 63 |
+
},
|
| 64 |
+
"calibrated_operating_point": {
|
| 65 |
+
"foreground_threshold": 0.5,
|
| 66 |
+
"seed_threshold": 0.5,
|
| 67 |
+
"boundary_threshold": 0.5,
|
| 68 |
+
"min_seed_size": 5,
|
| 69 |
+
"min_instance_size": 12,
|
| 70 |
+
"foreground_closing_iterations": 1,
|
| 71 |
+
"seed_opening_iterations": 0
|
| 72 |
+
},
|
| 73 |
+
"source_checkpoint_sha256": "77e78f5958adf77d59f9f530001efd63ce6d150fa16ce9614b6d502059e6fffe"
|
| 74 |
+
}
|
resattnunet3d/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:180db5516b7f51a281e61d39f17d45fcc49c1759584b1f4e2c769212ae1b51df
|
| 3 |
+
size 23727340
|
resattnunet3d/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,79 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "resattnunet3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_plus_synth",
|
| 19 |
+
"condition_label": "Real + synthetic volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261",
|
| 27 |
+
"synthetic_901",
|
| 28 |
+
"synthetic_902",
|
| 29 |
+
"synthetic_903",
|
| 30 |
+
"synthetic_904",
|
| 31 |
+
"synthetic_908"
|
| 32 |
+
],
|
| 33 |
+
"validation_volume": "real_263",
|
| 34 |
+
"selected_step": 17000,
|
| 35 |
+
"selection": "best validation panoptic quality on real_263",
|
| 36 |
+
"best_val_pq": 0.6889164358160301,
|
| 37 |
+
"parameter_count": 5929559,
|
| 38 |
+
"input_normalization": {
|
| 39 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 40 |
+
"lo": 302.0,
|
| 41 |
+
"hi": 1921.0
|
| 42 |
+
},
|
| 43 |
+
"voxel_spacing_km": 0.5,
|
| 44 |
+
"patch_size_dhw": [
|
| 45 |
+
32,
|
| 46 |
+
160,
|
| 47 |
+
160
|
| 48 |
+
],
|
| 49 |
+
"sliding_window": {
|
| 50 |
+
"roi_size": [
|
| 51 |
+
32,
|
| 52 |
+
160,
|
| 53 |
+
160
|
| 54 |
+
],
|
| 55 |
+
"overlap": 0.5,
|
| 56 |
+
"mode": "gaussian",
|
| 57 |
+
"blend": "logits, then sigmoid"
|
| 58 |
+
},
|
| 59 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 60 |
+
"global_operating_point": {
|
| 61 |
+
"foreground_threshold": 0.4,
|
| 62 |
+
"seed_threshold": 0.7,
|
| 63 |
+
"boundary_threshold": 0.5,
|
| 64 |
+
"min_seed_size": 3,
|
| 65 |
+
"min_instance_size": 6,
|
| 66 |
+
"foreground_closing_iterations": 1,
|
| 67 |
+
"seed_opening_iterations": 0
|
| 68 |
+
},
|
| 69 |
+
"calibrated_operating_point": {
|
| 70 |
+
"foreground_threshold": 0.4,
|
| 71 |
+
"seed_threshold": 0.5,
|
| 72 |
+
"boundary_threshold": 0.5,
|
| 73 |
+
"min_seed_size": 5,
|
| 74 |
+
"min_instance_size": 12,
|
| 75 |
+
"foreground_closing_iterations": 1,
|
| 76 |
+
"seed_opening_iterations": 0
|
| 77 |
+
},
|
| 78 |
+
"source_checkpoint_sha256": "17160c96e12d00e69e903f6252408dc854c6d65233ddd22f18d50eacaebc8603"
|
| 79 |
+
}
|
resattnunet3d/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c9d88e49b7b62335cef06c087e9e223eb6bb258cf07951a7ee6a9ba08863dafa
|
| 3 |
+
size 23727340
|
resunet3d/real_only/config.json
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "resunet3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_only",
|
| 19 |
+
"condition_label": "Real only volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261"
|
| 27 |
+
],
|
| 28 |
+
"validation_volume": "real_263",
|
| 29 |
+
"selected_step": 24000,
|
| 30 |
+
"selection": "best validation panoptic quality on real_263",
|
| 31 |
+
"best_val_pq": 0.6468635886700437,
|
| 32 |
+
"parameter_count": 5907555,
|
| 33 |
+
"input_normalization": {
|
| 34 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 35 |
+
"lo": 302.0,
|
| 36 |
+
"hi": 1921.0
|
| 37 |
+
},
|
| 38 |
+
"voxel_spacing_km": 0.5,
|
| 39 |
+
"patch_size_dhw": [
|
| 40 |
+
32,
|
| 41 |
+
160,
|
| 42 |
+
160
|
| 43 |
+
],
|
| 44 |
+
"sliding_window": {
|
| 45 |
+
"roi_size": [
|
| 46 |
+
32,
|
| 47 |
+
160,
|
| 48 |
+
160
|
| 49 |
+
],
|
| 50 |
+
"overlap": 0.5,
|
| 51 |
+
"mode": "gaussian",
|
| 52 |
+
"blend": "logits, then sigmoid"
|
| 53 |
+
},
|
| 54 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 55 |
+
"global_operating_point": {
|
| 56 |
+
"foreground_threshold": 0.4,
|
| 57 |
+
"seed_threshold": 0.7,
|
| 58 |
+
"boundary_threshold": 0.5,
|
| 59 |
+
"min_seed_size": 3,
|
| 60 |
+
"min_instance_size": 6,
|
| 61 |
+
"foreground_closing_iterations": 1,
|
| 62 |
+
"seed_opening_iterations": 0
|
| 63 |
+
},
|
| 64 |
+
"calibrated_operating_point": {
|
| 65 |
+
"foreground_threshold": 0.3,
|
| 66 |
+
"seed_threshold": 0.8,
|
| 67 |
+
"boundary_threshold": 0.5,
|
| 68 |
+
"min_seed_size": 5,
|
| 69 |
+
"min_instance_size": 12,
|
| 70 |
+
"foreground_closing_iterations": 1,
|
| 71 |
+
"seed_opening_iterations": 0
|
| 72 |
+
},
|
| 73 |
+
"source_checkpoint_sha256": "70baba16d01ac7bd377ec6d3d97b26ceec41525ab1bcba96664129ad611253ae"
|
| 74 |
+
}
|
resunet3d/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ccd94673958a6955cb39f8995f2f4c559c7051d84795fa239672d6cd2f794ea3
|
| 3 |
+
size 23637412
|
resunet3d/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,79 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "resunet3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_plus_synth",
|
| 19 |
+
"condition_label": "Real + synthetic volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261",
|
| 27 |
+
"synthetic_901",
|
| 28 |
+
"synthetic_902",
|
| 29 |
+
"synthetic_903",
|
| 30 |
+
"synthetic_904",
|
| 31 |
+
"synthetic_908"
|
| 32 |
+
],
|
| 33 |
+
"validation_volume": "real_263",
|
| 34 |
+
"selected_step": 31000,
|
| 35 |
+
"selection": "best validation panoptic quality on real_263",
|
| 36 |
+
"best_val_pq": 0.6708559358919156,
|
| 37 |
+
"parameter_count": 5907555,
|
| 38 |
+
"input_normalization": {
|
| 39 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 40 |
+
"lo": 302.0,
|
| 41 |
+
"hi": 1921.0
|
| 42 |
+
},
|
| 43 |
+
"voxel_spacing_km": 0.5,
|
| 44 |
+
"patch_size_dhw": [
|
| 45 |
+
32,
|
| 46 |
+
160,
|
| 47 |
+
160
|
| 48 |
+
],
|
| 49 |
+
"sliding_window": {
|
| 50 |
+
"roi_size": [
|
| 51 |
+
32,
|
| 52 |
+
160,
|
| 53 |
+
160
|
| 54 |
+
],
|
| 55 |
+
"overlap": 0.5,
|
| 56 |
+
"mode": "gaussian",
|
| 57 |
+
"blend": "logits, then sigmoid"
|
| 58 |
+
},
|
| 59 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 60 |
+
"global_operating_point": {
|
| 61 |
+
"foreground_threshold": 0.4,
|
| 62 |
+
"seed_threshold": 0.7,
|
| 63 |
+
"boundary_threshold": 0.5,
|
| 64 |
+
"min_seed_size": 3,
|
| 65 |
+
"min_instance_size": 6,
|
| 66 |
+
"foreground_closing_iterations": 1,
|
| 67 |
+
"seed_opening_iterations": 0
|
| 68 |
+
},
|
| 69 |
+
"calibrated_operating_point": {
|
| 70 |
+
"foreground_threshold": 0.4,
|
| 71 |
+
"seed_threshold": 0.8,
|
| 72 |
+
"boundary_threshold": 0.5,
|
| 73 |
+
"min_seed_size": 5,
|
| 74 |
+
"min_instance_size": 12,
|
| 75 |
+
"foreground_closing_iterations": 1,
|
| 76 |
+
"seed_opening_iterations": 0
|
| 77 |
+
},
|
| 78 |
+
"source_checkpoint_sha256": "084f1eb8125193990a418a5df767740ba6f908135528422295dea115d2e0ed4d"
|
| 79 |
+
}
|
resunet3d/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:30ddd4a6ed3fdea99e0159bb41231352d22a024751ba4ebab61a1c5490de75f3
|
| 3 |
+
size 23637412
|
segformer3d/real_only/config.json
ADDED
|
@@ -0,0 +1,73 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "segformer3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16
|
| 9 |
+
},
|
| 10 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 11 |
+
"output_channels": [
|
| 12 |
+
"foreground",
|
| 13 |
+
"seeds",
|
| 14 |
+
"boundary"
|
| 15 |
+
],
|
| 16 |
+
"output_activation": "logits (apply sigmoid)",
|
| 17 |
+
"condition": "real_only",
|
| 18 |
+
"condition_label": "Real only volumes",
|
| 19 |
+
"seed": 42,
|
| 20 |
+
"train_volumes": [
|
| 21 |
+
"real_253",
|
| 22 |
+
"real_255",
|
| 23 |
+
"real_257",
|
| 24 |
+
"real_259",
|
| 25 |
+
"real_261"
|
| 26 |
+
],
|
| 27 |
+
"validation_volume": "real_263",
|
| 28 |
+
"selected_step": 21000,
|
| 29 |
+
"selection": "best validation panoptic quality on real_263",
|
| 30 |
+
"best_val_pq": 0.6220155226102867,
|
| 31 |
+
"parameter_count": 2636067,
|
| 32 |
+
"input_normalization": {
|
| 33 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 34 |
+
"lo": 302.0,
|
| 35 |
+
"hi": 1921.0
|
| 36 |
+
},
|
| 37 |
+
"voxel_spacing_km": 0.5,
|
| 38 |
+
"patch_size_dhw": [
|
| 39 |
+
32,
|
| 40 |
+
160,
|
| 41 |
+
160
|
| 42 |
+
],
|
| 43 |
+
"sliding_window": {
|
| 44 |
+
"roi_size": [
|
| 45 |
+
32,
|
| 46 |
+
160,
|
| 47 |
+
160
|
| 48 |
+
],
|
| 49 |
+
"overlap": 0.5,
|
| 50 |
+
"mode": "gaussian",
|
| 51 |
+
"blend": "logits, then sigmoid"
|
| 52 |
+
},
|
| 53 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 54 |
+
"global_operating_point": {
|
| 55 |
+
"foreground_threshold": 0.4,
|
| 56 |
+
"seed_threshold": 0.7,
|
| 57 |
+
"boundary_threshold": 0.5,
|
| 58 |
+
"min_seed_size": 3,
|
| 59 |
+
"min_instance_size": 6,
|
| 60 |
+
"foreground_closing_iterations": 1,
|
| 61 |
+
"seed_opening_iterations": 0
|
| 62 |
+
},
|
| 63 |
+
"calibrated_operating_point": {
|
| 64 |
+
"foreground_threshold": 0.3,
|
| 65 |
+
"seed_threshold": 0.6,
|
| 66 |
+
"boundary_threshold": 0.5,
|
| 67 |
+
"min_seed_size": 5,
|
| 68 |
+
"min_instance_size": 12,
|
| 69 |
+
"foreground_closing_iterations": 1,
|
| 70 |
+
"seed_opening_iterations": 0
|
| 71 |
+
},
|
| 72 |
+
"source_checkpoint_sha256": "1f34c5aa28313ac1a452a6e0aa405fcd2a242718068d97f66d32dc24c48827b1"
|
| 73 |
+
}
|
segformer3d/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4a8953f6eae78112f47d20f366d001724954d2cc9516856734043b3da86dacb2
|
| 3 |
+
size 10554292
|
segformer3d/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "segformer3d",
|
| 3 |
+
"implementation": "custom (not released)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16
|
| 9 |
+
},
|
| 10 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 11 |
+
"output_channels": [
|
| 12 |
+
"foreground",
|
| 13 |
+
"seeds",
|
| 14 |
+
"boundary"
|
| 15 |
+
],
|
| 16 |
+
"output_activation": "logits (apply sigmoid)",
|
| 17 |
+
"condition": "real_plus_synth",
|
| 18 |
+
"condition_label": "Real + synthetic volumes",
|
| 19 |
+
"seed": 42,
|
| 20 |
+
"train_volumes": [
|
| 21 |
+
"real_253",
|
| 22 |
+
"real_255",
|
| 23 |
+
"real_257",
|
| 24 |
+
"real_259",
|
| 25 |
+
"real_261",
|
| 26 |
+
"synthetic_901",
|
| 27 |
+
"synthetic_902",
|
| 28 |
+
"synthetic_903",
|
| 29 |
+
"synthetic_904",
|
| 30 |
+
"synthetic_908"
|
| 31 |
+
],
|
| 32 |
+
"validation_volume": "real_263",
|
| 33 |
+
"selected_step": 53000,
|
| 34 |
+
"selection": "best validation panoptic quality on real_263",
|
| 35 |
+
"best_val_pq": 0.6497398092642781,
|
| 36 |
+
"parameter_count": 2636067,
|
| 37 |
+
"input_normalization": {
|
| 38 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 39 |
+
"lo": 302.0,
|
| 40 |
+
"hi": 1921.0
|
| 41 |
+
},
|
| 42 |
+
"voxel_spacing_km": 0.5,
|
| 43 |
+
"patch_size_dhw": [
|
| 44 |
+
32,
|
| 45 |
+
160,
|
| 46 |
+
160
|
| 47 |
+
],
|
| 48 |
+
"sliding_window": {
|
| 49 |
+
"roi_size": [
|
| 50 |
+
32,
|
| 51 |
+
160,
|
| 52 |
+
160
|
| 53 |
+
],
|
| 54 |
+
"overlap": 0.5,
|
| 55 |
+
"mode": "gaussian",
|
| 56 |
+
"blend": "logits, then sigmoid"
|
| 57 |
+
},
|
| 58 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 59 |
+
"global_operating_point": {
|
| 60 |
+
"foreground_threshold": 0.4,
|
| 61 |
+
"seed_threshold": 0.7,
|
| 62 |
+
"boundary_threshold": 0.5,
|
| 63 |
+
"min_seed_size": 3,
|
| 64 |
+
"min_instance_size": 6,
|
| 65 |
+
"foreground_closing_iterations": 1,
|
| 66 |
+
"seed_opening_iterations": 0
|
| 67 |
+
},
|
| 68 |
+
"calibrated_operating_point": {
|
| 69 |
+
"foreground_threshold": 0.3,
|
| 70 |
+
"seed_threshold": 0.6,
|
| 71 |
+
"boundary_threshold": 0.5,
|
| 72 |
+
"min_seed_size": 5,
|
| 73 |
+
"min_instance_size": 12,
|
| 74 |
+
"foreground_closing_iterations": 1,
|
| 75 |
+
"seed_opening_iterations": 0
|
| 76 |
+
},
|
| 77 |
+
"source_checkpoint_sha256": "f2dd33168bb3eec5928963949b5183721d900e5c9798dfdb8186687cc7c7e543"
|
| 78 |
+
}
|
segformer3d/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b1ff9803b7b0e55d425f73df45d4af7cadcd868e2929a1100229a4603c51f5ae
|
| 3 |
+
size 10554292
|
segresnet/real_only/config.json
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "segresnet",
|
| 3 |
+
"implementation": "monai.networks.nets.SegResNet",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"init_filters": 16,
|
| 9 |
+
"dropout_prob": 0.1
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_only",
|
| 19 |
+
"condition_label": "Real only volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261"
|
| 27 |
+
],
|
| 28 |
+
"validation_volume": "real_263",
|
| 29 |
+
"selected_step": 4000,
|
| 30 |
+
"selection": "best validation panoptic quality on real_263",
|
| 31 |
+
"best_val_pq": 0.6700788287147582,
|
| 32 |
+
"parameter_count": 4700931,
|
| 33 |
+
"input_normalization": {
|
| 34 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 35 |
+
"lo": 302.0,
|
| 36 |
+
"hi": 1921.0
|
| 37 |
+
},
|
| 38 |
+
"voxel_spacing_km": 0.5,
|
| 39 |
+
"patch_size_dhw": [
|
| 40 |
+
32,
|
| 41 |
+
160,
|
| 42 |
+
160
|
| 43 |
+
],
|
| 44 |
+
"sliding_window": {
|
| 45 |
+
"roi_size": [
|
| 46 |
+
32,
|
| 47 |
+
160,
|
| 48 |
+
160
|
| 49 |
+
],
|
| 50 |
+
"overlap": 0.5,
|
| 51 |
+
"mode": "gaussian",
|
| 52 |
+
"blend": "logits, then sigmoid"
|
| 53 |
+
},
|
| 54 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 55 |
+
"global_operating_point": {
|
| 56 |
+
"foreground_threshold": 0.4,
|
| 57 |
+
"seed_threshold": 0.7,
|
| 58 |
+
"boundary_threshold": 0.5,
|
| 59 |
+
"min_seed_size": 3,
|
| 60 |
+
"min_instance_size": 6,
|
| 61 |
+
"foreground_closing_iterations": 1,
|
| 62 |
+
"seed_opening_iterations": 0
|
| 63 |
+
},
|
| 64 |
+
"calibrated_operating_point": {
|
| 65 |
+
"foreground_threshold": 0.5,
|
| 66 |
+
"seed_threshold": 0.5,
|
| 67 |
+
"boundary_threshold": 0.5,
|
| 68 |
+
"min_seed_size": 5,
|
| 69 |
+
"min_instance_size": 12,
|
| 70 |
+
"foreground_closing_iterations": 1,
|
| 71 |
+
"seed_opening_iterations": 0
|
| 72 |
+
},
|
| 73 |
+
"source_checkpoint_sha256": "4ac39d2eff3582a389a65244d6d092f6f935f2ee886ba06c9f2219a89beccc8a"
|
| 74 |
+
}
|
segresnet/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ff21d2b772b3d252b27d1d3d43af1785a4f6a8d69e4c89eb76585e0205c54817
|
| 3 |
+
size 18812444
|
segresnet/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,79 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "segresnet",
|
| 3 |
+
"implementation": "monai.networks.nets.SegResNet",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"init_filters": 16,
|
| 9 |
+
"dropout_prob": 0.1
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_plus_synth",
|
| 19 |
+
"condition_label": "Real + synthetic volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261",
|
| 27 |
+
"synthetic_901",
|
| 28 |
+
"synthetic_902",
|
| 29 |
+
"synthetic_903",
|
| 30 |
+
"synthetic_904",
|
| 31 |
+
"synthetic_908"
|
| 32 |
+
],
|
| 33 |
+
"validation_volume": "real_263",
|
| 34 |
+
"selected_step": 7000,
|
| 35 |
+
"selection": "best validation panoptic quality on real_263",
|
| 36 |
+
"best_val_pq": 0.6671375694510983,
|
| 37 |
+
"parameter_count": 4700931,
|
| 38 |
+
"input_normalization": {
|
| 39 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 40 |
+
"lo": 302.0,
|
| 41 |
+
"hi": 1921.0
|
| 42 |
+
},
|
| 43 |
+
"voxel_spacing_km": 0.5,
|
| 44 |
+
"patch_size_dhw": [
|
| 45 |
+
32,
|
| 46 |
+
160,
|
| 47 |
+
160
|
| 48 |
+
],
|
| 49 |
+
"sliding_window": {
|
| 50 |
+
"roi_size": [
|
| 51 |
+
32,
|
| 52 |
+
160,
|
| 53 |
+
160
|
| 54 |
+
],
|
| 55 |
+
"overlap": 0.5,
|
| 56 |
+
"mode": "gaussian",
|
| 57 |
+
"blend": "logits, then sigmoid"
|
| 58 |
+
},
|
| 59 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 60 |
+
"global_operating_point": {
|
| 61 |
+
"foreground_threshold": 0.4,
|
| 62 |
+
"seed_threshold": 0.7,
|
| 63 |
+
"boundary_threshold": 0.5,
|
| 64 |
+
"min_seed_size": 3,
|
| 65 |
+
"min_instance_size": 6,
|
| 66 |
+
"foreground_closing_iterations": 1,
|
| 67 |
+
"seed_opening_iterations": 0
|
| 68 |
+
},
|
| 69 |
+
"calibrated_operating_point": {
|
| 70 |
+
"foreground_threshold": 0.3,
|
| 71 |
+
"seed_threshold": 0.5,
|
| 72 |
+
"boundary_threshold": 0.5,
|
| 73 |
+
"min_seed_size": 5,
|
| 74 |
+
"min_instance_size": 12,
|
| 75 |
+
"foreground_closing_iterations": 1,
|
| 76 |
+
"seed_opening_iterations": 0
|
| 77 |
+
},
|
| 78 |
+
"source_checkpoint_sha256": "f4de3018fee16e5a88e73b7d3d8593fed94c9d3aed168eed03f2da0a5cf1bdcf"
|
| 79 |
+
}
|
segresnet/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:517e84de76ddf2d64ec5b10c7e0f61eeaa1e3e8e519db8baa1523388d6f36156
|
| 3 |
+
size 18812444
|
swinunetr/real_only/config.json
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "swinunetr",
|
| 3 |
+
"implementation": "monai.networks.nets.SwinUNETR",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"feature_size": 24,
|
| 9 |
+
"use_checkpoint": true
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_only",
|
| 19 |
+
"condition_label": "Real only volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261"
|
| 27 |
+
],
|
| 28 |
+
"validation_volume": "real_263",
|
| 29 |
+
"selected_step": 14000,
|
| 30 |
+
"selection": "best validation panoptic quality on real_263",
|
| 31 |
+
"best_val_pq": 0.6681309527930587,
|
| 32 |
+
"parameter_count": 15703029,
|
| 33 |
+
"input_normalization": {
|
| 34 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 35 |
+
"lo": 302.0,
|
| 36 |
+
"hi": 1921.0
|
| 37 |
+
},
|
| 38 |
+
"voxel_spacing_km": 0.5,
|
| 39 |
+
"patch_size_dhw": [
|
| 40 |
+
32,
|
| 41 |
+
160,
|
| 42 |
+
160
|
| 43 |
+
],
|
| 44 |
+
"sliding_window": {
|
| 45 |
+
"roi_size": [
|
| 46 |
+
32,
|
| 47 |
+
160,
|
| 48 |
+
160
|
| 49 |
+
],
|
| 50 |
+
"overlap": 0.5,
|
| 51 |
+
"mode": "gaussian",
|
| 52 |
+
"blend": "logits, then sigmoid"
|
| 53 |
+
},
|
| 54 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 55 |
+
"global_operating_point": {
|
| 56 |
+
"foreground_threshold": 0.4,
|
| 57 |
+
"seed_threshold": 0.7,
|
| 58 |
+
"boundary_threshold": 0.5,
|
| 59 |
+
"min_seed_size": 3,
|
| 60 |
+
"min_instance_size": 6,
|
| 61 |
+
"foreground_closing_iterations": 1,
|
| 62 |
+
"seed_opening_iterations": 0
|
| 63 |
+
},
|
| 64 |
+
"calibrated_operating_point": {
|
| 65 |
+
"foreground_threshold": 0.4,
|
| 66 |
+
"seed_threshold": 0.5,
|
| 67 |
+
"boundary_threshold": 0.5,
|
| 68 |
+
"min_seed_size": 5,
|
| 69 |
+
"min_instance_size": 12,
|
| 70 |
+
"foreground_closing_iterations": 1,
|
| 71 |
+
"seed_opening_iterations": 0
|
| 72 |
+
},
|
| 73 |
+
"source_checkpoint_sha256": "eaa2ccf1e46ece704253a6ab1c525cd871d0e78cd1e7be6db6290aaef3cf0f8e"
|
| 74 |
+
}
|
swinunetr/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4cf25f32b1b29890ba8aff8114980b27e14962921a2d7c2ed876eba80fd9f547
|
| 3 |
+
size 70360660
|
swinunetr/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,79 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "swinunetr",
|
| 3 |
+
"implementation": "monai.networks.nets.SwinUNETR",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"feature_size": 24,
|
| 9 |
+
"use_checkpoint": true
|
| 10 |
+
},
|
| 11 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 12 |
+
"output_channels": [
|
| 13 |
+
"foreground",
|
| 14 |
+
"seeds",
|
| 15 |
+
"boundary"
|
| 16 |
+
],
|
| 17 |
+
"output_activation": "logits (apply sigmoid)",
|
| 18 |
+
"condition": "real_plus_synth",
|
| 19 |
+
"condition_label": "Real + synthetic volumes",
|
| 20 |
+
"seed": 42,
|
| 21 |
+
"train_volumes": [
|
| 22 |
+
"real_253",
|
| 23 |
+
"real_255",
|
| 24 |
+
"real_257",
|
| 25 |
+
"real_259",
|
| 26 |
+
"real_261",
|
| 27 |
+
"synthetic_901",
|
| 28 |
+
"synthetic_902",
|
| 29 |
+
"synthetic_903",
|
| 30 |
+
"synthetic_904",
|
| 31 |
+
"synthetic_908"
|
| 32 |
+
],
|
| 33 |
+
"validation_volume": "real_263",
|
| 34 |
+
"selected_step": 20000,
|
| 35 |
+
"selection": "best validation panoptic quality on real_263",
|
| 36 |
+
"best_val_pq": 0.6760594672330306,
|
| 37 |
+
"parameter_count": 15703029,
|
| 38 |
+
"input_normalization": {
|
| 39 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 40 |
+
"lo": 302.0,
|
| 41 |
+
"hi": 1921.0
|
| 42 |
+
},
|
| 43 |
+
"voxel_spacing_km": 0.5,
|
| 44 |
+
"patch_size_dhw": [
|
| 45 |
+
32,
|
| 46 |
+
160,
|
| 47 |
+
160
|
| 48 |
+
],
|
| 49 |
+
"sliding_window": {
|
| 50 |
+
"roi_size": [
|
| 51 |
+
32,
|
| 52 |
+
160,
|
| 53 |
+
160
|
| 54 |
+
],
|
| 55 |
+
"overlap": 0.5,
|
| 56 |
+
"mode": "gaussian",
|
| 57 |
+
"blend": "logits, then sigmoid"
|
| 58 |
+
},
|
| 59 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 60 |
+
"global_operating_point": {
|
| 61 |
+
"foreground_threshold": 0.4,
|
| 62 |
+
"seed_threshold": 0.7,
|
| 63 |
+
"boundary_threshold": 0.5,
|
| 64 |
+
"min_seed_size": 3,
|
| 65 |
+
"min_instance_size": 6,
|
| 66 |
+
"foreground_closing_iterations": 1,
|
| 67 |
+
"seed_opening_iterations": 0
|
| 68 |
+
},
|
| 69 |
+
"calibrated_operating_point": {
|
| 70 |
+
"foreground_threshold": 0.5,
|
| 71 |
+
"seed_threshold": 0.6,
|
| 72 |
+
"boundary_threshold": 0.5,
|
| 73 |
+
"min_seed_size": 5,
|
| 74 |
+
"min_instance_size": 6,
|
| 75 |
+
"foreground_closing_iterations": 1,
|
| 76 |
+
"seed_opening_iterations": 0
|
| 77 |
+
},
|
| 78 |
+
"source_checkpoint_sha256": "8466aad27350d65e2a044a3e93819ca04a238dce8f646691e8c9c03ab9c34688"
|
| 79 |
+
}
|
swinunetr/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:5a58bf8410aeea7ad3e6addbabb10b16eadcdd2c6ae0bfc9377bbc5330700efe
|
| 3 |
+
size 70360660
|
umamba/real_only/config.json
ADDED
|
@@ -0,0 +1,75 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "umamba",
|
| 3 |
+
"implementation": "custom (not released; uses mamba_ssm kernels)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4,
|
| 10 |
+
"d_state": 16
|
| 11 |
+
},
|
| 12 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 13 |
+
"output_channels": [
|
| 14 |
+
"foreground",
|
| 15 |
+
"seeds",
|
| 16 |
+
"boundary"
|
| 17 |
+
],
|
| 18 |
+
"output_activation": "logits (apply sigmoid)",
|
| 19 |
+
"condition": "real_only",
|
| 20 |
+
"condition_label": "Real only volumes",
|
| 21 |
+
"seed": 42,
|
| 22 |
+
"train_volumes": [
|
| 23 |
+
"real_253",
|
| 24 |
+
"real_255",
|
| 25 |
+
"real_257",
|
| 26 |
+
"real_259",
|
| 27 |
+
"real_261"
|
| 28 |
+
],
|
| 29 |
+
"validation_volume": "real_263",
|
| 30 |
+
"selected_step": 10000,
|
| 31 |
+
"selection": "best validation panoptic quality on real_263",
|
| 32 |
+
"best_val_pq": 0.6912856844280846,
|
| 33 |
+
"parameter_count": 6495331,
|
| 34 |
+
"input_normalization": {
|
| 35 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 36 |
+
"lo": 302.0,
|
| 37 |
+
"hi": 1921.0
|
| 38 |
+
},
|
| 39 |
+
"voxel_spacing_km": 0.5,
|
| 40 |
+
"patch_size_dhw": [
|
| 41 |
+
32,
|
| 42 |
+
160,
|
| 43 |
+
160
|
| 44 |
+
],
|
| 45 |
+
"sliding_window": {
|
| 46 |
+
"roi_size": [
|
| 47 |
+
32,
|
| 48 |
+
160,
|
| 49 |
+
160
|
| 50 |
+
],
|
| 51 |
+
"overlap": 0.5,
|
| 52 |
+
"mode": "gaussian",
|
| 53 |
+
"blend": "logits, then sigmoid"
|
| 54 |
+
},
|
| 55 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 56 |
+
"global_operating_point": {
|
| 57 |
+
"foreground_threshold": 0.4,
|
| 58 |
+
"seed_threshold": 0.7,
|
| 59 |
+
"boundary_threshold": 0.5,
|
| 60 |
+
"min_seed_size": 3,
|
| 61 |
+
"min_instance_size": 6,
|
| 62 |
+
"foreground_closing_iterations": 1,
|
| 63 |
+
"seed_opening_iterations": 0
|
| 64 |
+
},
|
| 65 |
+
"calibrated_operating_point": {
|
| 66 |
+
"foreground_threshold": 0.3,
|
| 67 |
+
"seed_threshold": 0.7,
|
| 68 |
+
"boundary_threshold": 0.5,
|
| 69 |
+
"min_seed_size": 5,
|
| 70 |
+
"min_instance_size": 12,
|
| 71 |
+
"foreground_closing_iterations": 1,
|
| 72 |
+
"seed_opening_iterations": 0
|
| 73 |
+
},
|
| 74 |
+
"source_checkpoint_sha256": "e254b1ee18ff6a7950c3780b915bb9bb3ebeda09e81eaa77a9b04a9eed229586"
|
| 75 |
+
}
|
umamba/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:625975ac59cdb8ca131eb09dbc90a29dd910da510d786eca5af166a0ab662ba3
|
| 3 |
+
size 25991716
|
umamba/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,80 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "umamba",
|
| 3 |
+
"implementation": "custom (not released; uses mamba_ssm kernels)",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"num_filter": 16,
|
| 9 |
+
"depth": 4,
|
| 10 |
+
"d_state": 16
|
| 11 |
+
},
|
| 12 |
+
"state_dict_note": "Custom architecture; definition not included in this repository.",
|
| 13 |
+
"output_channels": [
|
| 14 |
+
"foreground",
|
| 15 |
+
"seeds",
|
| 16 |
+
"boundary"
|
| 17 |
+
],
|
| 18 |
+
"output_activation": "logits (apply sigmoid)",
|
| 19 |
+
"condition": "real_plus_synth",
|
| 20 |
+
"condition_label": "Real + synthetic volumes",
|
| 21 |
+
"seed": 42,
|
| 22 |
+
"train_volumes": [
|
| 23 |
+
"real_253",
|
| 24 |
+
"real_255",
|
| 25 |
+
"real_257",
|
| 26 |
+
"real_259",
|
| 27 |
+
"real_261",
|
| 28 |
+
"synthetic_901",
|
| 29 |
+
"synthetic_902",
|
| 30 |
+
"synthetic_903",
|
| 31 |
+
"synthetic_904",
|
| 32 |
+
"synthetic_908"
|
| 33 |
+
],
|
| 34 |
+
"validation_volume": "real_263",
|
| 35 |
+
"selected_step": 7000,
|
| 36 |
+
"selection": "best validation panoptic quality on real_263",
|
| 37 |
+
"best_val_pq": 0.6836140569164155,
|
| 38 |
+
"parameter_count": 6495331,
|
| 39 |
+
"input_normalization": {
|
| 40 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 41 |
+
"lo": 302.0,
|
| 42 |
+
"hi": 1921.0
|
| 43 |
+
},
|
| 44 |
+
"voxel_spacing_km": 0.5,
|
| 45 |
+
"patch_size_dhw": [
|
| 46 |
+
32,
|
| 47 |
+
160,
|
| 48 |
+
160
|
| 49 |
+
],
|
| 50 |
+
"sliding_window": {
|
| 51 |
+
"roi_size": [
|
| 52 |
+
32,
|
| 53 |
+
160,
|
| 54 |
+
160
|
| 55 |
+
],
|
| 56 |
+
"overlap": 0.5,
|
| 57 |
+
"mode": "gaussian",
|
| 58 |
+
"blend": "logits, then sigmoid"
|
| 59 |
+
},
|
| 60 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 61 |
+
"global_operating_point": {
|
| 62 |
+
"foreground_threshold": 0.4,
|
| 63 |
+
"seed_threshold": 0.7,
|
| 64 |
+
"boundary_threshold": 0.5,
|
| 65 |
+
"min_seed_size": 3,
|
| 66 |
+
"min_instance_size": 6,
|
| 67 |
+
"foreground_closing_iterations": 1,
|
| 68 |
+
"seed_opening_iterations": 0
|
| 69 |
+
},
|
| 70 |
+
"calibrated_operating_point": {
|
| 71 |
+
"foreground_threshold": 0.5,
|
| 72 |
+
"seed_threshold": 0.7,
|
| 73 |
+
"boundary_threshold": 0.5,
|
| 74 |
+
"min_seed_size": 3,
|
| 75 |
+
"min_instance_size": 12,
|
| 76 |
+
"foreground_closing_iterations": 1,
|
| 77 |
+
"seed_opening_iterations": 0
|
| 78 |
+
},
|
| 79 |
+
"source_checkpoint_sha256": "c9aa6d87853e7cd20ab5a3354d82c8d2c2d463da3c26537fe3f587a7e923af5b"
|
| 80 |
+
}
|
umamba/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b38526f6266213c860cc31c12da1e8fa2d64d41da45c62515f7a42ca690b93be
|
| 3 |
+
size 25991716
|
unet/real_only/config.json
ADDED
|
@@ -0,0 +1,86 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "unet",
|
| 3 |
+
"implementation": "monai.networks.nets.UNet",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"channels": [
|
| 9 |
+
16,
|
| 10 |
+
32,
|
| 11 |
+
64,
|
| 12 |
+
128,
|
| 13 |
+
256
|
| 14 |
+
],
|
| 15 |
+
"strides": [
|
| 16 |
+
2,
|
| 17 |
+
2,
|
| 18 |
+
2,
|
| 19 |
+
2
|
| 20 |
+
],
|
| 21 |
+
"num_res_units": 2
|
| 22 |
+
},
|
| 23 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 24 |
+
"output_channels": [
|
| 25 |
+
"foreground",
|
| 26 |
+
"seeds",
|
| 27 |
+
"boundary"
|
| 28 |
+
],
|
| 29 |
+
"output_activation": "logits (apply sigmoid)",
|
| 30 |
+
"condition": "real_only",
|
| 31 |
+
"condition_label": "Real only volumes",
|
| 32 |
+
"seed": 42,
|
| 33 |
+
"train_volumes": [
|
| 34 |
+
"real_253",
|
| 35 |
+
"real_255",
|
| 36 |
+
"real_257",
|
| 37 |
+
"real_259",
|
| 38 |
+
"real_261"
|
| 39 |
+
],
|
| 40 |
+
"validation_volume": "real_263",
|
| 41 |
+
"selected_step": 27000,
|
| 42 |
+
"selection": "best validation panoptic quality on real_263",
|
| 43 |
+
"best_val_pq": 0.5787747756437983,
|
| 44 |
+
"parameter_count": 4807482,
|
| 45 |
+
"input_normalization": {
|
| 46 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 47 |
+
"lo": 302.0,
|
| 48 |
+
"hi": 1921.0
|
| 49 |
+
},
|
| 50 |
+
"voxel_spacing_km": 0.5,
|
| 51 |
+
"patch_size_dhw": [
|
| 52 |
+
32,
|
| 53 |
+
160,
|
| 54 |
+
160
|
| 55 |
+
],
|
| 56 |
+
"sliding_window": {
|
| 57 |
+
"roi_size": [
|
| 58 |
+
32,
|
| 59 |
+
160,
|
| 60 |
+
160
|
| 61 |
+
],
|
| 62 |
+
"overlap": 0.5,
|
| 63 |
+
"mode": "gaussian",
|
| 64 |
+
"blend": "logits, then sigmoid"
|
| 65 |
+
},
|
| 66 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 67 |
+
"global_operating_point": {
|
| 68 |
+
"foreground_threshold": 0.4,
|
| 69 |
+
"seed_threshold": 0.7,
|
| 70 |
+
"boundary_threshold": 0.5,
|
| 71 |
+
"min_seed_size": 3,
|
| 72 |
+
"min_instance_size": 6,
|
| 73 |
+
"foreground_closing_iterations": 1,
|
| 74 |
+
"seed_opening_iterations": 0
|
| 75 |
+
},
|
| 76 |
+
"calibrated_operating_point": {
|
| 77 |
+
"foreground_threshold": 0.5,
|
| 78 |
+
"seed_threshold": 0.8,
|
| 79 |
+
"boundary_threshold": 0.5,
|
| 80 |
+
"min_seed_size": 5,
|
| 81 |
+
"min_instance_size": 12,
|
| 82 |
+
"foreground_closing_iterations": 1,
|
| 83 |
+
"seed_opening_iterations": 0
|
| 84 |
+
},
|
| 85 |
+
"source_checkpoint_sha256": "cd54abfb4d08cc0450c955570e0f92eb2e0b7671a54a4c33915f45b43200ac13"
|
| 86 |
+
}
|
unet/real_only/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:bb223ae6dc779be27e73648c526e24b3e5ccd9c2397bf1d00d4affd8c1a61194
|
| 3 |
+
size 19237808
|
unet/real_plus_synth/config.json
ADDED
|
@@ -0,0 +1,91 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architecture": "unet",
|
| 3 |
+
"implementation": "monai.networks.nets.UNet",
|
| 4 |
+
"spatial_dims": 3,
|
| 5 |
+
"in_channels": 1,
|
| 6 |
+
"out_channels": 3,
|
| 7 |
+
"model_kwargs": {
|
| 8 |
+
"channels": [
|
| 9 |
+
16,
|
| 10 |
+
32,
|
| 11 |
+
64,
|
| 12 |
+
128,
|
| 13 |
+
256
|
| 14 |
+
],
|
| 15 |
+
"strides": [
|
| 16 |
+
2,
|
| 17 |
+
2,
|
| 18 |
+
2,
|
| 19 |
+
2
|
| 20 |
+
],
|
| 21 |
+
"num_res_units": 2
|
| 22 |
+
},
|
| 23 |
+
"state_dict_note": "MONAI networks were wrapped, so keys carry a 'network.' prefix; strip it to load into the bare MONAI class.",
|
| 24 |
+
"output_channels": [
|
| 25 |
+
"foreground",
|
| 26 |
+
"seeds",
|
| 27 |
+
"boundary"
|
| 28 |
+
],
|
| 29 |
+
"output_activation": "logits (apply sigmoid)",
|
| 30 |
+
"condition": "real_plus_synth",
|
| 31 |
+
"condition_label": "Real + synthetic volumes",
|
| 32 |
+
"seed": 42,
|
| 33 |
+
"train_volumes": [
|
| 34 |
+
"real_253",
|
| 35 |
+
"real_255",
|
| 36 |
+
"real_257",
|
| 37 |
+
"real_259",
|
| 38 |
+
"real_261",
|
| 39 |
+
"synthetic_901",
|
| 40 |
+
"synthetic_902",
|
| 41 |
+
"synthetic_903",
|
| 42 |
+
"synthetic_904",
|
| 43 |
+
"synthetic_908"
|
| 44 |
+
],
|
| 45 |
+
"validation_volume": "real_263",
|
| 46 |
+
"selected_step": 57000,
|
| 47 |
+
"selection": "best validation panoptic quality on real_263",
|
| 48 |
+
"best_val_pq": 0.6087093876585771,
|
| 49 |
+
"parameter_count": 4807482,
|
| 50 |
+
"input_normalization": {
|
| 51 |
+
"method": "x = clip((v - lo) / (hi - lo), 0, 1)",
|
| 52 |
+
"lo": 302.0,
|
| 53 |
+
"hi": 1921.0
|
| 54 |
+
},
|
| 55 |
+
"voxel_spacing_km": 0.5,
|
| 56 |
+
"patch_size_dhw": [
|
| 57 |
+
32,
|
| 58 |
+
160,
|
| 59 |
+
160
|
| 60 |
+
],
|
| 61 |
+
"sliding_window": {
|
| 62 |
+
"roi_size": [
|
| 63 |
+
32,
|
| 64 |
+
160,
|
| 65 |
+
160
|
| 66 |
+
],
|
| 67 |
+
"overlap": 0.5,
|
| 68 |
+
"mode": "gaussian",
|
| 69 |
+
"blend": "logits, then sigmoid"
|
| 70 |
+
},
|
| 71 |
+
"postprocessing": "foreground/seed thresholding + marker-controlled watershed",
|
| 72 |
+
"global_operating_point": {
|
| 73 |
+
"foreground_threshold": 0.4,
|
| 74 |
+
"seed_threshold": 0.7,
|
| 75 |
+
"boundary_threshold": 0.5,
|
| 76 |
+
"min_seed_size": 3,
|
| 77 |
+
"min_instance_size": 6,
|
| 78 |
+
"foreground_closing_iterations": 1,
|
| 79 |
+
"seed_opening_iterations": 0
|
| 80 |
+
},
|
| 81 |
+
"calibrated_operating_point": {
|
| 82 |
+
"foreground_threshold": 0.5,
|
| 83 |
+
"seed_threshold": 0.7,
|
| 84 |
+
"boundary_threshold": 0.5,
|
| 85 |
+
"min_seed_size": 5,
|
| 86 |
+
"min_instance_size": 12,
|
| 87 |
+
"foreground_closing_iterations": 1,
|
| 88 |
+
"seed_opening_iterations": 0
|
| 89 |
+
},
|
| 90 |
+
"source_checkpoint_sha256": "1f1bd91d9c40f7f90673980c170b7d4fd41ae9aadccb4ae001e95245ff86204a"
|
| 91 |
+
}
|
unet/real_plus_synth/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:94f6754e3356d728127247746f51c222699379268149ea9c20c202e884205e39
|
| 3 |
+
size 19237808
|