README.md

---
license: mit
tags:
  - image-segmentation
  - multilabel
  - unet
  - pytorch
  - medical-imaging
library_name: transformers
pipeline_tag: image-segmentation
---

# LN_segmentation_sweep

A unet model for multilabel image segmentation trained with sliding window approach.

## Model Description

- **Architecture:** unet
- **Input Channels:** 3
- **Output Classes:** 4
- **Base Filters:** 128
- **Window Size:** 128
- **Downsample Factor:** 1.0

### Model-Specific Parameters


## Training Configuration

| Parameter | Value |
|-----------|-------|
| Batch Size | 8 |
| Learning Rate | 7.77451918775676e-06 |
| Weight Decay | 0.00164040349077736 |
| Epochs | 100 |
| Patience | 10 |
| Dataset | GleghornLab/Semi-Automated_LN_Segmentation_10_11_2025 |

## Test Performance Metrics

| Metric | Mean | Class 0 | Class 1 | Class 2 | Class 3 |
|--------|------|--------|--------|--------|--------|
| Dice | 0.7781 | 0.7197 | 0.7614 | 0.7271 | 0.9040 |
| IoU | 0.6524 | 0.5708 | 0.6199 | 0.5929 | 0.8261 |
| F1 | 0.7781 | 0.7197 | 0.7614 | 0.7271 | 0.9040 |
| MCC | 0.7832 | 0.7308 | 0.7730 | 0.7440 | 0.8850 |
| ROC AUC | 0.9945 | 0.9945 | 0.9975 | 0.9917 | 0.9943 |
| PR AUC | 0.9076 | 0.8357 | 0.9108 | 0.9095 | 0.9743 |


## Usage

```python
import numpy as np
from model import MODEL_REGISTRY, SegmentationConfig

# Load model
config = SegmentationConfig.from_pretrained("aholk/LN_segmentation_sweep")
model = MODEL_REGISTRY["unet"].from_pretrained("aholk/LN_segmentation_sweep")
model.eval()

# Run inference on a full image with sliding window
image = np.random.rand(2048, 2048, 3).astype(np.float32)  # Your image here
probs = model.predict_full_image(
    image,
    dim=128,
    batch_size=16,
    device="cuda"  # or "cpu"
)
# probs shape: (num_classes, H, W) with values in [0, 1]

# Threshold to get binary masks
masks = (probs > 0.5).astype(np.uint8)
```


## Citation

If you use this model, please cite:

```bibtex
@software{windowz_segmentation,
  title={Multilabel Image Segmentation with Sliding Window U-Net},
  author={Gleghorn Lab},
  year={2025},
  url={https://github.com/GleghornLab/ComputerVision2}
}
```