Upload HF_README.md

HF_README.md

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+---
+license: mit
+tags:
+  - object-detection
+  - yolo
+  - biology
+  - computer-vision
+  - c-elegans
+  - worm-counting
+base_model: ultralytics/assets
+---
+
+# WormML — YOLOv11 Worm Counting Weights
+
+Pretrained YOLOv11-Large checkpoints for counting *C. elegans* worms across four imaging systems. Each model was trained on images from a specific camera and should be used with its matching preprocessing pipeline.
+
+## Models
+
+| File | Camera | Preprocessing |
+|------|--------|---------------|
+| `og_best.pt`  | OG (original lab microscope) | Hough circle crop → resize 1344×1344 |
+| `tau_best.pt` | Tau imaging system | Histogram equalisation + circle crop |
+| `lb_best.pt`  | LoopBio automated platform | Circle crop + colour inversion + augmentation |
+| `uva_best.pt` | UVA external dataset | No preprocessing |
+
+## Usage
+
+Download all weights with one command using the [WormML repository](https://github.com/tommyli88/wormml):
+
+```bash
+git clone https://github.com/tommyli88/wormml.git
+cd wormml
+pip install -r requirements.txt
+python scripts/download_weights.py
+```
+
+Or download a single camera:
+
+```bash
+python scripts/download_weights.py --camera og
+```
+
+Run inference on a preprocessed image:
+
+```python
+from ultralytics import YOLO
+
+model = YOLO("weights/og_best.pt")
+results = model("plate_image.jpg", conf=0.35, iou=0.30)
+print(f"Worm count: {len(results[0].boxes)}")
+```
+
+## Recommended Thresholds
+
+These confidence and IoU thresholds were tuned on each camera's validation set to minimise mean absolute error:
+
+| Camera | Confidence | IoU  |
+|--------|-----------|------|
+| OG     | 0.35      | 0.30 |
+| Tau    | 0.36      | 0.25 |
+| LB     | 0.265     | 0.30 |
+| UVA    | 0.32      | 0.30 |
+
+## Training
+
+All models use YOLOv11-Large (`yolo11l.pt`) trained for 100 epochs. Camera-specific hyperparameters (warmup epochs, box loss weight, learning rate, augmentation) are documented in the [configs](https://github.com/tommyli88/wormml/tree/main/configs) folder of the main repository.
+
+## Citation
+
+```bibtex
+@misc{wormml2024,
+  title  = {WormML: A Cross-Camera Pipeline for C. elegans Worm Counting},
+  year   = {2024},
+  note   = {\url{https://github.com/tommyli88/wormml}}
+}
+```