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package/bin/skills/segment-anything/SKILL.md

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+---
+name: segment-anything-model
+description: Foundation model for image segmentation with zero-shot transfer. Use when you need to segment any object in images using points, boxes, or masks as prompts, or automatically generate all object masks in an image.
+version: 1.0.0
+author: Synthetic Sciences
+license: MIT
+tags: [Multimodal, Image Segmentation, Computer Vision, SAM, Zero-Shot]
+dependencies: [segment-anything, transformers>=4.30.0, torch>=1.7.0]
+---
+
+# Segment Anything Model (SAM)
+
+Comprehensive guide to using Meta AI's Segment Anything Model for zero-shot image segmentation.
+
+## When to use SAM
+
+**Use SAM when:**
+- Need to segment any object in images without task-specific training
+- Building interactive annotation tools with point/box prompts
+- Generating training data for other vision models
+- Need zero-shot transfer to new image domains
+- Building object detection/segmentation pipelines
+- Processing medical, satellite, or domain-specific images
+
+**Key features:**
+- **Zero-shot segmentation**: Works on any image domain without fine-tuning
+- **Flexible prompts**: Points, bounding boxes, or previous masks
+- **Automatic segmentation**: Generate all object masks automatically
+- **High quality**: Trained on 1.1 billion masks from 11 million images
+- **Multiple model sizes**: ViT-B (fastest), ViT-L, ViT-H (most accurate)
+- **ONNX export**: Deploy in browsers and edge devices
+
+**Use alternatives instead:**
+- **YOLO/Detectron2**: For real-time object detection with classes
+- **Mask2Former**: For semantic/panoptic segmentation with categories
+- **GroundingDINO + SAM**: For text-prompted segmentation
+- **SAM 2**: For video segmentation tasks
+
+## Quick start
+
+### Installation
+
+```bash
+# From GitHub
+pip install git+https://github.com/facebookresearch/segment-anything.git
+
+# Optional dependencies
+pip install opencv-python pycocotools matplotlib
+
+# Or use HuggingFace transformers
+pip install transformers
+```
+
+### Download checkpoints
+
+```bash
+# ViT-H (largest, most accurate) - 2.4GB
+wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth
+
+# ViT-L (medium) - 1.2GB
+wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_l_0b3195.pth
+
+# ViT-B (smallest, fastest) - 375MB
+wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth
+```
+
+### Basic usage with SamPredictor
+
+```python
+import numpy as np
+from segment_anything import sam_model_registry, SamPredictor
+
+# Load model
+sam = sam_model_registry["vit_h"](checkpoint="sam_vit_h_4b8939.pth")
+sam.to(device="cuda")
+
+# Create predictor
+predictor = SamPredictor(sam)
+
+# Set image (computes embeddings once)
+image = cv2.imread("image.jpg")
+image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
+predictor.set_image(image)
+
+# Predict with point prompts
+input_point = np.array([[500, 375]])  # (x, y) coordinates
+input_label = np.array([1])  # 1 = foreground, 0 = background
+
+masks, scores, logits = predictor.predict(
+    point_coords=input_point,
+    point_labels=input_label,
+    multimask_output=True  # Returns 3 mask options
+)
+
+# Select best mask
+best_mask = masks[np.argmax(scores)]
+```
+
+### HuggingFace Transformers
+
+```python
+import torch
+from PIL import Image
+from transformers import SamModel, SamProcessor
+
+# Load model and processor
+model = SamModel.from_pretrained("facebook/sam-vit-huge")
+processor = SamProcessor.from_pretrained("facebook/sam-vit-huge")
+model.to("cuda")
+
+# Process image with point prompt
+image = Image.open("image.jpg")
+input_points = [[[450, 600]]]  # Batch of points
+
+inputs = processor(image, input_points=input_points, return_tensors="pt")
+inputs = {k: v.to("cuda") for k, v in inputs.items()}
+
+# Generate masks
+with torch.no_grad():
+    outputs = model(**inputs)
+
+# Post-process masks to original size
+masks = processor.image_processor.post_process_masks(
+    outputs.pred_masks.cpu(),
+    inputs["original_sizes"].cpu(),
+    inputs["reshaped_input_sizes"].cpu()
+)
+```
+
+## Core concepts
+
+### Model architecture
+
+```
+SAM Architecture:
+┌─────────────────┐     ┌─────────────────┐     ┌─────────────────┐
+│  Image Encoder  │────▶│ Prompt Encoder  │────▶│  Mask Decoder   │
+│     (ViT)       │     │ (Points/Boxes)  │     │ (Transformer)   │
+└─────────────────┘     └─────────────────┘     └─────────────────┘
+        │                       │                       │
+   Image Embeddings      Prompt Embeddings         Masks + IoU
+   (computed once)       (per prompt)             predictions
+```
+
+### Model variants
+
+| Model | Checkpoint | Size | Speed | Accuracy |
+|-------|------------|------|-------|----------|
+| ViT-H | `vit_h` | 2.4 GB | Slowest | Best |
+| ViT-L | `vit_l` | 1.2 GB | Medium | Good |
+| ViT-B | `vit_b` | 375 MB | Fastest | Good |
+
+### Prompt types
+
+| Prompt | Description | Use Case |
+|--------|-------------|----------|
+| Point (foreground) | Click on object | Single object selection |
+| Point (background) | Click outside object | Exclude regions |
+| Bounding box | Rectangle around object | Larger objects |
+| Previous mask | Low-res mask input | Iterative refinement |
+
+## Interactive segmentation
+
+### Point prompts
+
+```python
+# Single foreground point
+input_point = np.array([[500, 375]])
+input_label = np.array([1])
+
+masks, scores, logits = predictor.predict(
+    point_coords=input_point,
+    point_labels=input_label,
+    multimask_output=True
+)
+
+# Multiple points (foreground + background)
+input_points = np.array([[500, 375], [600, 400], [450, 300]])
+input_labels = np.array([1, 1, 0])  # 2 foreground, 1 background
+
+masks, scores, logits = predictor.predict(
+    point_coords=input_points,
+    point_labels=input_labels,
+    multimask_output=False  # Single mask when prompts are clear
+)
+```
+
+### Box prompts
+
+```python
+# Bounding box [x1, y1, x2, y2]
+input_box = np.array([425, 600, 700, 875])
+
+masks, scores, logits = predictor.predict(
+    box=input_box,
+    multimask_output=False
+)
+```
+
+### Combined prompts
+
+```python
+# Box + points for precise control
+masks, scores, logits = predictor.predict(
+    point_coords=np.array([[500, 375]]),
+    point_labels=np.array([1]),
+    box=np.array([400, 300, 700, 600]),
+    multimask_output=False
+)
+```
+
+### Iterative refinement
+
+```python
+# Initial prediction
+masks, scores, logits = predictor.predict(
+    point_coords=np.array([[500, 375]]),
+    point_labels=np.array([1]),
+    multimask_output=True
+)
+
+# Refine with additional point using previous mask
+masks, scores, logits = predictor.predict(
+    point_coords=np.array([[500, 375], [550, 400]]),
+    point_labels=np.array([1, 0]),  # Add background point
+    mask_input=logits[np.argmax(scores)][None, :, :],  # Use best mask
+    multimask_output=False
+)
+```
+
+## Automatic mask generation
+
+### Basic automatic segmentation
+
+```python
+from segment_anything import SamAutomaticMaskGenerator
+
+# Create generator
+mask_generator = SamAutomaticMaskGenerator(sam)
+
+# Generate all masks
+masks = mask_generator.generate(image)
+
+# Each mask contains:
+# - segmentation: binary mask
+# - bbox: [x, y, w, h]
+# - area: pixel count
+# - predicted_iou: quality score
+# - stability_score: robustness score
+# - point_coords: generating point
+```
+
+### Customized generation
+
+```python
+mask_generator = SamAutomaticMaskGenerator(
+    model=sam,
+    points_per_side=32,          # Grid density (more = more masks)
+    pred_iou_thresh=0.88,        # Quality threshold
+    stability_score_thresh=0.95,  # Stability threshold
+    crop_n_layers=1,             # Multi-scale crops
+    crop_n_points_downscale_factor=2,
+    min_mask_region_area=100,    # Remove tiny masks
+)
+
+masks = mask_generator.generate(image)
+```
+
+### Filtering masks
+
+```python
+# Sort by area (largest first)
+masks = sorted(masks, key=lambda x: x['area'], reverse=True)
+
+# Filter by predicted IoU
+high_quality = [m for m in masks if m['predicted_iou'] > 0.9]
+
+# Filter by stability score
+stable_masks = [m for m in masks if m['stability_score'] > 0.95]
+```
+
+## Batched inference
+
+### Multiple images
+
+```python
+# Process multiple images efficiently
+images = [cv2.imread(f"image_{i}.jpg") for i in range(10)]
+
+all_masks = []
+for image in images:
+    predictor.set_image(image)
+    masks, _, _ = predictor.predict(
+        point_coords=np.array([[500, 375]]),
+        point_labels=np.array([1]),
+        multimask_output=True
+    )
+    all_masks.append(masks)
+```
+
+### Multiple prompts per image
+
+```python
+# Process multiple prompts efficiently (one image encoding)
+predictor.set_image(image)
+
+# Batch of point prompts
+points = [
+    np.array([[100, 100]]),
+    np.array([[200, 200]]),
+    np.array([[300, 300]])
+]
+
+all_masks = []
+for point in points:
+    masks, scores, _ = predictor.predict(
+        point_coords=point,
+        point_labels=np.array([1]),
+        multimask_output=True
+    )
+    all_masks.append(masks[np.argmax(scores)])
+```
+
+## ONNX deployment
+
+### Export model
+
+```bash
+python scripts/export_onnx_model.py \
+    --checkpoint sam_vit_h_4b8939.pth \
+    --model-type vit_h \
+    --output sam_onnx.onnx \
+    --return-single-mask
+```
+
+### Use ONNX model
+
+```python
+import onnxruntime
+
+# Load ONNX model
+ort_session = onnxruntime.InferenceSession("sam_onnx.onnx")
+
+# Run inference (image embeddings computed separately)
+masks = ort_session.run(
+    None,
+    {
+        "image_embeddings": image_embeddings,
+        "point_coords": point_coords,
+        "point_labels": point_labels,
+        "mask_input": np.zeros((1, 1, 256, 256), dtype=np.float32),
+        "has_mask_input": np.array([0], dtype=np.float32),
+        "orig_im_size": np.array([h, w], dtype=np.float32)
+    }
+)
+```
+
+## Common workflows
+
+### Workflow 1: Annotation tool
+
+```python
+import cv2
+
+# Load model
+predictor = SamPredictor(sam)
+predictor.set_image(image)
+
+def on_click(event, x, y, flags, param):
+    if event == cv2.EVENT_LBUTTONDOWN:
+        # Foreground point
+        masks, scores, _ = predictor.predict(
+            point_coords=np.array([[x, y]]),
+            point_labels=np.array([1]),
+            multimask_output=True
+        )
+        # Display best mask
+        display_mask(masks[np.argmax(scores)])
+```
+
+### Workflow 2: Object extraction
+
+```python
+def extract_object(image, point):
+    """Extract object at point with transparent background."""
+    predictor.set_image(image)
+
+    masks, scores, _ = predictor.predict(
+        point_coords=np.array([point]),
+        point_labels=np.array([1]),
+        multimask_output=True
+    )
+
+    best_mask = masks[np.argmax(scores)]
+
+    # Create RGBA output
+    rgba = np.zeros((image.shape[0], image.shape[1], 4), dtype=np.uint8)
+    rgba[:, :, :3] = image
+    rgba[:, :, 3] = best_mask * 255
+
+    return rgba
+```
+
+### Workflow 3: Medical image segmentation
+
+```python
+# Process medical images (grayscale to RGB)
+medical_image = cv2.imread("scan.png", cv2.IMREAD_GRAYSCALE)
+rgb_image = cv2.cvtColor(medical_image, cv2.COLOR_GRAY2RGB)
+
+predictor.set_image(rgb_image)
+
+# Segment region of interest
+masks, scores, _ = predictor.predict(
+    box=np.array([x1, y1, x2, y2]),  # ROI bounding box
+    multimask_output=True
+)
+```
+
+## Output format
+
+### Mask data structure
+
+```python
+# SamAutomaticMaskGenerator output
+{
+    "segmentation": np.ndarray,  # H×W binary mask
+    "bbox": [x, y, w, h],        # Bounding box
+    "area": int,                 # Pixel count
+    "predicted_iou": float,      # 0-1 quality score
+    "stability_score": float,    # 0-1 robustness score
+    "crop_box": [x, y, w, h],    # Generation crop region
+    "point_coords": [[x, y]],    # Input point
+}
+```
+
+### COCO RLE format
+
+```python
+from pycocotools import mask as mask_utils
+
+# Encode mask to RLE
+rle = mask_utils.encode(np.asfortranarray(mask.astype(np.uint8)))
+rle["counts"] = rle["counts"].decode("utf-8")
+
+# Decode RLE to mask
+decoded_mask = mask_utils.decode(rle)
+```
+
+## Performance optimization
+
+### GPU memory
+
+```python
+# Use smaller model for limited VRAM
+sam = sam_model_registry["vit_b"](checkpoint="sam_vit_b_01ec64.pth")
+
+# Process images in batches
+# Clear CUDA cache between large batches
+torch.cuda.empty_cache()
+```
+
+### Speed optimization
+
+```python
+# Use half precision
+sam = sam.half()
+
+# Reduce points for automatic generation
+mask_generator = SamAutomaticMaskGenerator(
+    model=sam,
+    points_per_side=16,  # Default is 32
+)
+
+# Use ONNX for deployment
+# Export with --return-single-mask for faster inference
+```
+
+## Common issues
+
+| Issue | Solution |
+|-------|----------|
+| Out of memory | Use ViT-B model, reduce image size |
+| Slow inference | Use ViT-B, reduce points_per_side |
+| Poor mask quality | Try different prompts, use box + points |
+| Edge artifacts | Use stability_score filtering |
+| Small objects missed | Increase points_per_side |
+
+## References
+
+- **[Advanced Usage](references/advanced-usage.md)** - Batching, fine-tuning, integration
+- **[Troubleshooting](references/troubleshooting.md)** - Common issues and solutions
+
+## Resources
+
+- **GitHub**: https://github.com/facebookresearch/segment-anything
+- **Paper**: https://arxiv.org/abs/2304.02643
+- **Demo**: https://segment-anything.com
+- **SAM 2 (Video)**: https://github.com/facebookresearch/segment-anything-2
+- **HuggingFace**: https://huggingface.co/facebook/sam-vit-huge