Segment Anything Model — SAM: zero-shot image segmentation via points, boxes, masks

Segment Anything Model

SAM: zero-shot image segmentation via points, boxes, masks.

Skill metadata

Source	Bundled (installed by default)
Path	skills/mlops/models/segment-anything
Version	1.0.0
Author	Orchestra Research
License	MIT
Dependencies	segment-anything, transformers>=4.30.0, torch>=1.7.0
Tags	Multimodal, Image Segmentation, Computer Vision, SAM, Zero-Shot

Reference: full SKILL.md

The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.

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

# 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

# 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

import numpy as np
from segment_anything import sam_model_registry, SamPredictor

# Load model
sam = sam_model_registry["vit_h"](https://github.com/NousResearch/hermes-agent/blob/main/skills/mlops/models/segment-anything/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

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

# 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

# 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

# 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

# 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

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

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

# 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

# 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

# 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

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

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

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

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

# 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

# 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

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

# Use smaller model for limited VRAM
sam = sam_model_registry["vit_b"](https://github.com/NousResearch/hermes-agent/blob/main/skills/mlops/models/segment-anything/checkpoint="sam_vit_b_01ec64.pth")

# Process images in batches
# Clear CUDA cache between large batches
torch.cuda.empty_cache()

Speed optimization

# 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 - Batching, fine-tuning, integration
• Troubleshooting - 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