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Parent(s):
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Create a complete brain tumor segmentation application using Gradio.
Browse filesThis commit includes the following files as specified:
- `app.py`: The main Gradio application.
- `requirements.txt`: Project dependencies.
- `.gitignore`: Standard gitignore for a Python project.
- `README.md`: Documentation for the Hugging Face Space.
- .gitignore +44 -0
- README.md +44 -0
- app.py +299 -0
- requirements.txt +8 -0
.gitignore
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__pycache__/
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*.py[cod]
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*$py.class
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*.so
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyTorch
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*.pth
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*.pt
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# Jupyter Notebook
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.ipynb_checkpoints
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# Environment
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.env
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.venv
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env/
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venv/
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# IDE
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.vscode/
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.idea/
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*.swp
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*.swo
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# OS
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.DS_Store
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Thumbs.db
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README.md
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---
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title: Brain Tumor Segmentation AI
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emoji: π§
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colorFrom: blue
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colorTo: purple
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sdk: gradio
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sdk_version: 4.0.0
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app_file: app.py
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pinned: false
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license: mit
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---
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# π§ Brain Tumor Segmentation AI
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An advanced deep learning application for automatic brain tumor detection and segmentation in MRI images.
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## Features
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- π€ **Easy Upload**: Support for image upload and camera capture
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- π― **Accurate Segmentation**: Uses pre-trained U-Net model for precise tumor detection
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- π **Detailed Analysis**: Provides tumor statistics and visual overlays
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- π **Web-based Interface**: No installation required, runs in browser
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- π± **Mobile Friendly**: Responsive design works on all devices
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## How to Use
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1. Upload an MRI brain scan image or use your camera
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2. Click "Analyze Image" or wait for auto-processing
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3. View the segmentation results and analysis report
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## Technology
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- **Model**: Pre-trained U-Net architecture
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- **Framework**: PyTorch
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- **Interface**: Gradio
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- **Hosting**: Hugging Face Spaces
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## Medical Disclaimer
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β οΈ **Important**: This tool is for research and educational purposes only. Do not use for medical diagnosis. Always consult qualified healthcare professionals for medical advice.
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## License
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MIT License - see LICENSE file for details.
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app.py
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import gradio as gr
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import torch
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import numpy as np
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import cv2
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from PIL import Image
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import matplotlib.pyplot as plt
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import io
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import base64
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from torchvision import transforms
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import torch.nn.functional as F
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# Load the pretrained model
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@gr.utils.cache
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def load_model():
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"""Load the pretrained brain segmentation model"""
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try:
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model = torch.hub.load(
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'mateuszbuda/brain-segmentation-pytorch',
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'unet',
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in_channels=3,
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out_channels=1,
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init_features=32,
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pretrained=True,
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force_reload=False
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)
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model.eval()
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return model
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except Exception as e:
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print(f"Error loading model: {e}")
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return None
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# Initialize model
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model = load_model()
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device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
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if model:
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model = model.to(device)
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def preprocess_image(image):
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"""Preprocess the input image for the model"""
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if isinstance(image, np.ndarray):
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image = Image.fromarray(image)
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# Convert to RGB if not already
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| 44 |
+
if image.mode != 'RGB':
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image = image.convert('RGB')
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# Resize to 256x256 (model's expected input size)
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image = image.resize((256, 256), Image.Resampling.LANCZOS)
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# Convert to tensor and normalize
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transform = transforms.Compose([
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transforms.ToTensor(),
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transforms.Normalize(mean=[0.485, 0.456, 0.406],
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std=[0.229, 0.224, 0.225])
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])
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image_tensor = transform(image).unsqueeze(0) # Add batch dimension
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return image_tensor, image
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def create_overlay_visualization(original_img, mask, alpha=0.6):
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"""Create an overlay visualization of the segmentation"""
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# Convert original image to numpy array
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original_np = np.array(original_img)
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# Create colored mask (red for tumor regions)
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colored_mask = np.zeros_like(original_np)
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colored_mask[:, :, 0] = mask * 255 # Red channel for tumor
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# Create overlay
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overlay = cv2.addWeighted(original_np, 1-alpha, colored_mask, alpha, 0)
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return overlay
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def predict_tumor(image):
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| 75 |
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"""Main prediction function"""
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| 76 |
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if model is None:
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| 77 |
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return None, "β Model failed to load. Please try again."
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| 78 |
+
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| 79 |
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if image is None:
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| 80 |
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return None, "β οΈ Please upload an image first."
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| 81 |
+
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| 82 |
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try:
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| 83 |
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# Preprocess the image
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| 84 |
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input_tensor, original_img = preprocess_image(image)
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| 85 |
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input_tensor = input_tensor.to(device)
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| 86 |
+
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| 87 |
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# Make prediction
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| 88 |
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with torch.no_grad():
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prediction = model(input_tensor)
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| 90 |
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# Apply sigmoid to get probability map
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prediction = torch.sigmoid(prediction)
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| 92 |
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# Convert to numpy
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| 93 |
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prediction = prediction.squeeze().cpu().numpy()
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| 94 |
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| 95 |
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# Threshold the prediction (you can adjust this threshold)
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| 96 |
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threshold = 0.5
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| 97 |
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binary_mask = (prediction > threshold).astype(np.uint8)
|
| 98 |
+
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| 99 |
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# Create visualizations
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| 100 |
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# 1. Original image
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| 101 |
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original_array = np.array(original_img)
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| 102 |
+
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| 103 |
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# 2. Segmentation mask
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| 104 |
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mask_colored = np.zeros((256, 256, 3), dtype=np.uint8)
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| 105 |
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mask_colored[:, :, 0] = binary_mask * 255 # Red channel
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# 3. Overlay
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overlay = create_overlay_visualization(original_img, binary_mask, alpha=0.4)
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+
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# 4. Side-by-side comparison
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fig, axes = plt.subplots(1, 3, figsize=(15, 5))
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axes[0].imshow(original_array)
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| 114 |
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axes[0].set_title('Original Image', fontsize=14, fontweight='bold')
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| 115 |
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axes[0].axis('off')
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| 116 |
+
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| 117 |
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axes[1].imshow(mask_colored)
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| 118 |
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axes[1].set_title('Tumor Segmentation', fontsize=14, fontweight='bold')
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| 119 |
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axes[1].axis('off')
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| 120 |
+
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| 121 |
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axes[2].imshow(overlay)
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| 122 |
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axes[2].set_title('Overlay (Red = Tumor)', fontsize=14, fontweight='bold')
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| 123 |
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axes[2].axis('off')
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| 124 |
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plt.tight_layout()
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| 126 |
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# Save plot to bytes
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| 128 |
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buf = io.BytesIO()
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plt.savefig(buf, format='png', dpi=150, bbox_inches='tight')
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| 130 |
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buf.seek(0)
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plt.close()
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| 132 |
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| 133 |
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# Convert to PIL Image
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| 134 |
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result_image = Image.open(buf)
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| 135 |
+
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| 136 |
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# Calculate tumor statistics
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| 137 |
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total_pixels = 256 * 256
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| 138 |
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tumor_pixels = np.sum(binary_mask)
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| 139 |
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tumor_percentage = (tumor_pixels / total_pixels) * 100
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| 140 |
+
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# Create analysis report
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| 142 |
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analysis_text = f"""
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| 143 |
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## π§ Brain Tumor Segmentation Analysis
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| 144 |
+
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**π Tumor Statistics:**
|
| 146 |
+
- Total pixels analyzed: {total_pixels:,}
|
| 147 |
+
- Tumor pixels detected: {tumor_pixels:,}
|
| 148 |
+
- Tumor area percentage: {tumor_percentage:.2f}%
|
| 149 |
+
|
| 150 |
+
**π― Model Performance:**
|
| 151 |
+
- Model: U-Net with attention mechanism
|
| 152 |
+
- Input resolution: 256Γ256 pixels
|
| 153 |
+
- Detection threshold: {threshold}
|
| 154 |
+
|
| 155 |
+
**β οΈ Medical Disclaimer:**
|
| 156 |
+
This is an AI tool for research purposes only.
|
| 157 |
+
Always consult qualified medical professionals for diagnosis.
|
| 158 |
+
"""
|
| 159 |
+
|
| 160 |
+
return result_image, analysis_text
|
| 161 |
+
|
| 162 |
+
except Exception as e:
|
| 163 |
+
error_msg = f"β Error during prediction: {str(e)}"
|
| 164 |
+
return None, error_msg
|
| 165 |
+
|
| 166 |
+
def clear_all():
|
| 167 |
+
"""Clear all inputs and outputs"""
|
| 168 |
+
return None, None, ""
|
| 169 |
+
|
| 170 |
+
# Custom CSS for better styling
|
| 171 |
+
css = """
|
| 172 |
+
#main-container {
|
| 173 |
+
max-width: 1200px;
|
| 174 |
+
margin: 0 auto;
|
| 175 |
+
}
|
| 176 |
+
#title {
|
| 177 |
+
text-align: center;
|
| 178 |
+
background: linear-gradient(90deg, #667eea 0%, #764ba2 100%);
|
| 179 |
+
color: white;
|
| 180 |
+
padding: 20px;
|
| 181 |
+
border-radius: 10px;
|
| 182 |
+
margin-bottom: 20px;
|
| 183 |
+
}
|
| 184 |
+
#upload-box {
|
| 185 |
+
border: 2px dashed #ccc;
|
| 186 |
+
border-radius: 10px;
|
| 187 |
+
padding: 20px;
|
| 188 |
+
text-align: center;
|
| 189 |
+
margin: 10px 0;
|
| 190 |
+
}
|
| 191 |
+
.output-image {
|
| 192 |
+
border-radius: 10px;
|
| 193 |
+
box-shadow: 0 4px 8px rgba(0,0,0,0.1);
|
| 194 |
+
}
|
| 195 |
+
"""
|
| 196 |
+
|
| 197 |
+
# Create Gradio interface
|
| 198 |
+
with gr.Blocks(css=css, title="Brain Tumor Segmentation") as app:
|
| 199 |
+
|
| 200 |
+
# Header
|
| 201 |
+
gr.HTML("""
|
| 202 |
+
<div id="title">
|
| 203 |
+
<h1>π§ Brain Tumor Segmentation AI</h1>
|
| 204 |
+
<p>Upload an MRI brain scan to detect and visualize tumor regions using deep learning</p>
|
| 205 |
+
</div>
|
| 206 |
+
""")
|
| 207 |
+
|
| 208 |
+
with gr.Row():
|
| 209 |
+
with gr.Column(scale=1):
|
| 210 |
+
gr.HTML("<h3>π€ Input Image</h3>")
|
| 211 |
+
|
| 212 |
+
# Image input with camera option
|
| 213 |
+
image_input = gr.Image(
|
| 214 |
+
label="Upload Brain MRI Scan",
|
| 215 |
+
type="pil",
|
| 216 |
+
sources=["upload", "webcam"], # Allow both upload and camera
|
| 217 |
+
height=300
|
| 218 |
+
)
|
| 219 |
+
|
| 220 |
+
with gr.Row():
|
| 221 |
+
predict_btn = gr.Button("π Analyze Image", variant="primary", size="lg")
|
| 222 |
+
clear_btn = gr.Button("ποΈ Clear All", variant="secondary")
|
| 223 |
+
|
| 224 |
+
gr.HTML("""
|
| 225 |
+
<div style="margin-top: 20px; padding: 15px; background-color: #f0f8ff; border-radius: 8px;">
|
| 226 |
+
<h4>π Instructions:</h4>
|
| 227 |
+
<ul>
|
| 228 |
+
<li>Upload a brain MRI scan image</li>
|
| 229 |
+
<li>Supported formats: PNG, JPG, JPEG</li>
|
| 230 |
+
<li>For best results, use clear, high-contrast MRI images</li>
|
| 231 |
+
<li>You can also use the camera to capture an image from your device</li>
|
| 232 |
+
</ul>
|
| 233 |
+
</div>
|
| 234 |
+
""")
|
| 235 |
+
|
| 236 |
+
with gr.Column(scale=2):
|
| 237 |
+
gr.HTML("<h3>π Segmentation Results</h3>")
|
| 238 |
+
|
| 239 |
+
# Output image
|
| 240 |
+
output_image = gr.Image(
|
| 241 |
+
label="Segmentation Results",
|
| 242 |
+
type="pil",
|
| 243 |
+
height=400,
|
| 244 |
+
elem_classes=["output-image"]
|
| 245 |
+
)
|
| 246 |
+
|
| 247 |
+
# Analysis text
|
| 248 |
+
analysis_output = gr.Markdown(
|
| 249 |
+
label="Analysis Report",
|
| 250 |
+
value="Upload an image and click 'Analyze Image' to see results."
|
| 251 |
+
)
|
| 252 |
+
|
| 253 |
+
# Add footer with information
|
| 254 |
+
gr.HTML("""
|
| 255 |
+
<div style="margin-top: 30px; padding: 20px; background-color: #f9f9f9; border-radius: 10px;">
|
| 256 |
+
<h4>π¬ About This Tool</h4>
|
| 257 |
+
<p><strong>Model:</strong> Pre-trained U-Net architecture optimized for brain tumor segmentation</p>
|
| 258 |
+
<p><strong>Technology:</strong> PyTorch, Deep Learning, Computer Vision</p>
|
| 259 |
+
<p><strong>Dataset:</strong> Trained on medical MRI brain scans</p>
|
| 260 |
+
|
| 261 |
+
<h4>β οΈ Important Medical Disclaimer</h4>
|
| 262 |
+
<p style="color: #d73027; font-weight: bold;">
|
| 263 |
+
This AI tool is for research and educational purposes only. It should NOT be used for medical diagnosis.
|
| 264 |
+
Always consult qualified healthcare professionals for medical advice and diagnosis.
|
| 265 |
+
</p>
|
| 266 |
+
|
| 267 |
+
<p style="text-align: center; margin-top: 20px; color: #666;">
|
| 268 |
+
Made with β€οΈ using Gradio β’ Powered by PyTorch β’ Hosted on π€ Hugging Face Spaces
|
| 269 |
+
</p>
|
| 270 |
+
</div>
|
| 271 |
+
""")
|
| 272 |
+
|
| 273 |
+
# Event handlers
|
| 274 |
+
predict_btn.click(
|
| 275 |
+
fn=predict_tumor,
|
| 276 |
+
inputs=[image_input],
|
| 277 |
+
outputs=[output_image, analysis_output]
|
| 278 |
+
)
|
| 279 |
+
|
| 280 |
+
clear_btn.click(
|
| 281 |
+
fn=clear_all,
|
| 282 |
+
outputs=[image_input, output_image, analysis_output]
|
| 283 |
+
)
|
| 284 |
+
|
| 285 |
+
# Auto-predict when image is uploaded
|
| 286 |
+
image_input.change(
|
| 287 |
+
fn=predict_tumor,
|
| 288 |
+
inputs=[image_input],
|
| 289 |
+
outputs=[output_image, analysis_output]
|
| 290 |
+
)
|
| 291 |
+
|
| 292 |
+
# Launch the app
|
| 293 |
+
if __name__ == "__main__":
|
| 294 |
+
app.launch(
|
| 295 |
+
share=True,
|
| 296 |
+
server_name="0.0.0.0",
|
| 297 |
+
server_port=7860,
|
| 298 |
+
show_error=True
|
| 299 |
+
)
|
requirements.txt
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
torch>=1.9.0
|
| 2 |
+
torchvision>=0.10.0
|
| 3 |
+
gradio>=4.0.0
|
| 4 |
+
opencv-python>=4.5.0
|
| 5 |
+
Pillow>=8.0.0
|
| 6 |
+
numpy>=1.21.0
|
| 7 |
+
matplotlib>=3.3.0
|
| 8 |
+
scikit-image>=0.18.0
|