histox 0.1.1

Deep learning tools for digital histology

histox

histox is a powerful, open-source deep learning library for digital pathology. Built on top of Slideflow, it provides researchers and AI practitioners with a comprehensive toolkit for analyzing whole slide images (WSI) and building state-of-the-art computational pathology models.

🌐 Website: slideflow.dev

✨ Key Features

• End-to-end WSI analysis pipeline - From raw slides to trained models
• Robust slide processing - Automatic tile extraction with stain normalization
• Flexible learning paradigms
  • Strongly-supervised and weakly-supervised learning
  • Multiple Instance Learning (MIL) for slide-level labels
  • Self-Supervised Learning (SSL) for representation learning
  • Generative Adversarial Networks (GANs) for data augmentation
• Pre-trained foundation models - Integrated support for modern architectures
• Interpretability tools - Generate heatmaps, saliency maps, and mosaic visualizations
• Layer activation analysis - Understand model decision-making
• Uncertainty quantification - Measure model confidence

📋 Requirements

• Python: >= 3.7
• Deep Learning Framework (at least one):
  • PyTorch >= 1.9
  • TensorFlow >= 2.5, < 2.12

📦 Installation

From PyPI (Recommended)

pip install histox

From Source

git clone https://github.com/leicaohmu/histox
cd histox
pip install -e .

Optional GPU Support

Install with PyTorch GPU support:

pip install -e ".[torch]"

Or TensorFlow GPU support:

pip install -e ".[tf]"

NVIDIA RAPIDS acceleration (optional):

pip install -e ".[cucim]"

🚀 Quick Start Example

This example demonstrates how to train a lung cancer adenocarcinoma classifier using the included TCGA dataset.

1. Prepare Your Data Structure

project_root/
├── slides/                    # WSI files (.svs, .ndpi, etc.)
│   ├── TCGA-83-5908-01Z-00-DX1.svs
│   ├── TCGA-62-A46V-01Z-00-DX1.svs
│   └── ...
├── annotations.csv            # Slide labels
└── tfrecords/                # Output directory for processed data (auto-created)

2. Create Annotation File

Create annotations.csv with slide-level labels:

patient,subtype,site,slide
TCGA-83-5908,adenocarcinoma,Site-28,TCGA-83-5908-01Z-00-DX1
TCGA-62-A46V,adenocarcinoma,Site-124,TCGA-62-A46V-01Z-00-DX1
TCGA-44-2655,squamous,Site-29,TCGA-44-2655-01Z-00-DX1

(A complete dataset example is available in lung_labels.csv in this repository)

3. Initialize and Train

import histox as hx
import os

# Define paths
project_root = '/path/to/project'
annotations_file = '/path/to/annotations.csv'
slides_directory = '/path/to/slides'
tfrecords_directory = os.path.join(project_root, 'tfrecords')

# Create project
print("[1/5] Creating project...")
project = hx.create_project(
    root=project_root,
    annotations=annotations_file,
    slides=slides_directory,
    tfrecords=tfrecords_directory
)

# Extract tiles from slides
print("[2/5] Extracting tiles...")
project.extract_tiles(
    tile_px=299,        # Tile size in pixels
    tile_um=302,        # Tile size in micrometers
    workers=8           # Number of parallel workers
)

# Define model parameters
print("[3/5] Configuring model...")
params = hx.ModelParams(
    tile_px=299,
    tile_um=302,
    batch_size=32,
    model='xception',            # Base architecture
    learning_rate=0.0001,
    epochs=50,
    validation_fraction=0.2
)

# Train the model
print("[4/5] Training model...")
project.train(
    'subtype',                   # Column name for classification target
    params=params,
    save_predictions=True,
    multi_gpu=True               # Enable multi-GPU training if available
)

# Generate explanations
print("[5/5] Generating interpretations...")
project.generate_heatmaps()      # Attention/saliency visualizations
project.generate_mosaic_maps()   # Tile-level predictions

print("✓ Training complete!")

4. Evaluate and Interpret Results

# Access trained models and predictions
results = project.get_results('subtype')

# Generate patient-level predictions
slide_predictions = project.predict_slides('subtype')

# Create visualizations
heatmap = hx.Heatmap.from_project(
    project=project,
    outcome_name='subtype',
    model_idx=0
)
heatmap.save('/path/to/output/heatmap.png')

# Access detailed metrics
print(f"Validation Accuracy: {results['val_accuracy']:.4f}")
print(f"Validation AUC: {results['val_auc']:.4f}")

📊 Complete Workflow Example (Lung Cancer Dataset)

Here's a ready-to-run example using the included TCGA lung cancer data:

import histox as hx
import pandas as pd
import os

# Configuration
data_root = './datasets/lung_adeno_squam'
project_dir = './lung_project'

# The lung_labels.csv is already in the repository with TCGA samples
annotations_file = os.path.join(data_root, 'lung_labels.csv')
slides_dir = os.path.join(data_root, 'slides')  # Add actual .svs files here
tfrecords_dir = os.path.join(project_dir, 'tfrecords')

# Check available data
labels_df = pd.read_csv(annotations_file)
print(f"Total slides: {len(labels_df)}")
print(f"Subtypes: {labels_df['subtype'].unique()}")
print(labels_df.head())

# Step 1: Create project
try:
    project = hx.create_project(
        root=project_dir,
        annotations=annotations_file,
        slides=slides_dir,
        tfrecords=tfrecords_dir
    )
    print("✓ Project created successfully")
except Exception as e:
    print(f"Project already exists or error: {e}")

# Step 2: Extract tiles (if slides are available)
try:
    project.extract_tiles(
        tile_px=299,
        tile_um=302,
        workers=4,
        verbose=True
    )
    print("✓ Tiles extracted")
except Exception as e:
    print(f"Could not extract tiles: {e}")

# Step 3: Configure and train
params = hx.ModelParams(
    tile_px=299,
    tile_um=302,
    batch_size=32,
    model='xception',
    learning_rate=0.0001,
    epochs=30,
    validation_fraction=0.2
)

# Train on adenocarcinoma vs squamous classification
project.train(
    'subtype',
    params=params,
    save_predictions=True,
    multi_gpu=False  # Set to True if using multi-GPU
)

print("✓ Model training complete!")

🔧 Advanced Features

Multiple Instance Learning (MIL)

Use when you only have slide-level labels, not individual tile annotations:

params = hx.ModelParams(
    tile_px=299,
    model='xception',
    mil=True,                 # Enable MIL
    mil_method='attention',   # 'attention' or 'max-pooling'
    learning_rate=0.0001
)

project.train('diagnosis', params=params)

Self-Supervised Pre-training

Pre-train feature extractors without labeled data:

# Perform self-supervised learning on unlabeled slides
project.train_ssl(
    method='simclr',          # Self-supervised learning method
    epochs=100,
    batch_size=64,
    model='xception'
)

# Fine-tune on labeled data
project.train('diagnosis', params=params)

Stain Normalization

Automatic handling of staining variations across labs:

# Extract tiles with stain normalization
project.extract_tiles(
    tile_px=299,
    tile_um=302,
    stain_norm=True,          # Enable normalization
    norm_method='macenko'     # 'macenko' or 'reinhard'
)

Generate Heatmaps

Visualize model predictions across slides:

heatmap = hx.Heatmap.from_project(
    project=project,
    outcome_name='diagnosis',
    model_idx=0,
    cmap='RdYlBu_r'
)

# Save with metadata
heatmap.save(
    '/output/heatmap.png',
    high_res=True,
    stride=32
)

📚 Key Modules

Module	Purpose
histox.project	Main Project class for pipeline management
histox.dataset	Dataset handling and tile management
histox.model	Model architecture and training
histox.slide	WSI (Whole Slide Image) handling
histox.norm	Stain normalization algorithms
histox.heatmap	Heatmap generation and visualization
histox.stats	Statistical analysis and reporting

🎯 Supported Models

• CNN Architectures: Xception, ResNet-50, EfficientNet, InceptionV3, DenseNet
• Vision Transformers: ViT, DeiT
• Specialized Architectures: Cellpose (instance segmentation)

📖 Documentation

For detailed documentation and API reference:

• Slideflow Documentation
• GitHub Issues

🤝 Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/your-feature)
3. Commit your changes (git commit -am 'Add feature')
4. Push to the branch (git push origin feature/your-feature)
5. Open a Pull Request

📄 License

This project is licensed under the Apache License 2.0. See LICENSE file for details.

Note: This project is built on Slideflow. Please refer to the original project's license for additional terms.

🙏 Acknowledgments

• Slideflow - The powerful foundation this project is built upon
• TCGA - The Cancer Genome Atlas for dataset resources
• PyTorch & TensorFlow - Deep learning frameworks

📞 Support & Contact

• Email: [e-mail]
• Website: slideflow.dev
• Repository: github.com/leicaohmu/histox

🔗 Related Resources

• Slideflow Documentation
• TCGA Data Portal
• Digital Pathology Resources

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Status: Active development
Last Updated: 2026-04-11