Med-TDA Logo
  • Installation
    • Install from PyPI
    • Requirements
    • Install from Source
    • Development Installation
    • Verify Installation
    • Troubleshooting
      • Common Issues
      • Platform-Specific Notes
    • Virtual Environments
    • Updating MedTDA
    • Uninstallation
    • Next Steps
  • Quick Start
    • Installation
    • Basic Usage: Single Image
      • Working with 2D Images
      • Without a Mask
      • Using NumPy Arrays
    • Multiple Vectorization Methods
    • Preprocessing Options
    • Getting Barcodes
    • Batch Processing (Python)
    • Command-Line Interface
      • Single File
      • Batch Processing
      • Configuration Files
    • Outputs
      • Single File Processing
      • Batch Processing
    • Using Features in Machine Learning
    • Next Steps
    • Common Next Questions
  • User Guide
    • Overview
    • High-Level Workflow
    • Detailed Topics
      • Preprocessing
        • Overview
        • Supported Image Formats
        • Intensity Normalization
        • Resampling and Spacing
        • Windowing
        • Masking
        • ROI Cropping
        • Complete Preprocessing Example
        • Using the Preprocessor Directly
        • Best Practices
        • Troubleshooting
        • Next Steps
      • Persistent Homology
        • Overview
        • Persistent Homology Parameters
        • Filtration Types
        • Cubical Complex Construction
        • Homology Dimensions
        • Persistence Barcodes
        • Complete PH Configuration Examples
        • Performance Considerations
        • Troubleshooting
        • Best Practices
        • Next Steps
      • Vectorization
        • Overview
        • Available Methods
        • Persistence Statistics
        • Betti Curves
        • Persistence Images
        • Persistence Landscapes
        • Persistence Silhouettes
        • Entropy Summary
        • Lifespan Curves
        • Tropical Coordinates
        • Using Multiple Methods
        • Example Workflow
        • Next Steps
      • Batch Processing
        • Overview
        • Python Batch Processing
        • Command-Line Batch Processing
        • Using Configuration Files
        • Output Organization
        • Large-Scale Batch Processing
        • Best Practices
        • Troubleshooting
        • Example Complete Workflow
        • Next Steps
      • Preprocessing
      • Persistent Homology
      • Vectorization Methods
      • Batch Processing
    • Complete Feature Extractor Reference
      • Initialization Parameters
      • Methods
    • Common Patterns
      • Progressive Refinement
      • Comparing Vectorization Methods
      • Reusing Extractor for Multiple Images
    • Working with Different Image Types
      • 2D Images
      • 3D Medical Images
      • 4D Time Series
      • Multi-Label Masks
    • Best Practices
    • Performance Tips
    • Error Handling
    • Next Steps
  • Command-Line Interface (CLI)
    • Overview
    • Installation
    • Basic Usage
      • Single File
      • Batch Processing
      • Complete Example
    • Command-Line Arguments
      • General Options
      • Preprocessing Options
      • Persistent Homology Options
      • Vectorization Options
      • Parallelization Options
      • Logging Options
    • Configuration Files
      • YAML Format
      • Using Config Files
      • Benefits
    • Examples
      • Single File Examples
      • Batch Processing Examples
    • Output Files
      • Single File Mode
      • Batch Mode
      • batch_features.csv Format
    • Integration with Pipelines
      • Shell Scripts
      • Makefiles
      • Python Subprocess
      • Snakemake
      • Nextflow
    • Error Handling
      • Exit Codes
      • Checking Errors
      • Batch Error Handling
    • Performance Tips
      • Speed Optimization
      • Memory Optimization
      • Quality Settings
    • Troubleshooting
    • Full Help Output
    • Next Steps
  • API Reference
    • Overview
    • Quick Navigation
    • Typical Usage Pattern
    • Module Documentation
      • FeatureExtractor
        • Overview
        • Basic Usage
        • Class Documentation
        • Constructor Parameters
        • Methods
        • Complete Example
        • See Also
      • Preprocessor
        • Overview
        • Basic Usage
        • Class Documentation
        • Constructor Parameters
        • Methods
        • Normalization Methods
        • Windowing
        • ROI Cropping
        • Multi-Label Mask Handling
        • Complete Example
        • Common Patterns
        • See Also
      • PH Computer
        • Overview
        • Basic Usage
        • Functions
        • Parameters
        • Homology Dimensions
        • Complete Examples
        • Performance Tips
        • See Also
      • BarcodeExtractor
        • Overview
        • Basic Usage
        • Class Documentation
        • Constructor Parameters
        • Methods
        • Complete Examples
        • Common Use Cases
        • Performance Tips
        • See Also
      • Vectorizers
        • Overview
        • Quick Comparison
        • Functions
        • Complete Examples
        • See Also
      • Loaders
        • Overview
        • Functions
        • Validation Functions
        • Complete Examples
        • Supported Formats
        • Format Detection
        • Troubleshooting
        • Performance Tips
        • See Also
      • Utils
        • Overview
        • Functions
        • Complete Examples
        • Common Patterns
        • Performance Tips
        • See Also
      • CLI
        • Overview
        • Functions
        • Command-Line Arguments
        • Complete Examples
        • Configuration File Format
        • Batch CSV Format
        • Error Handling
        • Parallel Processing
        • Performance Tips
        • Internal Functions
        • See Also
    • Core Classes
      • FeatureExtractor
      • Preprocessor
      • BarcodeExtractor
    • Vectorization Functions
    • Utility Functions
    • Image Loading and Saving
    • Command-Line Interface
    • Indices and Tables
  • TDA Theory
    • Overview
    • Why TDA for Medical Images?
      • Capturing Complex Anatomy
      • Multi-Scale Analysis
      • Robustness to Noise
      • Clinical Applications
    • Core Concepts
    • Topological Features in Medical Images
      • H0: Connected Components
      • H1: Loops and Holes
      • H2: Voids and Cavities
    • Mathematical Foundation
    • Key Concepts Summary
    • Theory Sections
      • Persistent Homology
        • Introduction
        • Homology Groups
        • Birth and Death Times
        • Persistence Computation
        • Multi-Scale Analysis
        • Practical Examples
        • Mathematical Formulation
        • Connection to Medical Imaging
        • See Also
      • Filtrations
        • Introduction
        • What is a Filtration?
        • Building Filtrations from Images
        • Cubical Complexes
        • Construction Methods
        • Filtration Process
        • Multi-Dimensional Images
        • Practical Considerations
        • Mathematical Foundations
        • See Also
      • Barcodes and Diagrams
        • Introduction
        • Persistence Barcodes
        • Persistence Diagrams
        • Visualizing Barcodes and Diagrams
        • Interpretation Guide
        • Medical Image Examples
        • Noise Filtering
        • Statistical Analysis
        • Mathematical Foundations
        • See Also
      • Vectorization Methods
        • Introduction
        • Vectorization Strategies
        • Combining Methods
        • Multi-Dimensional Barcodes
        • See Also
    • Further Reading
      • Recommended Resources
    • Next Steps
    • See Also
  • Examples
    • Overview
    • Quick Links
    • Example Gallery
      • Basic Usage
        • Simple Feature Extraction
        • Using Masks
        • Different Image Formats
        • Accessing Barcodes
        • Multiple Vectorization Methods
        • Complete Workflow Examples
        • Using with Machine Learning
        • Tips and Best Practices
        • Common Pitfalls
        • Next Steps
        • See Also
      • Advanced Preprocessing
        • Custom Preprocessing Pipelines
        • Modality-Specific Preprocessing
        • Normalization Methods Comparison
        • Resampling Strategies
        • ROI Extraction and Cropping
        • Intensity Windowing
        • Handling Missing or Invalid Data
        • Performance Optimization
        • Complete Preprocessing Workflows
        • Next Steps
        • See Also
      • Batch Workflow
        • Basic Batch Processing
        • Error Handling
        • Parallel Processing
        • Progress Tracking
        • Different Vectorization Methods
        • Organized Output Structure
        • Dataset Creation
        • Quality Control
        • Complete Workflow Example
        • Next Steps
        • See Also
      • CLI Workflows
        • Basic CLI Usage
        • Configuration Files
        • Batch Processing
        • Output Formats
        • Advanced Workflows
        • Quality Control
        • Filtering and Selection
        • Preprocessing Exploration
        • Vectorization Parameter Tuning
        • Automation Scripts
        • Integration with ML Pipelines
        • Profiling and Optimization
        • Useful Aliases
        • Debugging
        • Next Steps
        • See Also
      • Interactive Tutorial
        • Overview
        • Tutorial Notebook
        • Running the Tutorial
        • Tutorial Contents
        • Sample Data
        • Contributing
        • Citation
        • Next Steps
        • See Also
    • Getting Started
    • For Production Use
    • Example Data
    • Example Categories
      • By Task
      • By Image Type
    • Code Patterns
      • Common Import Pattern
      • Basic Workflow
      • Error Handling
    • Next Steps
    • Contributing Examples
    • Tips for Using Examples
    • See Also
  • Frequently Asked Questions
    • Installation and Setup
      • How do I install MedTDA?
      • What are the system requirements?
      • Can I use MedTDA on Windows/Mac/Linux?
      • Dependencies won’t install - what should I do?
    • Getting Started
      • Where should I start?
      • What file formats are supported?
      • Can I use 2D images?
    • Common Errors and Solutions
      • ValueError: Image and mask shapes don’t match
      • MemoryError: Unable to allocate array
      • Empty barcodes / No features detected
      • RuntimeError: GUDHI failed to compute
    • Feature Extraction Questions
      • Which vectorization method should I use?
      • How do I choose between sublevel and superlevel?
      • What dimensions should I compute (H0, H1, H2)?
      • How many features will I get?
    • Performance and Optimization
      • How long does processing take?
      • How can I speed up processing?
      • How much RAM do I need?
      • Can I use GPU acceleration?
    • Machine Learning Integration
      • How do I integrate features with scikit-learn?
      • Should I normalize features?
      • How do I do feature selection?
      • Can I combine multiple vectorization methods?
    • Results Interpretation
      • What do the barcode plots mean?
      • How do I interpret persistence statistics?
      • What’s a “good” persistence value?
      • Why are my features all similar/different between groups?
    • Troubleshooting
      • Code runs but gives unexpected results
      • “Module not found” errors
      • Processing hangs / takes forever
    • Where to Get Help
      • I read the FAQ but still have questions
      • How do I report a bug?
      • Can I request a feature?
      • How can I contribute?
    • See Also
  • Changelog
    • [Unreleased]
    • [1.0.0] - 2024-01-15
      • Added
        • Core Features
        • Vectorization Methods
        • File Format Support
        • Preprocessing
        • Command-Line Interface
        • Visualization
        • Documentation
      • Changed
      • Deprecated
      • Removed
      • Fixed
      • Security
    • [0.3.0] - 2023-11-20
      • Added
      • Changed
      • Fixed
    • [0.2.0] - 2023-09-10
      • Added
      • Changed
      • Fixed
    • [0.1.0] - 2023-07-01
      • Added
      • Known Issues
    • Version History Summary
    • Migration Guides
      • Migrating from 0.3.x to 1.0.0
      • Migrating from 0.2.x to 0.3.x
      • Migrating from 0.1.x to 0.2.x
    • Release Cycle
    • Deprecation Policy
    • Contributing to Changelog
    • External Links
    • Acknowledgments
    • See Also
  • Contributing to MedTDA
    • Ways to Contribute
    • Getting Started
      • Quick Start
      • Prerequisites
    • Development Setup
      • 1. Fork and Clone
      • 2. Create Environment
      • 3. Install in Development Mode
      • 4. Install Pre-commit Hooks
    • Development Workflow
      • 1. Create a Branch
      • 2. Make Your Changes
      • 3. Write Tests
      • 4. Update Documentation
      • 5. Run Code Quality Checks
      • 6. Commit Your Changes
      • 7. Push and Create Pull Request
    • Code Guidelines
      • Style Guide
      • Type Hints
      • Error Handling
    • Testing Guidelines
      • Test Structure
      • Test Types
      • Fixtures
    • Documentation Guidelines
      • Documentation Types
      • Writing Style
      • Code Examples
    • Pull Request Process
      • Checklist Before Submitting
      • Review Process
    • Community Guidelines
      • Code of Conduct
      • Reporting Issues
    • Getting Help
    • Recognition
    • See Also
  • References
    • Persistent Homology Foundations
      • Core Theory
      • Computational Methods
    • Vectorization Methods
      • Surveys and Comparative Studies
      • Persistence Images
      • Persistence Landscapes
      • Other Vectorizations
    • Medical Imaging Applications
      • General Medical Imaging TDA
      • Brain Imaging
      • Tumor and Lesion Analysis
      • Vascular Imaging
      • Cardiac Imaging
    • Statistical Analysis
      • Statistical Methods for Persistence
      • Distance and Stability
    • Machine Learning with TDA
      • Deep Learning Integration
      • Feature Learning
    • Software and Tools
      • Core Libraries
      • Visualization
      • Medical Imaging Libraries
    • Textbooks and Tutorials
      • Topological Data Analysis
      • Medical Image Analysis
    • Online Resources
      • Tutorials and Courses
      • Datasets
      • Code Repositories
    • Citing MedTDA
    • Related Projects
    • Contributing References
    • See Also
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