HABIT Documentation

HABIT (Habitat Analysis: Biomedical Imaging Toolkit) — preprocessing → habitat segmentation → feature extraction → machine learning.

Warning

For research and education only. Not for clinical diagnosis or treatment.

Learning path

1. Installation — Install

2. Demo tutorial — Run the demo

3. Web GUI (under development) — Web GUI (under development; CLI recommended)

4. How-to guides — Step-by-step with your data

5. Configuration Reference — YAML reference

6. Feature reference — Feature definitions (papers)

7. Issues → FAQ

Tutorial

• Installation
  • Windows lightweight installer
  • Source install
• Demo tutorial
  • Prepare data
  • Run (5 steps)

Web GUI

• Web GUI (under development)

How-to guides

• How-to guides

Configuration

• Configuration Reference
  • Configuration recipe catalog
  • Preprocessing Configuration
  • DICOM Sort Configuration
  • Habitat Segmentation Configuration
  • Feature Extraction Configuration
  • Traditional Radiomics Configuration
  • Machine Learning Configuration
  • Model Comparison Configuration
  • Auxiliary Tools and Data Configuration

Feature reference

• Feature reference
  • Traditional Radiomics
  • Non-radiomics Morphology
  • Whole / Each Habitat Radiomics
  • MSI Features
  • ITH Score

Command reference

• Command reference
• Auxiliary commands

FAQ

• FAQ

Background

• Habitats and clustering

Developer

• Developer Guide
  • Design Philosophy
  • Core Concepts and Mental Model
  • Architecture
  • Complete Request Lifecycle
  • Code Map
  • Configuration System
  • Subsystems
  • Extension and Plugin Guide
  • Invariants and Architecture Contracts
  • Contributor Workflow
  • Contributing
  • Recommended reading order
• Customization and Extension Guide
  • Overview
  • Extension principles
  • Custom preprocessors
  • Custom feature extractors
  • Custom clustering algorithms
  • Custom models
  • Custom feature selectors
  • Best practices
  • FAQ
  • Next steps
• API Reference
  • Python API
  • Image and geometry API
  • Low-level radiomics API
  • habitat_analysis module
  • machine_learning module
  • preprocessing module
  • habit.core.dicom_sort
  • Plugin discovery API
  • API contracts, provenance, and errors
  • common module
  • utils module
  • CLI Commands API
  • Command-oriented API notes
• Upstream Dependencies and Documentation Links
  • Image preprocessing (habit preprocess)
  • Habitat segmentation (habit get-habitat)
  • Habitat features and traditional radiomics (habit extract / habit radiomics)
  • Machine learning (habit model / habit cv)
  • Model comparison (habit compare)
  • ICC / Test–retest / other
  • ROI delineation (external tools)
• Changelog
  • Version 2.0 (2026-01-25)
  • Version 1.x
  • Future Roadmap
  • See Also
• Acknowledgments
  • Core developers
  • Future developers
  • Clinical collaborators
  • Special thanks
  • Open source community
  • How to contribute
  • Contact

• GitHub: https://github.com/lichao312214129/HABIT