Habitat Analysis: Biomedical Imaging Toolkit (HABIT)

Tumor habitat analysis and intratumoral heterogeneity quantification for clinical and radiomics research. Workflows are driven by YAML configs: preprocessing, habitat segmentation, feature extraction, and optional machine learning.

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Documentation

Online docs: https://lichao312214129.github.io/HABIT

Local build: cd docs && make html → docs/build/html/index.html

Suggested learning path

Workflow chapters

Tools & more

Bundled config templates

After cloning or unpacking the repo, use the config/ folder at the project root (sibling to the habit/ Python package). See config/README_CONFIG.md and Configuration reference.

Install & demo data

Python 3.10–3.14. Full steps: Installation.

conda create -n habit python=3.10 -y
conda activate habit
pip install -U pip
pip install habitat-analysis -i https://pypi.org/simple
habit --version
# import name: import habit

Optional: napari for habit view (see Installation). PyRadiomics is separate when you need radiomics. Other capabilities are extras — missing ones raise OptionalDependencyError with the exact pip install command, e.g.:

pip install "habitat-analysis[ml,analysis]"

• Source: GitHub (dev: pip install -e .)

• Demo data (two packs):

  1. Imaging (habitat / preprocess / feature extract): preprocessed.zip (code 9bi3). After extract you must have demo_data/preprocessed/images/ and demo_data/preprocessed/masks/ next to config/ (no nested processed_images). If zip top level is preprocessed/, extract into demo_data/; if images/+masks/, put under demo_data/preprocessed/.
  2. Tabular ML (habit model / habit cv): ml_data.zip (code atnp). Extract at project root to get demo_data/ml_data/ (e.g. breast_cancer_dataset.csv). If zip top level is ml_data/, extract into demo_data/.

  Habitat-only demos need pack 1; add pack 2 only for ML demos. See Quickstart

Support & citation

• Issues: GitHub Issues
• Citation: see CITATION.cff
• License: Apache License 2.0. Free for academic and commercial use; the only obligation is to retain the copyright and license notices and to ship NOTICE with redistributions. When HABIT supports scientific work, the authors request -- but do not require as a license condition -- that you cite it