🫁🧠🔴 Organ Segmentation – MED-PROJECTS

A clean, modular Python package for Brain MRI, Liver CT, and Lung CT segmentation.

Repo Structure

organ_segmentation/
│
├── segmentation/          # One class per organ
│   ├── brain.py           # BrainSegmentor
│   ├── liver.py           # LiverSegmentor
│   └── lungs.py           # LungSegmentor
│
├── utils/                 # Shared code (no duplication!)
│   ├── metrics.py         # Dice coefficient, Hausdorff distance
│   ├── preprocessing.py   # NIfTI loading, normalization, Otsu threshold
│   ├── visualization.py   # Plotly 3-D viewer + matplotlib 2-D slices
│   └── io_helpers.py      # Kaggle download, file discovery
│
├── notebooks/             # Thin Colab demo scripts
│   ├── brain_demo.py
│   ├── liver_demo.py
│   └── lung_demo.py
│
└── main.py                # CLI: python main.py --organ brain --input file.nii.gz

Features

• 3D visualization using matplotlib/pyvista/plotly/skimage/Nibabel/scipy/Numpy
• Automated segmentation using trained deep learning models
• Organ-specific models
• User-friendly script execution

collaborators

janawaleed135

Janamostafa-star gannaali061-stack

Evaluation metric

LIVER

Lung

brain

Screenshots

Liver

Lungs

Brain

3D Visualization

Liver

Lungs

brain

CLI

python main.py --organ brain  --input brain.nii.gz
python main.py --organ liver  --input liver.nii.gz --export liver.html
python main.py --organ lungs  --input lung.nii.gz  --gt gt.nii.gz

Dependencies

nibabel
numpy
scipy
scikit-image
plotly
matplotlib
kagglehub

Installation

pip install -r requirements.txt