README.md

---
title: MONAI WholeBody CT Segmentation
emoji: 🏥
colorFrom: blue
colorTo: green
sdk: gradio
sdk_version: 6.2.0
app_file: app.py
pinned: false
license: apache-2.0
tags:
- medical-imaging
- segmentation
- ct-scan
- monai
- 3d-segmentation
short_description: 'Whole‑body CT segmentation demo using MONAI’s SegResNet '
---

# 🏥 MONAI WholeBody CT Segmentation

**Automatic 3D segmentation of 104 anatomical structures from CT scans**

## Overview

This application uses MONAI's pre-trained **SegResNet** model trained on the [TotalSegmentator](https://github.com/wasserth/TotalSegmentator) dataset to automatically segment 104 different anatomical structures from whole-body CT scans.

## Features

- 🔬 **104 Anatomical Structures**: Segments organs, bones, muscles, and vessels
- 📊 **Interactive Visualization**: Navigate through axial, coronal, and sagittal views
- 🎨 **Color-coded Overlay**: Each structure has a distinct color for easy identification
- ⚡ **GPU Accelerated**: Uses CUDA when available for faster inference

## Supported Structures

| Category | Structures |
|----------|------------|
| **Major Organs** | Liver, Spleen, Kidneys, Pancreas, Gallbladder, Stomach, Bladder |
| **Cardiovascular** | Heart (4 chambers), Aorta, Vena Cava, Portal Vein, Iliac vessels |
| **Respiratory** | Lung lobes (5), Trachea, Esophagus |
| **Skeletal** | Vertebrae (C1-L5), 24 Ribs, Hip bones, Femur, Humerus, Scapula, Clavicle |
| **Muscles** | Gluteal muscles, Iliopsoas, Autochthon |
| **Other** | Brain, Face, Adrenal glands, Small/Large bowel |

## Usage

1. **Upload** a CT scan in NIfTI format (`.nii` or `.nii.gz`)
2. Click **Run Segmentation** and wait for processing (1-5 minutes)
3. **Explore** the results using the slice sliders and view controls
4. Check the **Detected Structures** panel to see all identified anatomy

## Model Details

- **Architecture**: SegResNet (MONAI)
- **Resolution**: 3.0mm isotropic (low-resolution model)
- **Training Data**: TotalSegmentator dataset
- **Output**: 105 channels (background + 104 structures)

## References

- [MONAI Model Zoo](https://monai.io/model-zoo.html)
- [TotalSegmentator Paper](https://pubs.rsna.org/doi/10.1148/ryai.230024)
- [TotalSegmentator GitHub](https://github.com/wasserth/TotalSegmentator)

## License

This model is released under the Apache 2.0 License. The TotalSegmentator dataset is released under CC BY 4.0.

## Citation

If you use this model, please cite:

```bibtex
@article{wasserthal2023totalsegmentator,
  title={TotalSegmentator: robust segmentation of 104 anatomical structures in CT images},
  author={Wasserthal, Jakob and others},
  journal={Radiology: Artificial Intelligence},
  year={2023}
}
```