# Lung-Lobes-Segmentation-in-CT-Scans

Python and C++ implementation on vessel and fissure segmentation in Lung CT Scans based on [Bianca's work](https://pdfs.semanticscholar.org/ddd9/8a73eab745841ba41a13633be76ab1f9c8b0.pdf)

## Usage

**For lung and pulmonary vessel segmentation**. 

I create a ipython notebook for this part (in lung_segmentation.ipynb except the last two parts).

**For pulmonary fissure segmentation**. 

Compile the two C++ files for fissure segmentation.

1. cmake .

2. make

3. 

    Use vector-based region growing for fissure segmention. 

    ```Python

    ./vector_region_growing ORIGINAL_CT.mhd FISSURE_EXTRACT.mhd

    ```

    Use intensity-based region growing for removing small regions.

    ```Python

    ./region_growing FISSURE_EXTRACT.mhd FISSURE_EXTRACT_REFINED.mhd

    ```

4. Running the last two sections in the ipython notebook to generate fissure mask and final lung-vessel-fissure mask. 

## Results

The result of lung segmentation:  

![ ](images/lung.png)

----

The result of vessel segmentaton:  

![ ](images/vessel.png)

And in 3D view:  

![ ](images/vessel3d.png)

----

The result of fissure segmentation:   

(From left to right: original, after vector-based region growing, after intensity-based region growing)

![ ](images/fissure.png)

The 3D maps of Lung-Vessel-Fissure for 9 cases:  

![ ](images/maps.png)

## Dataset

The dataset I used is [LOLA11](https://lola11.grand-challenge.org), which contains 55 CT Scans.