Lung Segmentation

Manual Segmentation of lung CT images in python from open-cv, matplotlib, numpy, and pydicom. This was inspired by SciXChange Medical Physics labs which were done in MatLab.

Instructions

1. Clone the repository
2. Create a virtual environment: virtualenv venv.
3. Activate the virtual environment:venv\Scripts\activate
4. Download the requirements: pip install -r requirements.txt
5. Download and extract slices.zip from the database L. Sorensen
6. Ensure the path is correct when loading the image!

Brief Overview

The main segmenter is in the ctimage.py file, which holds a class that has the functions that creates the masks and other necessary images.

manualThreshold.py

An interactable program in matplotlib that will let you determine a threshold. It will display the original ct image, the binary mask, and the processed lung mask which will highlight emphysemic areas (dark areas).

calculateEmphysema.py

A simple program that will display the thresholded images and percentage of emphysemic areas.

dicom.py (WORK IN PROGRESS)

Similar to manualThreshold.py, except it loades in DICOM format images. It is current a WIP as normalization is needed.

Credits

For the databases:

1. L. Sørensen, S. B. Shaker, and M. de Bruijne, Quantitative Analysis of Pulmonary Emphysema using Local Binary Patterns, IEEE Transactions on Medical Imaging 29(2): 559-569, 2010. [PDF to publication]

2. VIA-ELCAP Public Access