3D Segmentation of Vertebra using Volumetric Network
This is an example of the CT images of vertebra segmentation from spineweb
Prerequisities
The following dependencies are needed:
- numpy
- SimpleITK
- opencv-python
- tensorflow
- keras
- pandas
- scikit-learn
- matplotlib
- plotly
How to Use
1、Preprocess
Vertebra Detection
- analyze the ct image,and get the slice thickness and window width and position along with generating 3D interactive plot and extraction of masks:run the GenerateMasks.ipynb
- generate vertebra ct image and mask:run the get2dScans.py
- generate patch(128,128,128) of vertebra image and mask:run the preparePatches.py
- save vertebra data and mask into csv file run the saveDetailsToCSV.py
2、Segmentation of Vertebra
- To train and generate the result run VNet.py