ninadmn / 3D-Segmentation-of-Vertebra-using-Volumetreic-Network

Thesis project on 3D instance segmentation of vertebra using Mask RCNN

8 stars 0 forks source link

readme

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

the VNet model

To train and generate the result run VNet.py