README.md

Helmsley 3D MIP Project - ML

A repo for 3D medical MRI image visualization and organ (colon) segmentation for Crohn's Disease using deep Convolutional Neural Network and curve/plane reconstruction algorithms

Demo Video:

• Youtube Link

Quick Access to Relevant Components of this Project

• The Google Drive Folder
• MICCAI 2019 Paper
• Tutorial for Nautilus Clusters using Kubernetes
• Previous Presentation Slides
• Integrated API for Prediction and Centerline Extraction

Frameworks and Libraries Utilized

• Pickle
• Python 2.7 & Python 3.6.8
• OpenCV
• PyDicom
• Keras with Tensorflow Kernel
• Python.h - C_API for wrapping the python scripts in a C++ Interface

Developers Team

• Wanze (Russell) Xie - (https://github.com/russellxie7)
• Zifeng Li - ()
• Trevor Hedstrom - ()

Comments

• All the raw and processed data include the png/dicom segmented masks and nrrd files for 3D slicer (data for training): https://drive.google.com/drive/u/2/folders/130arK9MAYJD8Pq-1-6TU2y9fOTO5rJ5n
• Saved models (hdf5 files): https://drive.google.com/drive/u/2/folders/1IM0TxECQgww1rflAW-mgwIhlyKa5Qbw3