anguoyang / 3d-unet

Tensorflow, Pytorch, and Chainer implementations of 3D UNet

3D UNet implementation [WIP] [Contribution Welcome]

This repository includes Tensorflow (v1.0), PyTorch, and Chainer (v2.0) implementations of 3D UNet, semantic segmentation neural network for 3D voxel data.

NOTE: This is not official implementation.

The original paper is: Özgün Çiçek, Ahmed Abdulkadir, S. Lienkamp, Thomas Brox & Olaf Ronneberger. 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation. Medical Image Computing and Computer-Assisted Intervention (MICCAI), Springer, LNCS, Vol.9901, 424--432, Oct 2016

Data preparation

Download SLIVER07 dataset. You need to register to download it.

Please let me know if you know better 3D voxel dataset to apply 3D convolutional neural network!

PyTorch implementation

Requirements

• pytorch-0.1.11

Training

cd pytorch

Chainer implementation

Requirements

• Python 2.7.11+
  • Chainer 1.21.0.1+
  • numpy 1.9+
  • scipy 0.16+
  • six
  • matplotlib
  • tqdm
  • cv2 (opencv)

GPU memory requirement and Result

Now in prep.

LICENSE

MIT LICENSE.

Author

shiba24, April 2017.