lehougoogle / quip_cnn_segmentation

CNN based segmentation codes

Nuclear image synthesis and segmentation code

This repository contains source code for the following paper:
Robust Histopathology Image Analysis: to Label or to Synthesize? Hou, Le and Agarwal, Ayush and Samaras, Dimitris and Kurc, Tahsin M and Gupta, Rajarsi R and Saltz, Joel H. Computer Vision and Pattern Recognition (CVPR), 2019

You need the following python2 libraries to run this software:

tensorflow  
scipy  
numpy  
json  
pickle
cv2 

If you want to obtain initial synthetic images with nuclear masks, please read training-data-synthesis/README.md
If you want to train your nuclei segmentation model, or use our trained nuclei segmentation model, please read segmentation-of-nuclei/README.md

This software uses several open source repositories, especially this one

Trained model and released segmentation results

We also include:

1. A Dockerfile with trained model here
2. Segmentation results we've already generated here with readme.