CNN for tumor location and RF for image based classification.
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README.md

CNN for tumor detection on whole slede images(WSI)

This project is for the tumor area detection on whole slide images(WSI), using Python 3, keras, and Tensorflow.
效果图
The repository includes:

  • Preprocess
  • Train and predict
  • Postprocess
  • Random forest

Requirements

  • Python 3.6.x or above
  • Tensoflow 1.6.x
  • Openslide
  • sk-learn
  • sk-image
  • open-cv
  • numpy, sciPy

Preprocess

There are have broad categories:

  1. Finding Region of Interest(ROI)
  2. Exatract Patches from ROI
  3. Data augumentation

get _ mask.py
get _ patches.py

Keras Finetuming

Patches classfier for normal and tumor patch

train _ images _ classifier.py
evl _ images.py

Postprocess

There are have broad categories:

  1. get consecutive patches for heatmaps
  2. get heatmaps for all trainset slide

Random forest

This is slide based classifier using what we get in above steps!!