unet for image segmentation
Branch: master
Clone or download
zhixuhao Update model.py
merge --> concatenate
Latest commit d171fd0 Nov 27, 2018
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data/membrane update Jun 9, 2018
img update readme Apr 24, 2017
README.md update Jun 9, 2018
data.py update Jun 9, 2018
dataPrepare.ipynb Update dataPrepare.ipynb Jun 22, 2018
main.py update Jun 9, 2018
model.py Update model.py Nov 27, 2018
trainUnet.ipynb update Jun 9, 2018

README.md

Implementation of deep learning framework -- Unet, using Keras

The architecture was inspired by U-Net: Convolutional Networks for Biomedical Image Segmentation.


Overview

Data

The original dataset is from isbi challenge, and I've downloaded it and done the pre-processing.

You can find it in folder data/membrane.

Data augmentation

The data for training contains 30 512*512 images, which are far not enough to feed a deep learning neural network. I use a module called ImageDataGenerator in keras.preprocessing.image to do data augmentation.

See dataPrepare.ipynb and data.py for detail.

Model

img/u-net-architecture.png

This deep neural network is implemented with Keras functional API, which makes it extremely easy to experiment with different interesting architectures.

Output from the network is a 512*512 which represents mask that should be learned. Sigmoid activation function makes sure that mask pixels are in [0, 1] range.

Training

The model is trained for 5 epochs.

After 5 epochs, calculated accuracy is about 0.97.

Loss function for the training is basically just a binary crossentropy.


How to use

Dependencies

This tutorial depends on the following libraries:

  • Tensorflow
  • Keras >= 1.0

Also, this code should be compatible with Python versions 2.7-3.5.

Run main.py

You will see the predicted results of test image in data/membrane/test

Or follow notebook trainUnet

Results

Use the trained model to do segmentation on test images, the result is statisfactory.

img/0test.png

img/0label.png

About Keras

Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. It was developed with a focus on enabling fast experimentation. Being able to go from idea to result with the least possible delay is key to doing good research.

Use Keras if you need a deep learning library that:

allows for easy and fast prototyping (through total modularity, minimalism, and extensibility). supports both convolutional networks and recurrent networks, as well as combinations of the two. supports arbitrary connectivity schemes (including multi-input and multi-output training). runs seamlessly on CPU and GPU. Read the documentation Keras.io

Keras is compatible with: Python 2.7-3.5.