# Cardiac MRI Segmentation

![build status](https://travis-ci.org/chuckyee/cardiac-segmentation.svg?branch=master)

This repository contains code and models to identify the right ventricle in

cardiac MRI images. The

[project](http://ai-on.org/projects/cardiac-mri-segmentation.html) is one of

the open calls for research from Francois Chollet's [AI Open

Network](http://ai-on.org/).

For the problem description, models and results, please see the blog post

[here](https://chuckyee.github.io/cardiac-segmentation/).

## Installation

The main code is written as a Python package named `rvseg'. After cloning this

repository to your machine, install with:

```bash

cd cloned/path

pip install .

```

You should then be able to use the package in Python:

```python

import matplotlib.pyplot as plt

from rvseg import patient, models

p = patient.PatientData("RVSC-data/TrainingSet/patient01")

# Explore p.images, p.endocardium_masks, etc.

```

## Running models

Scripts for model training and evaluation are located under /scripts/.

```bash

python -u scripts/train.py defaults.config

```

Note: this package is written with the Tensorflow backend in mind -- (batch,

height, width, channels) ordered is assumed and is not portable to Theano.