3D_UNet for Cardiac MRI image segmentation

This repository contains code for 3D-UNet for cardiac MRI image segmentation tasks.
Main file:
3D_Cardiac_UNet.ipynb
Helper functions:
utilities.py
read_cardiac_MRI_segments.py
Pure_SA_3D_8x8_2.architecture.py
preprocess_on_fly.py
metrics.py

The notebook contains both training code and the inference code.

How to run in your local

1. Open the notebook and remove all the commands related to Google Colab and Goole Drive
2. Adjust the paths to directories containing dataset in your computer accordingly
3. Create a Python virtual environment
4. Install the dependencies in the file: requirements.txt
5. Run all the cells in the notebook

How to run in Google Colab

1. Open the notebook in Google Colab.
2. Upoad all the files in this repository in the '/content' folder using Files tab in Colab notebook.
3. Make sure to place the data in the Google Drive and and fix the paths in the notebook accoridingly
4. Run all the cells of the notebook.