ce-coronary-artery

Repository for automatic segmentation of contrast enhanced (ce) coronary arteries.

Overview

This projet utilizes the ImageCAS dataset
- Contains 1000 contrast enhanced CT angiography images with 1000 corresponding coronary artery labels
The Hausdorff loss function is utilized throughout the training process
The (.....TBD) model is utilized

Goals

Introduce a state of the art coronary artery segmentation model
- Measured in terms of dice coefficient, hausdorff distance, overlap, ...
Introduce the vendor neutral, GPU optimizzed Hausdorff loss function

virtual environment setup

Prerequisite

You should login in to the cluster.
You can be in any node(server). I recommand you to login to the free CPU server.

Install Mini-conda

We are using Mini-conda for enviornment.

run cd first to get to the default path.
then run the following commands.
Before running: if you don't want to install conda to directory /miniconda, change the path in the scripts.

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh

After running the scripts:

run ~/miniconda3/bin/conda init bash

Now, you should be able to use conda commands.

run conda --version to make sure your conda is ready.
if you are still not able to use conda commands, try source .bashrc, which restart/refresh the bash shell.

Create Env

conda create --name imagecas python=3.9 to create a virtual environment with python version 3.9
conda activate imagecas to run the virtual environment
conda install pip to install pip package manager for the virtual environment
you have to check if you are using the correct pip by pip --version and see the path of the pip. It should be some path that contains miniconda3 like .../miniconda3/env/imagecas...
if your pip is not having the correct path, contact Liam. (I think you should delete the pyenv settings in .bashrc or .bash_profile Andrew :))
[unnecessary] you can check if you are using the correct python version by python --version and see the path of the pip

Install Dependencies

cd to the directory you clone this repo. If you didn't clone the repo, clone it first, then open it in terminal.
run pip install -r requirements.txt
done :)

Run the project with marimo

in your environment, do pip install marimo
run marimo edit [filename] --host 0.0.0.0 --port [num] to run the marimo file, an example is marimo edit newTest.py --host 0.0.0.0 --port 1234
do ssh port forwarding mentioned in Zulip group chat

MolloiLab/ce-coronary-artery