OpenVessel

OpenVessel is an open-source Flask app that segments out portions of DICOM files using machine learning hosted on celery workers, and displays the result as a 3D objects using VTK.

DEMO

Installation

On Windows

Get the repository

git clone https://github.com/OpenVessel/Vessel-app.git

Make the Virtual Environment (Optional)

python3 -m venv vessel_env  
vessel_env\Script\activate   

Install requirements

pip3 install -r requirements.txt

Installing VTK

One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of DICOM files.

Directions to install VTK on Windows

Installing Redis

Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.

Directions to install Redis

Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.

Open config.py and find these lines

class Config: 

	...
	 
     ### Celery Workers ##########  
    CELERY_BROKER_URL='redis://localhost:6379/0'  
    CELERY_RESULT_BACKEND='redis://localhost:6379/0'

Change the redis://localhost:6379/0 to whatever port your Redis server is running on.

On MacOS

Get the repo

git clone https://github.com/OpenVessel/Vessel-app.git 

Make the Virtual Environment (Optional)

python3 -m venv vessel_env  
vessel_env\Script\activate   

Install requirements

pip3 install -r requirements.txt

Installing VTK

One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of dicom files.

brew install vtk

Installing Redis

Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.

Install Redis

brew install redis

Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.

Open config.py and find these lines

class Config:  

	...

     ### Celery Workers ##########  
    CELERY_BROKER_URL='redis://localhost:6379/0'  
    CELERY_RESULT_BACKEND='redis://localhost:6379/0'

Change the redis://localhost:6379/0 to whatever port your Redis server is running on.

Running the App

Initialize the database

We use Flask-SQLAlchemy to connect to our SQLite database, and Flask-Migrate by Miguel Grinberg to update the database as we make changes.

In order to run the Flask app you need to have a database. First make your current working directory the Back-end folder in the repo.

cd Vessel-app/vessel_app/Back-end

Run these commands to initialize the database.

flask db init
flask db migrate
flask db upgrade

Running the Flask app

Make sure you are in the Back-end directory then run

flask run

and the website will run on a local port for you!