MRI Viewer

A web application for analyzing and visualizing VTI files.

Created for the Institute for Clinical and Experimental Medicine in Prague, Czech Republic.

Powered by Trame, VTK, and Vuetify.

Features

• Upload, manage, and render .vti files
• Slice data in different orientations and positions
• Pick points and cells to see the values of data arrays in them
• Zoom, translate, and rotate data
• Play sequences of .vti files
• Switch between files
• Switch between data arrays
• Switch between representations (points, slice, surface, surface with edges, and wireframe)
• Switch between color maps (cool to warm and grayscale)
• Switch between languages (Czech and English only)
• Switch between dark and light themes
• Read the user guide directly in the web application
• and more...

Docs

User documentation is available here.

Technical documentation is available here.

Installing

1. Create a virtual environment:

python -m venv .venv

2. Activate the virtual environment:

source ./.venv/Scripts/activate

3. Install packages:

pip install -e .

Running

1. Run as a web application:

mri-viewer

2. Run as a desktop application:

mri-viewer --app

3. Run in JupyterLab:

pip install -r ./jupyter/requirements.txt
jupyter-lab

Docker

1. Build the image:

docker build -t mri-viewer .

2. Run the Docker container:

docker run -it --rm -p 8080:80 -v mri-viewer-deploy:/deploy mri-viewer

Instead of creating a named volume with -v mri-viewer-deploy:/deploy, you can mount the ./docker directory from the git repository to /deploy in the container using -v ./docker:/deploy.

3. Open the web application in your browser: http://localhost:8080