Creating a Segmentation App Including Including Visualization with Clara-Viz

This tutorial shows how to create an organ segmentation application for a PyTorch model that has been trained with MONAI, and provide interactive visualization of the segmentation and input images with Clara Viz integration.

Setup

# Create a virtual environment with Python 3.10.
# Skip if you are already in a virtual environment.
conda create -n monai python=3.10 pytorch torchvision jupyterlab cudatoolkit=12.2 -c pytorch -c conda-forge
conda activate monai

# Launch JupyterLab if you want to work on Jupyter Notebook
jupyter-lab

Executing from Jupyter Notebook

• Creating a Segmentation App Including Visualization with MONAI Deploy App SDK
  • Creating Operators and connecting them in Application class
    • Setup environment
    • Download/Extract input and model/bundle files from Google Drive
    • Set up environment variables
    • Set up imports
    • Determining the Input and Output for the Model Bundle Inference Operator
    • Creating Application class
  • Executing app locally
    • app.py
    • __main__.py
  • Packaging app

Download 03_segmentation_viz_app.ipynb