Docker Image

In order to support a completely reproducible analysis environment, Vizgen provides a Docker image of the Vizgen Post-processing Tool vpt that can be deployed locally, in a high-performance compute (HPC) environment, or in the cloud. The docker image contains vpt and all dependencies, as well as:

  • Nextflow

  • AWS CLI v2

  • Example segmentation algorithm json files

  • Simple Nextflow pipeline suitable for deploying vpt in a HPC environment

The docker image may be downloaded using docker pull:

docker pull vzgdocker/vpt
Python Package Index

The Vizgen Post-processing Tool vpt is available as a Python package. The package may be installed using pip:

pip install vpt[all]

The functionality of vpt requires the following system libraries:

  • libgl

  • libvips (version >=8.12)

These libraries are available on Windows, MacOS, or Linux. Development and testing of vpt is done using Ubuntu 22.04. Users encountering difficulty installing the Python package in their local environment are encouraged to try the Docker distribution.


The Vizgen Post-processing Tool vpt may be installed from source code by cloning the GitHub Repository and installing using poetry:

git clone
cd vizgen-postprocessing
poetry install --all-extras
Post-Install Verification

After installation, users can verify that vpt is properly configured by running:

vpt --help

If vpt was installed through poetry or in a virtual environment, the environment may need to be activated. For example:

poetry run vpt --help