Overview

The Vizgen Post-processing Tool vpt accepts two types of inputs to specify how to run segmentation:

• Command line arguments

• Segmentation algorithm .json file parameters

Command line arguments generally relate to properties of the computing platform running vpt and are expected to vary with each experiment. For example, the location of files and optimal number of parallel processes depend on the computer running vpt and are set with command line arguments. These arguments are described in the Command Line Interface section.

In contrast, the segmentation algorithm .json file describes a series of steps to perform on the input data that are independent of the computing environment. Using the same segmentation algorithm on a series of experiments ensures that they are processed identically and reproducibly.

In addition to this documentation, several working example segmentation algorithm json files are provided that can serve either as a ready-made segmentation definition, or as a template for a custom workflow. These files are available on the vpt GitHub Repository (https://github.com/Vizgen/vizgen-postprocess) or in the Docker Image.