Slicer CLI

3D Slicer, the free and open-source software package for image analysis and visualization, developed in part by Kitware, has seen recent changes that enhance its flexibility, scalability, and ease-of-use. After significant improvements to extension/plugin support in 2012, a major step completed this year is the CLI AutoRun feature.

The Command Line Interface (CLI) model provides a simple mechanism for incorporating command line programs as Slicer modules. These command line modules are self-describing, emitting an XML description of its command line arguments. Slicer uses this XML description to automatically construct a Graphical User Interface (GUI) for the module.

CLI AutoRun

In order to give more interactivity to Slicer, an “AutoRun” button has been added to all the CLI modules:

When enabled, AutoRun allows CLI modules to be automatically executed:

  • Anytime a parameter is changed: Searching for the best parameter combination within the parameter space of an algorithm can be somewhat labor intensive. By instantaneously running the CLI module as soon as a parameter is changed by the user, Slicer becomes much closer to the WYSIWYG (What-You-See-Is-What-You-Get) interface.
  • Anytime an input data is being modified: This new feature opens up a wide variety of interesting possibilities. For example, a pipeline of filters can now be created such that changes to any input data are automatically propagated downstream by triggering the execution of the pipeline filters.

The following short presentation illustrates a few use cases for the AutoRun feature:


Slicer AutoRun demo on vimeo


AutoRun is already available in the nightly builds of Slicer, and will be part of the next Slicer 4.3 release. Stay tuned for the release announcement!

This work was supported in part by the Air Force Research Laboratory, under Contract No. D22009D10.

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