A CLI (command Line Interface) is a standalone executable file that can be run either directly or from within the Slicer application. We have developed a series of CLIs that encapsulates pipelines with advanced imaging functionalities. They can help both developers and clinicians to extract and analyze different lung phenotypes, and are mainly based on VTK, ITK and Teem libraries. 

The CLIs are distributed in 6 categories according to their functionality.

• Particles: High level tools that use algorithms based on particles to segment and clasify airways and vessels.
• Segmentation: Segmentationof different parts of the ling following our Chest Conventions.
• Registration: Lung registration tools.
• Processing: Processing tools that are usually required as a previous step for another higher level tools, but that can be used independiently.
• Quantification: Quantification of different general image statistics.
• Utils: Auxiliary tools that are used by different CLIs.