ITK-SNAP is a stand-alone software application used to segment structures in 3D medical images and other utilities [1] - http://www.itksnap.org/pmwiki/pmwiki.php.

Within CaPTk specifically, ITK-SNAP is tightly integrated as a tool used for segmentation, accepting files chosen through the CaPTk interface and returning results for further use within CaPTk. ITK-SNAP uses a combination of random forests and level sets to obtain precise segmentations of structures [1]. Please see the following video for detailed instructions: https://www.youtube.com/watch?v=-gBcFxKf-7Q

References:

1. P.Yushkevich, Y.Gao, G.Gerig, "ITK-SNAP: An interactive tool for semi-automatic segmentation of multi-modality biomedical images", Conf Proc IEEE Eng Med Biol Soc. 2016:3342-3345, 2016, DOI:10.1109/EMBC.2016.7591443.