Cancer Imaging Phenomics Toolkit (CaPTk)
Segmentation Usage

Geodesic Segmentation

The geodesic distance based segmentation is a semi-automatic technique to generate masks for specific tissue types.


A single image with distinct boundaries for tissue needing to be segmented. [1]



ITK-SNAP is a stand-alone software application used to segment structures in 3D medical images and other utilities. 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 very precise segmentations of generic tissues [2]. Please see the following video for detailed instructions:


[1] B. Gaonkar, L. Shu, G. Hermosillo, Y. Zhan, Adaptive geodesic transform for segmentation of vertebrae on CT images. Conference Papers SPIE Medical imaging, 2014 (Oral)

[2] P. Yushkevich, Y. Gao, G. Gerig. ITK-SNAP: An interactive tool for semi-automatic segmentation of multi-modality biomedical images. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2016.