Cancer Imaging Phenomics Toolkit (CaPTk)  1.3.0
Segmentation Usage

Overview | Pre-Processing | Interaction | Segmentation | Quantitative Imaging Feature Panel | Specialized Applications | Stand Alone CLIs

Segmentation applications

Geodesic Distance Transform based

The geodesic distance transform based segmentation is a semi-automatic technique to delineate structures of distinct intensity.

REQUIREMENTS: A single image with distinct boundaries for the structure that needs to be segmented. [1]


  • Using Label 1 from the drawing tab, annotate a continuous region of the tissue you would like to segment in the image.
  • After that, select "Geodesic Segmentation" from the Applications menu.
  • The mask is populated within ~5 minutes.
  • This application is also available as with a stand-alone CLI for data analysts to build pipelines around.


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 precise segmentations of structures [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 (Oral), 2014
[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

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