Cancer Imaging Phenomics Toolkit (CaPTk)  1.9.0
Geodesic Distance Transform-based Segmentation

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].


  1. Load in CaPTk the image that you want to segment.
  2. Using Label 1 from the drawing tab, annotate a region of the tissue you would like to segment in the image.
  3. Launch the application using the 'Applications' -> 'Geodesic Segmentation' menu option.
  4. The mask is populated within ~5 minutes, showing the progress at the bottom right corner of CaPTk.
  5. The mask is visualized automatically in the visualization panels.
  6. You can revise the resulted segmentation mask (Label:1), by selecting the "Geodesic" preset and changing the "Threshold" at the bottom right corner of CaPTk.
  • This application is also available as with a stand-alone CLI for data analysts to build pipelines around, and can run in the following format:
    ${CaPTk_InstallDir}/bin/GeodesicSegmentation.exe -i C:/inputImage.nii.gz -m C:/maskWithOneLabel.nii.gz -o C:/outputImage.nii.gz -t 20