RT-UTILS: A minimal Python library for RT Struct manipulation

RT-Utils has been developed to allow physicians and other users to view the results of segmentation performed on a series of DICOM images. It allows you to

  • create or load RT Structs,
  • extract 3d masks from RT Struct ROIs,
  • easily add one or more regions of interest, and
  • save the resulting RT Struct in just a few lines!
  • merge two existing RT Structs to one file.

How it works

RT-Utils provides a builder class to faciliate the creation and loading of an RT Struct. From there, you can add ROIs through binary masks and optionally input the colour of the region along with the region name.

The format for the ROI mask is an nd numpy array of type bool. It is an array of 2d binary masks, one plane for each slice location within the DICOM series. The slices should be sorted in ascending order within the mask. Through these masks, we extract the contours of the regions of interest and place them within the RT Struct file. Note that there is currently only support for the use of one frame of reference UID and structured set ROI sequence. Also note that holes within the ROI may be handled poorly.

RT-UTILS was developed by Asim ShresthaAdam WatkinsKevin Lam and Carlos Uribe at QURIT Lab at the University of British Columbia.

Github Website

Readme (Users Guide)

Installation Guide

RT-Utils is a tool designed to allow users to easily view the results of machine learning models performing tasks like image segmentation on medical image data.

Asim Shrestha,
Full Stack Developer Intern (2021-2022)
QuritLab, University of British Columbia (UBC),
British Columbia Cancer Research (BCCR),
Vancouver, BC, Canada

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