Open-source Informatics Tools for Radiotherapy Research

This is the companion website to the book chapter "Open-source Informatics for Radiotherapy Research," by Joseph Deasy and Aditya Apte, in the book "Informatics in Radiation Oncology," ed. George Starkschall and Alfredo ('Al') Siochi, CRC Press (2013)

Last updated:  October, 2013, by Joe Deasy, PhD. (deasyj mskcc org ; you know what to do).  We intend to update it at some unspecified frequency.  If you have suggested improvements, additions, or corrections, please email me.

This page lists radiotherapy-specific informatics tools and resources and a few more general image handling and statistical modeling tools.  General DICOM tools are referenced below, but are not the focus.

No fitness is implied for any of these tools for treatment-related data processing or decision making. 

Many of these tools are open-source and have widely varying quality.  This list is not meant to be comprehensive. 

DICOM-RT introduction pages

What is DICOM?  Here is a nice presence courtesy of Elekta:

Introductory course given by the Swiss Society of Radiobiology and Medical Physics (SGMP).  Informative slide sets are provided.

Last updated:  July 2003.

Structure of DICOM

DICOM for RT introduction by Andrew Reilly.  This pdf slide show gives examples of DICOM-RT troubleshooting as well as a list of useful tools (most are relisted here).

RT Plan structure

Law, M. Y. and B. Liu (2009). "Informatics in radiology: DICOM-RT and its utilization in radiation therapy." Radiographics 29(3): 655-667.  This is a useful short paper discussing the basics of Radiation Oncology information flow and DICOM-RT.  A figure from the paper:

RT workflow figure
      from Law and Liu, 2009.

General DICOM resource pages

A useful, brief, introduction to DICOM, as well as useful links, can be found at  "A single DICOM file contains both a header (which stores information about the patient's name, the type of scan, image dimensions, etc), as well as all of the image data (which can contain information in three dimensions)."

The Wikipedia DICOM page is very informative, at

A comprehensive of free radiology software (relevant to PACS, RIS, and DICOM) can be found at  

DICOM Servers/PACs

The Conquest DICOM project

Conquest is a full-featured DICOM server that handles DICOM-RT.  Marcel Van Herk and collaborators have developed and released Conquest as an open-source package.  The homepage is at  Conquest is actively supported.  Conquest has many features, including image format conversion, rules-based-forwarding, image viewing, archiving, compression, archive merging, series merging, etc.

Conquest server
      screen grab


ClearCanvas is an open-source PACs server, embedded within an application framework with a plug-in architecture.  The ClearCanvas viewer is entirely web-based (using the Microsoft silverlight viewer), with server-side image processing. The ClearCanvas image server can be downloaded from

According to the website, ClearCanvas can handle some RT-specific image data, but does not handle RT-plan files (i.e., the DICOM component with the beam apertures, etc.).

Some interesting plug-ins that extend ClearCanvas functionality are described at

Advanced plug-ins include tools for dynamic contrast enhanced imaging analysis.

Of note, ClearCanvas implements AIM, a standard for image annotation.  The homepage of AIM is at

The ClearCanvas

OSIRIX, an open-source DICOM PACs workstation and server

The home webpage is at  However, at this time OSIRIX does not support RT-specific data objects, such as dose distributions.  Also, the FDA-cleared version is (understandably) not free/open-source.  An OSIRIX app is available for the iPhone/iPad.  Here is a screenshot of the FDA-cleared version:



Tools to anonymize radiotherapy (DICOM-RT) data

The DICOMPiler

The DICOMPiler, developed by the Image Guided Therapy Center at Washington University in St. Louis, is a DICOM reciever that can be used to conveniently anonymize DICOM series for subsequent submission in research protocols.  The DICOMPiler can be found at   Helpful instructions on the use of the DICOMPiler can be found here.  CERR can also be used to anonymize data (see entry below.)


The DVTk project

DVTk is an open-source project to diagnose and validate DICOM traffic (DVTk: Dicom Validation Toolkit).  It has further developed high-quality DICOM-related applications, including an anonymizer, editor, and a viewer.  From the home page (  "DVTk is an open source project for testing, validating and diagnosing communication protocols and scenario's in medical environments. It supports DICOM, HL7 and IHE integration profiles."

DVTk webinar

Tools to manipulate radiotherapy data

CERR:  A Computational Environment for Radiotherapy Research.

CERR is a widely used open-source system, based on the Matlab platform, that has comprehensive tools for manipulating radiotherapy data.  CERR has extensive import/export, visualization, image registration, IMRT dose calculation, contouring, complication/control estimation tools, etc.  The CERR homepage is at  The CERR Wiki is at


The dicompyler

Dicompyler is an ambitious open-source software system, based on the widely used python language, that has many viewer and data analysis features.  In some ways, dicompyler parallels CERR.  The dicompyler homepage is at  Dicompyler has a flexible plugin architecture, and a convenient graphical view of DICOM inputs.

dicompyler dicom
      browser window


RT_Image is an open-source software package developed by Edward (Ted) Graves, of Stanford University, that provides fairly general RT image viewing and data analysis tools.  RT_Image can be downloaded from  RT_Image has particularly strong PET-image viewing and analysis tools, including image contouring, registration, adn segmentation tools, as it grew from those applications.


SlicerRT:  an open-source tool for radiotherapy data manipulation and processing built on Slicer.

Pinter, C., Lasso, A., Wang, A., Jaffray, D., & Fichtinger, G. (2012). "SlicerRT: Radiation therapy research toolkit for 3D Slicer". Medical physics, 39, 6332.

This paper was published just after the book chapter went to print.  Further information about this powerful package can be found at

Here is the a screen shot from the paper by Pinter et al.:
SlicerRT screen shot

Exporting/creating DICOM-RT structures

Gorthi S., Bach Cuadra M., Thiran J, "Exporting Contours to DICOM-RT Structure Set," The Insight Journal - 2009 January - June.  This paper and associated open-source code details methods for exporting structures in DICOM-RT format using ITK (see entry for ITK, below).

Medical Image viewing (general)

Slicer is an impressively comprehensive open-source, cross-platform, software tool for visualizing and manipulating medical image data.  Some RT related capabilities have recently been added.  There is a dicomRT import capability, that imports structures and doses, based on the plastimatch software system.  Slicer has been referenced in over 200 publications to date.

ITK, the Insight segmentation and registration ToolKit (ITK)

ITK is an extensive, stable, widely used open source toolkit developed by the National Library of Medicine to support image handling, analysis, registration and segmentation.  The ITK homepage can be found at

XiP:  the eXtensible Imaging Platform and DICOM WG-23

Ca-Big has sponsored the development of XiP, the eXtensible Imaging Platform.  XiP is a platform of opensource tools to perform rapid prototyping of medical image processing and visualization algorithms.  XiP utilizes an emerging protocol, DICOM WG-23 for Application Hosting Interfaces, which has the goal of a being a widely adopted architecture for plugins.  Thus, a researcher who writes a WG-23 compliant plugin could potentially transfer the plugin with little or no change to commercial systems that (hopefully) adopy the WG-23 standard.

Although XiP has great promise as a possible radiotherapy research platform, RT specific data elements, such as dose distributions, have not yet been implemented.

The ca-BIG home page of XiP is

The wiki for XiP is

A powerpoint presentation on XiP that also describes WG-23 is given at


Slicer, a powerful opensource system for image viewing and analysis.

The Slicer system is now widely used in various areas of image-based medicine.  The home page can be found at  SlicerRT, a package referenced above, was built using Slicer.  Slicer is deeply integrated with the ITK and VTK toolkits as well as many community contributed extensions.

Image Processing (general)


A particularly powerful image processing package is ImageMagick, the result of an ongoing open source project, containing a large library of image manipulation command-line routines.  ImageMagick can be found here


ImageJ is another powerful open-source image processing toolkit.  ImageJ, unlike imageMagick, can be used either as a library or as a stand-alone application.  Many plug-ins have been developed for imageJ.  The home page for imageJ is

Deformable Image Registration

Deformable image registration is a general technology, and many of the best tools are general.

Plastimatch ( is a deformable image registration system developed by Greg Sharp and collaborators at Massachusetts General Hospital/Harvard Medical School.

Statistical modeling (general) 

The R-language

There are many open-source statistical modeling packages for general use.  The most well-developed suite of tools has been developed around the R language, which was based on the Bell Labs product, S.  R contains a massive number of freely-available routines, written by many thousands of contributors.

The wikipedia entry for S is at

The official website of the R language is at

Radiotherapy dose response statistical modeling

DREES:  The Dose REsponse Explorer System.

Our group has developed a package to implement general model selection in the 'meso' modeling range (i.e. tens or hundreds of potential predictor variables, but not thousands or millions).

DREES, the Dose-REsponse Explorer System, implements multivariable logistic modeling building using cross validation techniques to test the stability of model selection.  It is open-source but written in the Matlab language.  DREES can be found at