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Software Resources

This page will contain links to information on image viewing and image processing software. This will (eventually) include information about freeware applications that are known to be useful, as well as in-house software. Users are encouraged to edit existing information and to add information about their own favorite tools.

Wright Group


The OCCIviewer imaging platform was developed by the Tech Office of the Ontario Consortium of Cardiac Imaging. The latest version (1.1) is available for Windows and Linux. Primarily intended for cardiac imaging, it also has features for DICOM reading, 3D display, thin-plate spline warping, multiple ROI stats, & image filtering. Developers can extend it with the plugin SDK.


Vurtigo (external link) is a real-time 3D visualization platform for guiding interventions. It is written in C++ using Qt and VTK. Vurtigo is currently under active development with the primary use case being the guidance of cardiovascular interventions in the MR scanner. Install packages for the latest release 2.0 are available for Ubuntu Linux 10.04 and 11.10 and Mac OSX 10.6+ from our Downloads page (external link).

Martel Group


  • SedeenViewer. Although it can be used as a general purpose image viewer, it has been designed for viewing digital microscopy images. It has the ability to load and overlay multiple images with independent opacity settings for the purpose of manual registration. It also provides tools for automated registration, segmentation, and markups including regions of interest and annotations.

Registration Tools

  • Rig2d. A general purpose tool for 2D rigid registration. This is based on the ITK registration library and provides a configuration file which allows the transformation, optimiser, similarity metric and other parameters to be modified without having to recompile code.
  • Rig3d. A general purpose tool for 3D rigid registration. 3D version of Rig2d.
  • Stacker. A 2D rigid rgistration tool for aligning serial sections.
  • Volumizer. Converts a series of 2D images into an Analyze 7.5 (or MetaImage) volume.

Compression Tools

  • Tiffcrop. Converts or crops TIFF (or Big-TIFF) images created by TissueScope?.
  • Sedeen Viewer. A JPEG-2000 image viewer with TIFF (or Big-TIFF) support.

Statistical Tools

  • GMM. A Gaussian mixture model (GMM) package for statistical data modeling.
  • KMeans. A K-Means? package for statistical data modeling.

MRI Bias Correction

  • Pabic. An algorithm for estimating the bias field in MR images.
  • N3. An implementation of the N3 algorithm for estimating the bias field in MR images.

Validation Tools

  • Hausdorff. Calculates the Hausdorff distance for two binary masks.
  • MDCP. Calculates the mean distance to closest point (MDCP) for two binary masks.
Please contact Danoush for more details of the Martel group software.

Licensed software

  • IDL (Interactive Data Language). This is an image processing package similar to MATLAB. Licences are currently held by various groups and are administered by Research Computing.

Freely available downloads

  • MRIcro. This package is geared towards neuroimaging but is also a useful medical image viewer that provides support for Analyze and DICOM images. It is written and supported by Chris Rorden at the University of South Carolina (external link)
  • CImg (external link). An open-source utility library for image i/o implemented as a series of templates stored in a single header file. Includes native support for uncompressed graphics formats including, among others, BMP, TIF, GIF and Analyze7.5. Capabilities can be extended with external packages such as XMedCon (external link) for DICOM image handling and ImageMagick (external link) for compressed image formats (JPG, etc.).

Created by: amartel Last Modification: Thursday 22 of March, 2012 07:03:45 EDT by labonny

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