Three new programs for serious science.

Recently added to I Do Imaging are three advanced programs: two image segmentation programs from a very productive collaboration in Vancouver, and a Matlab-based dynamic PET analysis package from Umeå University in Sweden.

TurtleSeg is an advanced 3D image segmentation program developed by a prolific team at Simon Fraser University and the University of British Columbia.  Employing a 3D Livewire algorithm named TurtleMap 3D, also developed by the same team, this program uses minimal interactive guidance to automatically perform and iteratively refine  a full 3D segmentation.  The concept is that the user, with Livewire assistance, generates a small number of nonparallel 2D contours on orthogonal or oblique planes, from which the program generates a dense set of parallel segmentation contours defining a full 3D volume.  As the segmentation progresses, the program can present the user with the plane to contour which would best assist the segmentation.  The results are shown in real time as a 3D rendering.  This is a very well-implemented program, with a thorough website offering documentation, including video guides, and a full manual.  TurtleSeg can read and write a wide range of commonly-used 3D file formats, can store and edit existing contours, and can export the segmentation as an image mask or surface mesh.  The program was developed as part of an MSc project and makes effective use of a wide range of free software, particularly the imaging toolkits ITK for segmentation and VTK for image processing and visualization, and also Qt for the graphical interface.  Using the program for the first time, and with minimal anatomical knowledge, I was able to perform an acceptable aortic segmentation within half an hour.  TurtleSeg is a particularly well-implemented project.

Another, more specialized program from the same collaboration is LiveVessel.  It is designed to perform 2D segmentation of vessels from colour photographs, in particular retinal images.  The development of the segmentation process and its underlying algorithm are described in two publications included in the program’s website.  To perform a segmentation, the user defines the start seed point and traverses the vessel with the mouse, while the application calculates the optimal path and boundaries of the vessel in real time. There’s a video on the site that shows how this process reduces the user input to about as minimal as it can be while still providing guidance. This program is written in a combination of Matlab scripts and MEX-files, which need to be compiled before use.  I was able to compile within Matlab on both Windows and Macintosh systems, however as LiveVessel uses the Signal Processing Toolbox, which I don’t have access to, I was unable to run the application.   LiveVessel looks to be a good implementation of a solution to a specialist need, and is well grounded in original research.

ImLook4D is a Matlab application for the analysis of dynamic PET scans, from Jan Axelsson in Sweden.  This is specialized software for a specialized application, and emphasizes the definition and analysis of volumes of interest over time (hence the 4D).  The program may easily be extended by means of drop-in Matlab scripts, and there are a large number of scripts provided with the program.  It’s also able to import and export its working set to the ImageJ environment for further analysis.  It has native capacity to read and write Dicom and ECAT files, as well as raw binary files.  If you work in the rather esoteric field of PET image analysis, you will be familiar with the features offered by this program.  It’s also quite likely that you are a user or programmer of Matlab, which makes this program doubly useful.