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Sunday, December 26th, 2010, 12:33 pm

Search for Cardiac Analysis Code

During the holidays I decided to see what else is out there which is already free/libre software like my own work, which thus can be merged for comparative purposes. It would be valuable to have applied to my work some comparison to existing tracking algorithms which deal with cardiac images. A decade-old paper from Osman et al. covers the very popular HARP and states in its abstract that it offers an “image processing technique for rapid analysis of tagged cardiac magnetic resonance image sequences.[...] Results from the new method are shown to compare very well with a previously validated tracking algorithm.” It’s not easy to gain access even to code samples of complete frameworks that facilitate benchmarking, so the search ascended to SourceForge. I uploaded some projects of mine to SourceForge about 8.5 years ago and hoped that others would do the same. A search in SourceForge for “cardiac” yields about a dozen results (at the time of writing), but there are empty entries in the code repositories where there ought to be complete projects. The Cardiac MR toolbox for Matlab, for instance, is an empty project:

[roy@blueberry cmr-toolbox]$ svn co cmr-toolbox
Checked out revision 0.
[roy@blueberry cmr-toolbox]$ ls
[roy@blueberry cmr-toolbox]$ cd cmr-toolbox/
[roy@blueberry cmr-toolbox]$ ls
[roy@blueberry cmr-toolbox]$

The same goes for Neonatal Rat Cardiac Action Potential, but the Evaluation of Cardiac MR Segmentation project (all of them written for MATLAB but ought to be compatible with Octave) contains some LGPL-licensed code. Repository access (SVN):

svn co cardiac-mr

Looking at MATLAB Central for some more existing code I find an old BSD-licensed function but almost nothing else when searching for “Cardiac”. Since the literature review phase and the subsequent finding of some data [1, 2, 3] there has been almost no room for code reuse, so I had to code everything from scratch. I will soon publish the code (GPLv3-licensed), but in a more scientific society more code would have already been out there for others to collaborate and build upon the work of others.

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