SIRF (Synergistic Image Reconstruction Framework) for Biomedical Imaging

The CCP (Collaborative Computational Project) in synergistic image reconstruction for biomedical imaging (SyneRBI), formerly known as CCP PET-MR (Collaborative Computational Project in synergistic PET-MR image reconstruction), project has led to the on-going development of the SIRF (Synergistic Image Reconstruction Framework) software, which is an Open Source toolkit for the reconstruction of PET and MRI raw data. The aim is to provide code simple enough to easily perform a reconstruction, yet powerful enough to be able to handle real, full-size datasets. Our strategy in achieving this aim is to employ available Open Source reconstruction software written in advanced programming languages such as C++ and provide basic-user-friendly interfaces to it written in script languages, primarily Matlab and Python. The interface style permits a reconstruction to be performed in stages, allowing the user to inspect or modify data, or insert their own code.

The code builds upon existing Open Source software packages for medical image reconstruction. At the outset, these packages are STIR for PET reconstruction, Gadgetron for MRI and NiftyReg for registration/resampling. SIRF provides MATLAB and Python interfaces to these underlying reconstruction engines. This is done by wrapping the engines in a C++ layer, and then placing a C-interface between the wrapped C++ engines and the MATLAB and Python interfaces.