Institute of Nuclear Medicine


Open Source Software Packages at INM

Our research and its translation to practice relies on a considerable amount of software. We lead and contribute to several Open Source Software projects. This increases dissemination, collaboration and software quality.

We currently lead the following 3 projects:


STIR (http://stir.sourceforge.net/) is Open Source Software for tomographic image reconstruction [1]. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET and SPECT, but other application areas and imaging modalities can be added. STIR is written in C++ but its interface in Python and MATLAB is growing in functionality.

STIR is available since 2000 and has been developed at several institutions. It is used by many researchers world-wide and has more than 200 citations. At INM, we maintain STIR and of course also contribute to its development.


CCP PET-MR (http://www.ccppetmr.ac.uk/) is an EPSRC-funded Collaborative Computational Project (CCP) ( http://www.ccp.ac.uk/ ) in synergistic PET-MR image reconstruction, led by Dr Kris Thielemans. To enable researchers to develop and test new reconstruction algorithms for dual-modality imaging, we are developing a common software platform into 3D and 4D reconstruction of PET-MR data. This will be achieved by standardisation of data formats, creating tools to export data in these data formats, and interfacing to packages such as STIR (http://stir.sourceforge.net/ ) (and Gadgetron ( http://gadgetron.github.io/ ). Researchers can use the software via Python and MATLAB interfaces.


PETPVC (https://github.com/UCL/PETPVC) is software for Partial Volume Correction of PET images, but it can be used for other modalities as well. It was developed in collaboration with the Clinical Imaging Research Centre (Singapore) (https://www.circ.nus.edu.sg/).

In addition, we use many different Open Source packages, including

NifTK (http://cmictig.cs.ucl.ac.uk/research/software), a translational imaging platform developed by TIG/CMIC at UCL; the Insight Segmentation and Registration Toolkit (ITK) (https://itk.org/)and the Monte Carlo simulation packages GATE (http://www.opengatecollaboration.org/)and SIMIND (http://www.msf.lu.se/forskning/the-simind-monte-carlo-program).

[1] Thielemans K., Tsoumpas C., Mustafovic S., Beisel T., Aguiar P., Dikaios N., and Jacobson M.W., STIR: Software for Tomographic Image Reconstruction Release 2, Physics in Medicine and Biology, 57 (4), 2012 pp.867-883. http://dx.doi.org/10.1088/0031-9155/57/4/867