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STIR Users' & Developers' Meeting

Dr Kris Thielemans & Dr Charalampos Tsoumpas

Thursday, 5 November 2015 from 18:30 to 20:30 (PST)

STIR Users' & Developers' Meeting

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STIR event Ended Free  

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Event Details

STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on image reconstruction in emission tomography (PET and SPECT) but other imaging modalities can be added in the future. During this annual meeting experienced users and developers will present their recent work with STIR with the emphasis on software and algorithmic development. Additional time will be allocated for discussion between the speakers and the audience. 

The event is free but priority will be given to those that have reserved, as only limited space is available. For additional information please visit STIR website: We may have some food available if we find  sponsorship.



18.30 Opening 

18.35 Custom input file format class for reading arbitrary crystal positions into STIR by Jannis Fischer (ETH Zürich)

Abstract: In the SAFIR project, a high-rate capable preclinical PET insert is developed. Simulations of different geometries were performed using Geant4. Images are reconstructed using STIR, which has been extended by classes to read crystal positions from a text file to quickly reconstruct data from any of the approximately cylindrical crystal arrangements. It is planned to later implement an integration into the ray-tracing algorithm for better matching the scanner geometry in the actual iterative reconstruction.


18.55 Using an External Optimization Algorithm for PET reconstruction with STIR in MATLAB by Yu-Jung Tsai, Matthias J. Ehrhardt and Kris Thielemans (UCL)

Abstract: Calling STIR from MATLAB makes the library more flexible. With efficient STIR functionalities and robust MATLAB toolboxes, quick prototyping can be achieved for evaluating new reconstruction algorithms or analyzing methods. In this presentation, we are going to give an example of how to combine STIR projectors with an open source optimization algorithm, namely L-BFGS-B (limited-memory Broyden-Fletcher-Goldfarb- Shanno with boundary constraints). It will be concentrated on practice and will not include too much background about the algorithm. The users should be able to deal with any algorithms available in MATLAB using similar steps.


19.15 Incorporation of a two metre long PET scanner in STIR by Charalampos Tsoumpas, Christopher Brain and Thomas Dyke (Uni. Leeds)

Abstract: This investigation incorporates a total-body 2 metre long PET scanner in STIR library and demonstrates the capabilities and weaknesses of FBP and OSEM reconstruction and single scatter simulation algorithms. It was found that sensible images are reconstructed but at the expense of high memory and processing time demands. FBP requires 4 hrs on a single core; OSEM (MPI-version): 2 hrs per iteration if ran in parallel on 15-cores of a high performance computer. The single scatter simulation algorithm shows that on a short scale, up to a fifth of the scanner length, the assumption that the scatter between direct rings is similar to the scatter between the oblique rings is approximately valid. However, for more extreme cases this assumption is no longer valid, which illustrates that consideration of the oblique rings within the single scatter simulation will be necessary, if this scatter correction is the method of choice.


19.30 New features in STIR 3.1 and future developments by Kris Thielemans (UCL)

Abstract: This talk gives an overview of the new features in the 3.1 release (currently in testing phase), including OpenMP support for multi-core machines, Maximum-Likelihood estimation of normalisation factors and randoms for PET. This release will also include support for Siemens mMR data. We will also discuss the future of STIR and its connection with the software of the CCP for Synergistic PET-MR Reconstruction (


20.00 General Discussion & Closing

Do you have questions about STIR Users' & Developers' Meeting? Contact Dr Kris Thielemans & Dr Charalampos Tsoumpas

When & Where

Town & Country Hotel
500 Hotel Cir N
San Diego, California 92108

Thursday, 5 November 2015 from 18:30 to 20:30 (PST)

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Dr Kris Thielemans & Dr Charalampos Tsoumpas

Kris Thielemans is a Reader at University College London (UCL) and is an IEEE senior member. He received his Ph.D degree in String Theory from KU Leuven in 1994. Prior to UCL, he has been working as a Researcher at Hammersmith (London, UK) for the Medical Research Council and General Electric, and at King’s College London (KCL). His research interests encompass all aspects of quantitative PET image reconstruction with emphasis on the development of advanced reconstruction techniques for PET and SPECT including motion correction. He developed along with others STIR which has been cited more than 250 times.


Charalampos Tsoumpas is a Lecturer in Medical Imaging at the University of Leeds since 2013 and Visiting Assistant Professor at Icahn School of Medicine at Mount Sinai since 2014. He received his Ph.D. degree in Parametric Image Reconstruction from Imperial College London in 2008 and worked as a post-doctoral fellow at KCL on PET-MR. He is a Senior Member of IEEE and Fellow of Higher Education Academy. He has contributions in more than 40 peer-reviewed papers, 20 IEEE conference records and two patents with GE Healthcare. His research interests include statistical iterative image reconstruction and acquisition system modelling for more accurate and precise PET and PET-MR imaging. 

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