Exchange Programme

Funded researcher exchange scheme

The CCP in synergistic reconstruction for biomedical imaging has funding to facilitate the exchange of staff and students between institutions, one of which must be a UK institution. Proposals are invited for full or part funding to enable the short term (up to 2 weeks) exchange of students and early career researchers (ECR). Such exchanges should further the aims for the CCP as detailed on the website. Proposals for exchanges should be submitted to David Atkinson or Julian Matthews and should include:

• A description of the purpose, the activities planned, and how the exchange will benefit the CCP (1 page max).
• A short CV of the student or postdoctoral researcher.
• The costs being requested with justification (1 page max).
• A PDF letter or email of support from the host institution.
• A PDF letter or email of support from the student’s supervisor or postdoctoral/ECR researcher’s line manager.

Ideally you should allow for 6-8 weeks from your request to notification of the funding decision. Following your visit we will ask you for a short report including a statement of outcomes for dissemination to the EPSRC as a case study and possible website publication.

Successful applications MUST submit the report within 2 months after the visit

Funded internship opportunities

Internships Funded by the CCP SyneRBI. We have launched some potentially funded internship opportunities for scientists based in the UK or abroad. If interested, please directly contact the corresponding person.

Host: Dr Matthias Ehrhardt, University of Bath (me549@bath.ac.uk)
Topic: Advanced Image Reconstruction with Machine Learning Training Algorithms
Summary: Image reconstruction is usually formulated as an optimization problem. Mathematically these are challenging since they are large-scale and may be nonsmooth. Similar problems are encountered in machine learning which has boosted research in this direction over the last decade. In this project we want to study algorithms invented for machine learning in the context of tomographic image reconstruction.

Host: Dr Daniel Deidda, National PhysicalLaboratory, Teddington, UK (daniel.deidda@npl.co.uk)
Topic 1: implementing vendor specific calibration factors
Calibration functionality has recently been implemented into the STIR library for both SPECT and PET. Every vendor however may have a different way to save calibration information in the raw data. This project aims at the implementation of reading functionality of calibration factors for any possible Scanner (examples: Siemens mMR/mCT, GEsigna etc.)

Topic 2: Parallelisation of SPECT reconstruction
SPECT image reconstruction is available in STIR, however reconstruction of real data with full PSF modelling is currently time demanding. A Github branch that attemps to make SPECT reconstruction faster using open MP is available but not complete. This project aims at the parallelisation of SPECT image reconstruction using previous code as starting point.

Opportunities specifically for scientists based in the UK who wish to visit overseas centres (note that visa restrictions may apply):

Host: Dr Christoph Kolbitsch, PTB, Berlin, Germany (Christoph.Kolbitsch@ptb.de)
Topic 1: Temporal regularisation 
For the reconstruction of motion resolved images or for dynamic images showing contrast changes after injection of a contrast agent temporal regularisation can utilise the data redundancy between different dynamics. The aim of the project would be to extend existing spatial regularisation along a dynamic dimension.

Topic 2: GPU-acceleration 
Gadgetron offers the possibility of GPU-acceleration for non-Cartesian MR image reconstruction. The aim of this project would be to extend the current MR acquisition models to be able to use this acceleration.

Host: Professor Charalampos Tsoumpas, University Medical Center Groningen, Netherlands (c.tsoumpas@rug.nl)
Topic 1: Integrate Siemens Biograph Vision Quadra PET/CT scanner in STIR library
At UMCG we have recently installed a long axial field of view PET scanner that can acquire high quality PET imaging. STIR library is an open access software package that can reconstruct data acquired from various PET scanners, but it is not updated for the Siemens Biograph Vision Quadra PET/CT scanner. This project aims to incorporate the scanner in the open-source package so that image reconstruction and associate corrections are possible and comparable to the images as produced by the scanner’s reconstruction software.

Topic 2: Integrate MR Solutions PET-MRI scanner in STIR library
At UMCG we have recently installed a preclinical PET-MRI scanner that can acquire simultaneous images from both PET and MRI. STIR library is an open access software package that can reconstruct data acquired from various PET scanners, but it is not updated for this specific PET-MRI scanner. This project aims to incorporate the scanner in the open-source package so that image reconstruction and associate corrections are possible and comparable to the images as produced by the scanner’s reconstruction software.

Successful Grant Reports

Exchange at Department of Nuclear Medicine & Molecular Imaging, University Medical Center Groningen, University of Groningen, Jan-Apr 2025 by Aparna Jayaraj, PhD Physics, School of Physics and Astronomy, University of Edinburgh Scatter Correction for Long Axial Field of View PET Scanners in STIR Library Report Aparna Jayaraj, PhD Physics, School of Physics and Astronomy, University of Edinburgh The Single Scatter Simulation (SSS) method implemented in Software for Tomographic Image Reconstruction (STIR) was originally designed for scanners with a short axial field of view (aFOV) [1, 2]. This implementation is limited to estimating scatter in direct planes and approximates scatter from oblique planes by nearest-neighbour interpolation, which is an inaccurate approximation for LAFOV PET systems. In LAFOV scanners, scatter contributions from oblique planes become significant, and the scatter distribution varies with both the axial length and the axial angle of the system. SSS doesn’t model multiple scatters or scatter originating from outside the FOV. Explicit 3D modelling would improve accuracy but requires substantial computation time and extensive tail fitting, often limited by poor statistics in high attenuation regions. In total-body PET scanners, accounting for both direct and indirect Lines of Response (LORs), makes scatter estimation computationally intensive, requiring careful upsampling and scaling strategies. The primary objective of this exchange project is to extend the SSS method for LAFOV PET scanners with a focus on speed, accuracy and memory effeciency. In the long term, the goal is to develop the scatter correction method for time-of-flight (TOF) PET scanners with LAFOV.	Full pdf report
Exchange at University Medical Centre Groningen (UMCG), Groningen, Netherlands, Nov 2023 – Jul 2024, by Viet Dao, University of Leeds, Leeds, UK. Summary The primary aim of this project was to successfully read and utilise listmode data from the Siemens Biograph Vision and Siemens Biograph Vision Quadra scanners. Using phantom or patient data from the University Medical Centre Groningen, the goal was to generate data necessary for developing motion detection and motion tracking algorithms. One potential candidate for motion detection explored was Bottom-Up Segmentation (BUS), which could be used with listmode data to achieve high temporal and spatial resolution in motion detection.	Full pdf report.
Exchange at University College London, UK, 18 Sep 2023 – 17 Mar 2024, by Tommaso Ferri, Politecnico di Milano, Milan, Italy. Summary Traditional X-ray radiotherapy is increasingly being sidelined by high-energy charged particle irradiation techniques…	Full pdf report.
Exchange at University College London, UK, 13 Nov – 12 Dec 2022, by Matthew Strugari, Dalhousie University, Halifax, NS, Canada. Summary Initially written for support of PET and MR data…	Full pdf report.
Exchange at University College London, UK, 20 Jan – 3 Apr 2020, by Eric Einspanner, UKL, Leipzig, Germany Summary Due to comparatively long measurement times…	Full pdf report.
Exchange at University College London, UK, 7-24 Nov 2019, by Harry Marquis, School of Physics, University of Sydney (USYD), Sydney, Australia Summary The purpose of the research exchange visit…	Full pdf report.
Exchange at University College London, UK, 25 October – 12 December 2018, by Ashley Gillman, CSIRO and University of Queensland, Brisban, Australia. Summary This exchange was co-funded by CCP PET-MR and CSIRO…	Full pdf report.
Exchange at University College London, UK, July-August 2018, by Johannes Mayer, Physikalisch-Technische Bundesanstalt (PTB), Berlin, Germany Summary The purpose of the exchange was the integration…	Full pdf report.
Exchange at University College London, UK, July-September 2018, by Ashley Gillman, CSIRO and University of Queensland, Brisban, Australia. Summary Due to the distance travelled…	Full pdf report.
Exchange at University College London, UK, 17 October 2017, by Palak Wadhwa, University of Leeds. Summary This exchange programme was proposed to contribute…	Full pdf report.
Exchange at the Medical Imaging Research Center, KUL, Leuven, Belgium, 18–30 April 2017, by Yu‑Jung Tsai Summary The main intention of the visit…	Full pdf report.
Exchange at the Frédéric Joliot Hospital (SHFJ), CEA Orsay, France, by Ottavia Bertolli, 12 January 2017 Summary The purpose of the exchange was…	Full pdf report.
Exchange at UCL Daniel Deidda, Q1 2016 Summary The purpose of the exchange programme…	Full pdf report.