Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

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 (

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 (

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 (

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 (

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

Report for Exchange programme at UCL Daniel Deidda, Division of Biomedical Imaging and Department of Statistics, University of Leeds: Q1 2016

Abstract: The purpose of the exchange programme was to process and reconstruct list-mode data acquired from the Siemens PET-MR scanner as processing data from a PET-MR scanner is not straightforward, generally due to the incompatibility between the format of the scanner and the user software. In addition, Reconstruction taking into account attenuation, normalisation, random and scatter effects is an essential step. During the visit to UCL the main achievements were: that all necessary datasets are now readable; a script now exists for di erent reconstruction algorithms; and that reconstructions were successfully performed creating a range of images. We plan to make this script available to other users of the Siemens PET-MR scanner.

Full pdf report. 

Report for Exchange programme at the Frédéric Joliot Hospital (SHFJ) at CEA, Orsay, France by Ottavia Bertolli University College London January 12, 2017

Summary: The purpose of the exchange was to become familiar with the data acquisition process with the GE PET-MR system and with the use of the respiratory tracking device currently utilized in the centre (that is a pressure belt), and to acquire patient data with MR sequences that could allow the detection of an MR navigator (as representative of the internal respiratory motion of the organs). Moreover, data acquired with the GE PET-MR scanner were meant to be used as test datasets for the utilization of a feature of the STIR code, that allows the user to unlist the listmode files into sinograms (after the recent addition of the scanner to the library).

Full pdf report.

Report for Exchange programme at the Medical Imaging Research Center, Katholieke Universiteit Leuven (KUL), Leuven, Belgium, 18-30 April 2017, by Yu-Jung Tsai, a PhD student of UCL, London, UK

Summary:The main intention of the visit was to explore the use of a spatially variant penalty strength in penalized image reconstruction using anatomical information. As Parallel Level Sets (PLS) has shown promising results in literature, it was chosen to be incorporated into the previously proposed preconditioned algorithm (L-BFGS-B-PC) for achieving both good image quality and fast convergence rate. Since the penalty function has been well-studied by the host group, the other purpose of this exchange was to learn from their knowledge and experience on parameter optimization for PLS. The software developed (on top of STIR) during the visit can be used as a starting-point for integration into the CCP PETMR software which would allow users to utilize PLS with anatomical information derived from MR images during PET reconstructions. During this visit I interacted with several members of the group of Prof. J. Nuyts, most intensively with Dr Anna Turco and Dr Georg Schramm. In addition to helping me build up essential knowledge for the proposed joint project, they also provided plenty information regarding live in the center and the city so that I could get used to the new environment quickly and have a productive visit.

Full pdf report.

Report for exchange programme at University College London, UK, 17 October 2017, by Palak Wadhwa, University of Leeds.

Summary: This exchange programme was proposed to contribute towards the current devel-opments in Synergistic Image Reconstruction Framework (SIRF) to read and reconstruct positron emission tomography (PET) raw data from GE SIGNA PET/magnetic resonance (MR) scanner. There were three main challenges that were faced during PET data reconstruction with SIRF for real data produced by GE SIGNA PET/MR scanner prior to this exchange programme. These challenges included:
1. Random data correction: Randoms correction could not be carried out for the data acquired by GE SIGNA scanner.
2. Rotated images: There was a view angle o set between GE reconstructed image and SIRF for reconstructed images.
3. Time of Flight (ToF) reconstructions: Reconstructions with recent ToF code (to be included in SIRF) for real phantom data from the scanner was not validated. This ToF code will allow SIRF users to be able to reconstruct real ToF-PET data from GE SIGNA PET/MR (a scanner with 390 ps timing resolution) with all data corrections.
This visit was aimed to resolve all the above challenges. Additionally, PET/MR datasets were acquired using VQC calibration phantom provided by GE with GE SIGNA scanner located at Imanova, UK with the help of Dr. Gaspar Delso. This VQC phantom data was used to validate the rotation angle between GE and STIR. The dataset was also used to validate the random correction after the code was included in STIR. This dataset will prove to be bene cial for PET and MR data alignment that will be included within SIRF and will be made open source via Dementia Platform United Kingdom (DPUK). Another dataset with 2 GE-68 spheres as discussed in section 2.2, was collected at Imanova and this was used to validate the ToF code as discussed later in this report. Finally, all the code-based developments and outcomes of the visit are aimed to be available within SIRF as a part of this exchange programme.

Full pdf report.

Report for exchange programme at University College London, UK, July-September 2018, by Ashley Gillman, CSIRO and University of Queensland, Brisban, Australia.

Due to the distance travelled for this exchange, it was decided that the exchange should take place
between multiple host facilities and over a longer period of time, in this case two months, than
typical CCP PETMR Exchanges. Additionally, due to the extra cost, the exchange was funded by
CSIRO, CCP PETMR and University of Queensland. The project was originally divided between
two projects, which became four projects during the exchange. These were: implementing HKEM
into STIR and SIRF; developing a motion modelling technique to capture discontinuous lung
motion; developing PET data-driven head motion estimation techniques; and implementing
geometrical awareness and consistency into STIR and SIRF. Due to the increased scope of work
and limited time, all projects require some additional work for completion. However, this was a
worthwhile trade-off, as the benefit from the short time on exchange was maximised.

Full pdf report.

Report for exchange programme at University College London, UK, July-August 2018, by Johannes Mayer, Physikalisch-Technische Bundesanstalt (PTB), Berlin, Germany

The purpose of the exchange was the integration of a numerical simulation framework for dynamic PET-MR data into the Synergistic Image Reconstruction Framework (SIRF).
The exchange was part of a larger effort to implement a simulation framework able to produce MR and PET rawdata in a format which makes simulation results compatible with standard image reconstruction packages such as SIRF. In addition, the simulation framework should also provide ground truth motion information on the displacement of organs due to respiratory and cardiac motion to validate image registration and motion correction methods.
After implementing the MR part of the framework at PTB, Berlin, the simulation was able to simulate the MR acquisition process. The goal of the exchange was to integrate the PET rawdata simulation and to design and implement the software structures to simulate dynamic processes (e.g. respiration, heart beat, contrast uptake) for both modalities.

Full pdf report.

Report for exchange programme at University College London, UK, 25 October - 12 December 2018, by Ashley Gillman, CSIRO and University of Queensland, Brisban, Australia.

This exchange was co-funded by CCP PET-MR and CSIRO.
In this exchange, I aimed to achieve four primary goals: to make progress on (1) the development of an automated pipeline for PET reconstruction from raw data extracted from the scanner through to reconstructed equivalent to manufacturer DICOM output; to (2) apply the recently integrated HKEM technique in STIR/SIRF to a larger dataset in order to determine its effectiveness in a 18F-Florbetaben study; to (3) learn from UCL’s experience in kinetic modelling of dynamic PET for use at CSIRO; and finally, to (4) develop the work to be presented at MIC on PCA motion regression to be expanded into a journal publication. Given the broad scope of work to be achieved, most of the visit was spent developing plans and preliminary implementations of the intended products, and work will be continued by myself in Australia.

Full pdf report.

Report for exchange programme at University College London, UK, 7-24 Nov 2019, by Harry Marquis, School of Physics, University of Sydney (USYD), Sydney, Australia

The purpose of the research exchange visit to UCL was to familiarise myself with the
algorithms developed within the CCP PET-MR for PET reconstruction with MR sideinformation,
and to investigate PET-MR synergistic reconstruction using the SIRF software.
Another purpose of this visit was to see if these algorithms could be extended to SPECT
reconstruction using PET side-information as a potential method for Partial Volume
Correction (PVC) in theranostic PET/SPECT studies, for improved activity estimates in small
lesions in the reconstructed SPECT image.

After attending the SIRF conference/symposium in Chester I headed down to London to
begin my research exchange visit to UCL. The first few days of my visit was spent setting up
SIRF and STIR natively on my Macbook so that I could begin testing and debugging the
implementation of anatomical priors using the algorithms developed within the CCP for PETMR.
Once I had STIR and SIRF installed on my laptop I started investigating PET and
SPECT reconstruction using Daniel Deidda’s Hybrid Kernelised Expectation Maximisation
(HKEM) algorithm developed for PET reconstruction using MR side-information as an
anatomical prior. A few bugs and potential improvements were discovered throughout my
investigations; this led to several Github issues raised as well as suggestions for future
additions and alterations to the HKEM algorithm implemented in STIR.

Since my visit to UCL I have been using the HKEM algorithm in STIR to investigate the
potential of PET-SPECT synergistic reconstruction for the theranostic pairing Copper-64
(Cu-64) PET and Copper-67 (Cu-67) SPECT as a method for PVC; using clinical data from a
meningioma cohort. The initial results have been very promising and has led to an abstract
submission to the SNMMI 2020 conference: “SPECT/CT-based Dosimetry in PRRT: Using
Theranostics to Minimise the Impact of the Partial Volume Effect”.

Full pdf report.

Report for exchange programme at University College London, UK, 20 Jan - 3 Apr 2020, by Eric Einspanner, UKL, Leipzig, Germany

Due to comparatively long measurement times in PET/MR imaging, patient
movements during the measurement are likely. These lead to artefacts which
have a negative impact on the visual assessment and quantitative validity of
the image data and, in the worst case, lead to misinterpretations. Simultaneous
PET/MR systems allow the registration of movements and enable correcting
the PET data.
In order to assess the effectiveness of the motion correction methods, it is necessary
to carry out measurements on phantoms that are reproducible moved. For
this purpose an experimental setup was developed for specific movements during
my master thesis in Germany. Due to a cooperation between Leipzig (UKL) and
London the data I measured during my master thesis could be used. An MR-compatible
robotic system (Innomotion by INNOMEDIC GmbH) was used to
generate rigid movements of a brain-like phantom acquired on a Siemens mMR.
Different motion estimates were compared with the robot-induced motion.

Full pdf report.

Report for exchange programme at University College London, UK, November 13 - December 12, 2022, by Matthew Strugari, Department of Physics and Atmospheric Science,
Dalhousie University, Halifax, NS, Canada

A pinhole-SPECT library was successfully integrated and released in STIR v5.1.0 on January 14, 2023, making it the first open-source code available for reconstructing pinhole-SPECT datasets. SIRF was subsequently expanded in v3.4.0 by adding a PinholeSPECTUBMatrix acquisition model to allow for the use of SIRF’s advanced optimization algorithms when reconstructing pinhole-SPECT data. The extension of SIRF was successfully tested with a proof-of-concept application in multi-radionuclide SPECT using a GATE Monte-Carlo model of the Cubresa Spark single-pinhole preclinical SPECT system.

Full pdf report.