Image Reconstruction: the Sparse Way

Lead Research Organisation: University College London
Department Name: Computer Science

Abstract

The ability to image the inside of an object is one of the driving forces of scientific progress. Applications occur in almost all areas of science and engineering, including the whole of medical imaging, non-destructive testing, geophysics and material science. In industry imaging is frequently employed for process monitoring and quality assurance. A further important application is security monitoring like for instance airport luggage screening.Medical imaging is the application which affects the general public the most. In medicine a wide range of imaging modalities is used to assist the diagnosis. Commonly used techniques include Magnetic Resonance Imaging (MRI) and X-ray Computed Tomography (CT). Unfortunately, even using state-of-the-art imaging equipment these procedures can be either very time consuming, as in the case of an MRI scan or the patient is exposed to ionising radiation which is potentially harmful, like in CT. Both procedures would greatly benefit from reducing the number of measurements, which are necessary to reconstruct the image without compromising its diagnostic value. This almost sounds like a lost cause but it turns out it is not!Think about compression algorithms such as JPEG, which allow to significantly reduce the size of an image and later are able to restore it seemingly without visual losses. We say images are compressible. Compression standards like JPEG exploit this fact by efficiently representing images with significantly fewer numbers than the number of pixels in the original image. Mathematically, this is achieved by representing the image in a basis in which most of its coefficients are so small that they can be set to zero without visibly diminishing the quality of the image. We call such a representation sparse.Would it not be great if one could directly acquire an image in this compact representation?In recent years this question has been affirmatively answered. It turns out that under certain assumptions it is indeed possible to make such compressed measurements and to subsequently recover the image almost completely. For applications like MRI and CT this means shorter scanning times and reduced radiation exposure.However, to be able to benefit from this new sensing paradigm it is necessary to modify both, the measurement procedure and the reconstructing algorithm. This fellowship addressed exactly this problem for a wide range of imaging modalities including, CT, Tomosynthesis and Optical Tomography. It develops new ways of data acquisition and new algorithms to reconstruct the image from this data. It addresses some fundamental issues concerned with the conditions on the design of the measurement and limits of what is feasible under these conditions. It explores ways of further improving the reconstruction by incorporating prior knowledge on the object. The new Sparse Way of imaging has the potential to push boundaries of what is achievable at present in terms of resolution, data acquisition time, and radiation dose. In close collaboration with experimentalists at UCL the developed methodology will be tested on real-life applications. The research will benefit from collaboration with leading experts in the field and Rapiscan Systems, manufacturer of a wide range of security monitoring equipment.Imaging is an essential technology in science and engineering. Advances in many areas depend on a steady progress of existing imaging techniques and the development of novel approaches. The research community working on sparsity-enhanced imaging has been steadily growing over the last couple of years and it has the potential to take the lead in the more general field of imaging in the future. This fellowship will be at the forefront of this exciting research area, addressing timely and relevant real-life problems. It will strengthen the expertise of the UK in image reconstruction by delivering contributions, which will have a major impact in the field.

Planned Impact

The applications of imaging extend to many areas of science and engineering, medical diagnosis, industrial process monitoring and quality assurance, security monitoring and many others. New acquisition and reconstruction schemes for faster and more robust imaging using substantially fewer measurements have the potential to improve upon the existing technology in many of these areas. The commercial beneficiaries are Rapiscan Systems and Dexela. Rapiscan will benefit from the development of Sparse CT. The ideas are immediately applicable to Rapiscan hardware and therefore can lead to commercial deployment in airport security CT scanners in a relatively short time. In the long run this will lead to faster and more accurate luggage screening in airports. Dexela will profit from the research on Tomosynthesis, which has the potential to significantly improve the currently achievable image quality. Advancing their technology Dexela will enhance its position against international competition. Betcke will regularly visit both companies and give presentations on the progress of the project. Under an appropriate licensing agreement the developed software will be made available and assistance in its deployment e.g. through demonstration sessions will be provided to both companies. In general manufacturers of CT, Tomosynthesis, BLT and DOT equipment will benefit from the expertise generated through the fellowship. Betcke will give presentations at mathematical, engineering and medical imaging conferences to ensure the dissemination to a wide range of audiences including the manufacturers of medical equipment to increase potential of further exploitation of the ideas. The results will be published in peer reviewed journals in those fields. The Henry Moseley X-ray Imaging Facility at the University of Manchester will benefit from the development of Sparse CT and sparsity-enhanced reconstruction algorithms. Under an appropriate licensing agreement the developed software will be made available at the facility thereby greatly increasing its exposure to other academics and the industry. Commercial exploitation of the work (patents, software licenses) will be pursued through the UCLi office who have considerable experience in such negotiations, and who have already negotiated licences for some of the previous image reconstruction software developments. Once the technology is mature enough for medical applications, the NHS will benefit from availability of more cost-efficient medical imaging equipment. Physicians and patients will benefit from new faster, more flexible and lower dose or even non-invasive diagnostic tools providing better quality results, which will increase the success rate in image assisted diagnosis. Betcke will engage in dissemination to schools and lay audiences working with the UCL Outreach office and participate in events organised by the Biomedical Optics Research Laboratory group in Medical Physics, such as e.g. the Royal Society summer exhibitions. Betcke will maintain a website documenting the progress of the project in general terms suitable for broader audiences to ensure that the research is reaching other communities for which it might be of interest. The fellowship will allow Betcke to quickly establish herself as a fully independent researcher making essential contributions at the frontiers of mathematics, science and engineering. The research visits will enable Betcke to build up long term collaborations with leading experts in the field, which will last beyond the time of the fellowship. Betcke has a very successful collaboration history with Rapiscan during her time at the University of Manchester including effective knowledge transfer to Rapiscan engineers and a filed patent application. The collaboration with Rapiscan during the fellowship will further strengthen Betcke's relationship to this important industrial partner.

Publications

10 25 50
 
Description With W. Lionheart we developed, refined a patented a series of approximative method for reconstruction from a novel X-ray CT geometry with an entire ring of sources and entire cylinder of detectors as in Rapiscan Systems RTT [Inverse Problems 29(11) 115003, Inverse Problems 29(11) 115004, US Patent 8204173]. This geometry presented a challenge to the available methods, as a data which it collected was in the sense of integral geometry severely limited. I consulted teams at UCLA and University of Manchester assisting in hardware implementation and evaluation of performance of one of those methods.

With C. Reid and R. Speller we investigated an optimal setup of an On-Belt Tomosynthesis (limited angle cheap scanning technology, which integrates in the airport system of luggage conveyer belts), [Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 652(1), 108 - 111]. Some of our findings are being applied to a new system developed at University of Antwerp, iMinds-VisionLab, Antwerp (E. Janssens, J.Sijbers).

Jointly with N. Calvert, R. Speller, E. Morton we performed feasibility studies of a new modality: Time of Flight Compton Scatter imaging for Cargo container imaging [IEEE TNS, accepted, Proceedings of IPAC2014]. Experimental aspects of this research are funded by other grants and partly Rapiscan (STFC Global Challenge Concepts).

We investigated a broader role of sparsity in enhancing the solution of ill-posed problems. Our results showed that employing randomness can help to reduce the number of measurements for DOT, even without employing the nonlinear L1 solver in the reconstruction step (presentation at SPARS'11), while more pronounced effect is expected for time resolved measurements (subject of a new collaboration with Consiglio Nazione delle Ricerche, Milano, for which we were given RS International Exchange grant).
In joint work with S. Arridge we explored the compressibility of the sensitivity maps in DOT to significantly reduce the memory requirements for the numerical solution of the inverse problem (paper in preparation). A byproduct of this research is a Matlab Toolbox for construction of wavelets on meshes, which will be released after publication of the results. Our numerical experiments indicated regularising properties of sensitivity map compression, which we are interested in examining further in a future.
Priors like TV are established means of regularization of inverse problems. When applying Krylov method to an ill-posed problem it is well known that the components of the solution corresponding to the largest singular values converge quickly while convergence of high frequency components can be very slow. With L. Harhanen (Helsinki) and S. Arridge (UCL) we developed an iterated preconditioned LSQR method for inverse problems on unstructured grids with accelerated convergence by means of priorconditioning of the projection subspaces to contain the high frequency features of the solution [Inverse Problems 30(7) 075009].

Jointly with S. Arridge (PI), P. Beard, B. Cox and E. Zhang we were awarded an EPSRC grant EP/K009745/1 for the development of a dynamic high resolution Photoacoustic Tomography (PAT) system and the corresponding enabling mathematics. This project harmonises well with my Fellowship, while bringing in new exciting PAT specific mathematical challenges. PAT is particularly attractive as it achieves both high contrast and resolution through coupling two physical processes: light absorption and emission of sound. The PAT scanner at UCL utilizes the Fabry Perot sensor, which enables high spatial resolution measurements of the emitted sound waves. However, at present, this data takes several minutes to build up, so the imaging is limited to specimens that are static in time. In this project we aim to make this process hundreds of times faster, using light patterns to interrogate the sensor. We then recover the PAT image from such measurements building on ideas of compressed sensing. In the first stage of this project we developed a prototype Single Pixel Fabry Perot camera. We obtained a 5 fold speed up alone by reconstructing the full PAT data from a subset (20%) of patterned measurements. We hold a UK patent for this system [PCT/GB2014/051910]. In the mean time this project has resulted in many publications both journal and conference, please refer to EP/K009745/1 record on resource fish.
Exploitation Route The data acquisition and reconstruction methods we developed are applicable to wider scope of problems. For instance the Iterated LSQR method is applicable to Tomosynthesis problems (e.g. On-Belt Tomosynthesis).

We ourselves are taking many of the developments forward. Examples inlace the collaboration with University of Antwerp, iMinds-VisionLab, Antwerp,E. Janssens, J.Sijbers (supported by COST SMS); the new collaboration with Consiglio Nazione delle Ricerche, Milano supported by RS International Exchange grant); work on Dynamic PAT scanner (supported by EP/K009745/1).

The outcomes from EP/K009745/1, with some work still ongoing. We are broadening our interest in dynamic imaging (IMPACT studentship with CurveBeam for dynamic weight bearing foot imaging). Work on ToF Compton Scatter imaging is ongoing and we are investigating options for further funding.
Sectors Aerospace, Defence and Marine,Healthcare,Manufacturing, including Industrial Biotechology,Security and Diplomacy

 
Description Jointly with Rapiscan Systems we hold a patent for multi-sheet rebinning methods. The optimal surface rebinning method is being considered for including in Rapiscan RTT airport luggage CT scanner (consulting UCLA, University of Manchester). I developed a large Matlab package for rebinning methods, which is used by our research team and Rapiscan but cannot be made public domain due to confidentiality agreement. Some of the ideas in the Fellowship inspired further work for different applications (Dynamic PAT EP/K009745/1, RS Travel grant with Consiglio Nazione delle Ricerche, Milano) and led to patent filing PCT/GB2014/051910 for Dynamic PAT scanner. The methodology developed has wider applicability and we and our collaborators are using them in different applications e.g. On-Belt-Tomosynthesis in different setups. The same applies to numerical methods and developed software.
First Year Of Impact 2013
Sector Aerospace, Defence and Marine,Healthcare,Security and Diplomacy
Impact Types Economic

 
Description COST MP1207 Small scientific mission to host E. Janssens, (University of Antwerp, iMinds-VisionLab,Antwerp)
Amount € 760 (EUR)
Organisation European Cooperation in Science and Technology (COST) 
Sector Public
Country Belgium
Start 05/2014 
End 05/2014
 
Description EPSRC responsive mode grant. Simon arrange (PI). I was applying as Research Co-I as I did not have a permanent position at that time. We are in negotiations with EPSRC to change my status to Co-I.
Amount £657,726 (GBP)
Funding ID EP/K009745/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2013 
End 12/2016
 
Description Post break award
Amount £10,000 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 05/2015 
End 07/2015
 
Description RS International Exchanges Scheme
Amount £11,970 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2014 
End 08/2016
 
Description STFC Global Challenge Concepts. This scheme only allows to name PI, here P. Nolan from Liverpool, but this bid built on the work of our (with Robert Speller, UCL) PhD student Nick Calvert.
Amount £45,598 (GBP)
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 05/2014 
End 04/2015
 
Description Consulting for Rapiscan Systems on a joint project with University of Manchester 
Organisation Rapiscan Systems
Country United States 
Sector Private 
PI Contribution Private consulting for Rapiscan Systems on a joint project with University of Manchester, Department of Mathematics to facilitate evaluation of Optimal Surface Rebinning Algorithm (an algorithm which I developed for image reconstruction from Rapiscan RTT system, will soon be submitted) in terms of speed and reconstruction quality , March 2012 - August 2012
Collaborator Contribution Partial GPU implementation. Evaluation of the performance and reconstruction quality. Parameter studies.
Impact Partial port to GPU. further code optimisation. Understanding of image reconstruction quality and artefacts.
Start Year 2012
 
Description Consulting for Rapiscan Systems on a joint project with University of Manchester 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Private consulting for Rapiscan Systems on a joint project with University of Manchester, Department of Mathematics to facilitate evaluation of Optimal Surface Rebinning Algorithm (an algorithm which I developed for image reconstruction from Rapiscan RTT system, will soon be submitted) in terms of speed and reconstruction quality , March 2012 - August 2012
Collaborator Contribution Partial GPU implementation. Evaluation of the performance and reconstruction quality. Parameter studies.
Impact Partial port to GPU. further code optimisation. Understanding of image reconstruction quality and artefacts.
Start Year 2012
 
Description Consulting for Rapiscan Systems on a project with UCLA 
Organisation Rapiscan Systems
Country United States 
Sector Private 
PI Contribution Privately paid consulting on a joint project with UCLA, Electrical Engineering (Prof Dejan Markovic) to facilitate FPGA implementation of Optimal Surface Rebinning Algorithm (algorithm which I developed for image reconstruction from Rapiscan RTT system), March 2011 - February 2012.
Collaborator Contribution Prof Dejan Markovic's team were implementing the algorithm I developed on an FPGA.
Impact FPGA code for Optimal Surface Rebinning algorithm
Start Year 2011
 
Description Consulting for Rapiscan Systems on a project with UCLA 
Organisation University of California, Los Angeles (UCLA)
Country United States 
Sector Academic/University 
PI Contribution Privately paid consulting on a joint project with UCLA, Electrical Engineering (Prof Dejan Markovic) to facilitate FPGA implementation of Optimal Surface Rebinning Algorithm (algorithm which I developed for image reconstruction from Rapiscan RTT system), March 2011 - February 2012.
Collaborator Contribution Prof Dejan Markovic's team were implementing the algorithm I developed on an FPGA.
Impact FPGA code for Optimal Surface Rebinning algorithm
Start Year 2011
 
Description Rapiscan, Nick Calvert funding 
Organisation Rapiscan Systems
Country United States 
Sector Private 
PI Contribution Jointly with Robert Speller we are supervising Nick's PhD. Nick is working on a project with Rapiscan Cargo division on time of flight Compton Scatter Imaging.
Collaborator Contribution Part of the stipend for Nick via IMPACT scheme (40k). In-kind contribution: consulting, performing experiments and use of LINAC X-ray source on Rapiscan site. Part of funding for experiments performed at VELA STFC facility.
Impact - STFC Global Challenge Concepts, "Time of flight X-ray imaging for security applications" jointly with N. Calvert, R. Speller (UCL), E. Morton, A. Deacon, J. Ollier, M. Procter (Rapiscan), D. Judso, J. Cresswel, P. Nolan (PI) (Liverpool), £45,598 total. - IEEE Trans.Nucl.Sci. paper accepted "Feasibility Study of Time-of-Flight Compton Scatter Imaging Using Picosecond Length X-ray Pulses" - McIntosh P.A. et al (2014). VELA: A new accelerator technology developed platform for industry Proceedings of IPAC2014, Dresden, Germany
Start Year 2011
 
Title APPARATUS AND METHOD FOR PERFORMING PHOTOACOUSTIC TOMOGRAPHY 
Description A method and apparatus are provided for performing photoacoustic tomography with respect to a sample that receives a pulse of excitation electromagnetic radiation and generates an acoustic field in response to said pulse. One embodiment provides an apparatus comprising an acoustically sensitive surface, wherein the acoustic field generated in response to said pulse is incident upon said acoustically sensitive surface to form a signal. The apparatus further comprises a source for directing an interrogation beam of electromagnetic radiation onto said acoustically sensitive surface so as to be modulated by the signal; means for applying a sensitivity pattern to the interrogation beam; and a read-out system for receiving the interrogation beam from the acoustically sensitive surface and for determining a value representing a spatial integral of the signal across the acoustically sensitive surface, wherein said spatial integral is weighted by the applied sensitivity pattern. The apparatus is configured to apply a sequence of sensitivity patterns to the interrogation beam and to determine a respective sequence of values for said weighted spatial integral for generating a photoacoustic image. 
IP Reference WO2014207440 
Protection Patent application published
Year Protection Granted 2014
Licensed No
Impact - Developed prototype scanner at UCL and first reconstruction methods - Pattern interrogation scanner presented on SPIE Photonics 2014 - Real time ultrasonic field mapping system presented on SPIE Photonics 2015 - Image reconstruction presented at AIP 2014 (in mini symposium), LMS Inverse Day on Hybrid and Multimodal Imaging July 2014 (invited)
 
Title System and Method for Image Reconstruction by Using Multi-Sheet Surface Rebinning 
Description The present application is directed toward the generation of three dimensional images in a tomography system having X-ray sources offset from detectors, in particular in a system where the sources are located on a plane, while detectors are located on multiple parallel planes, parallel to the plane of sources and all the planes of detectors lie on one side of the plane of sources. A controller operates to rebin detected X-rays onto a non-flat surface, perform two dimensional reconstruction on the surface, and generate the three dimensional image from reconstructed images on the plurality of surfaces. 
IP Reference US2011091007 
Protection Patent granted
Year Protection Granted 2011
Licensed No
Impact Algorithm for image reconstruction from a novel geometry as featured in Rapican Systems RTT machines.