MPHY3000/MPHYM000: Medical Physics Projects 2015/16

Below is a list of Medical Physics projects being offered for undergraduate students in the Department. To find out more about a project and/or to indicate your interest in taking it, please email the first supervisor by clicking on his/her name.


  • A Project Outline is due on Monday October 12, 2015. Your supervisor must also complete a Project Risk Assessment Form. Students are required to hand in the form with two copies of their outline to Vikki Crowe or James Vallerine in the Medical Physics Departmental Office (second floor of the Malet Place Engineering Building).
  • Project Progress Reports are due by Monday January 18, 2016. Two copies should be handed to Vikki Crowe or James Vallerine in the Medical Physics Departmental Office.
  • Project talks will be held on Wednesday March 16, 2016 in Rooms 1.19 and 2.14 of the Malet Place Engineering Building.
  • Final Reports are due by Wednesday March 23, 2016. Please hand in two copies to James Vallerine in the Medical Physics Departmental Office.

Project information

Total number of projects listed below: 36
Number of projects still available: 26

Characterization of energy-resolved single-photon-counting x-ray detectors for application in phase-contrast imaging

Supervisors: Dr. Marco Endrizzi and Dr. Alberto Astolfo

Student: (Project available)

Single-photon-counting detectors offer unique capabilities for x-ray imaging in terms of noise performance and energy resolution. This project involves a complete characterization of a detector based on this technology encompassing classical parameters such as noise and spatial resolution, but also more sophisticated and method-specific ones like signal spill-out between adjacent pixels and detector response as a function of energy. The parameters extracted with this analysis will enable the quantitative interpretation of the acquired data and the inclusion of the realistic detector performance into simulation software. Some familiarity with the basics of data acquisition and analysis (e.g. Matlab, ImageJ) will be useful.

Optimisation of data reconstruction for laboratory-based X-ray phase-contrast imaging using indirect conversion detectors

Supervisors: Dr. Marco Endrizzi and Dr. Paul Diemoz

Student: (Project available)

Large area, indirect conversion detectors are an attracting option for the translation of X-ray phase-contrast imaging into a standard laboratory tool. One of the prototypes available in the X-ray phase-contrast lab is based on such detector technology and, due to the shape of its point spread function, it requires the use of a “line-skipped” design mask. In practice, this means that only every second column of the detector is used and half of the data collected are simply not used. This project is focussed on the inclusion of this information into the standard reconstruction algorithms with the aim to provide images of higher quality at no additional cost. The student will develop an understanding of the basic principles of image formation and data collection. Existing software will be used to simulate the experimental set-up and, once an optimized data processing strategy is identified, it will be tested on experimental data. Familiarity with programming (e.g. Matlab) will be helpful.

Comparison of two x-ray phase-contrast techniques through simulations of image contrast and signal-to-noise ratio

Supervisors: Dr. Paul Diemoz and Dr. Marco Endrizz

Student: (Project available)

X-ray phase-contrast imaging (XPCi) techniques have emerged in recent years, which are based on exploiting interference and refraction effects, instead of x-ray absorption, to generate image contrast. The strong research interest they have attracted is due to their ability to increase the image contrast, which enables the detection of features invisible to conventional x-ray methods. The simplest XPCi technique, free-space propagation (FSP), is based on moving the detector further away from the sample, so as to produce interference fringes that can be recorded by the detector. The XPCi group at UCL, instead, has been developing and investigating a more advanced method, called edge illumination (EI), which requires the additional use of two absorption masks before the sample and the detector, respectively. The aim of this project is to quantify the improvement in contrast and signal-to-noise ratio provided by the EI technique compared to FSP, for a variety of different acquisition parameters (ex. feature size, source size, x-ray energy, etc.), and to determine under which conditions the advantages of EI are largest. The comparison will be based on existing simulation software developed within the group. If time allows, some experimental data will be also made available to validate the results of the simulations. The student will have the opportunity to learn how to use a matlab simulation code, understand the different metrics defining the image quality, analyze simulation data and ultimately compare simulated and experimental results.

Wave and ray-optics approaches to the modelling of x-ray phase contrast imaging

Supervisors: Dr. Paul Diemoz and Prof. Alessandro Olivo

Student: (Project available)

X-ray phase-contrast imaging (XPCi) allows the generation of images with highly improved contrast compared to conventional x-ray imaging techniques. While the latters are based on measuring the attenuation of a photon beam when passing through different parts of the sample, XPCi exploits the interference/refraction effects experienced by the photons. Our group developed a new implementation of XPCi, the edge illumination (EI) technique, which was proven to work efficiently with standard x-ray sources and laboratory equipment. It has therefore great potential for applications in many fields of x-ray investigation, such as materials science, biomedical and clinical imaging. There are two basic ways to model x-ray phase contrast imaging. The wave-optics approach, based on Fresnel/Kirchoff diffraction integrals, is very rigorous but time consuming. The ray-tracing approach, instead, offers a substantial simplification, however at the cost of accuracy. The phase contrast group at UCL has developed software to simulate phase contrast images following both approaches. The student will be provided with this software and will use it to investigate how the two models compare in different experimental situations, and establish under what set of conditions ray optics can be considered a satisfying approximation. The student will gain skills in simulation methods, data analysis, image analysis and familiarize with the basic concepts of optics. A reasonably sound mathematical background is required.

Optimization of experimental parameters for x-ray imaging with edge-illumination

Supervisors: Dr. Peter Modregger and Prof. Alessandro Olivo

Student: (Project available)

Modern x-ray imaging with the edge-illumination technique offers the exciting possibility to take advantage of the generally superior phase contrast over the traditional absorption contrast. This project is aimed at optimizing specific experimental parameters for dose efficiency, which will be vital for the translation of edge-illumination into a tool for medical diagnostics. It requires the student to develop an understanding of image quality assessment, the physics of the image formation process, and the numerical simulation thereof. It is expected that the entirety of the project consists of numerical simulations. Prior experience with Matlab or Python is required. Knowledge in optics/imaging is useful.

Performance comparison of different data analysis algorithms for x-ray imaging with edge-illumination

Supervisors: Dr. Peter Modregger and Gibril Kallon

Student: (Project available)

Modern x-ray imaging with the edge-illumination technique offers the exciting possibility to take advantage of the generally superior phase contrast over the traditional absorption contrast. This project is aimed at identifying the particular advantages and limitations of different approaches to data analysis. The student will acquire an understanding of image quality assessment, noise transfer and numerical implementation of data retrieval algorithms. It is expected that the entirety of the project consists of numerical simulations. The comparison will be performed on mostly synthetic data and experimental data as available. Prior experience with either Matlab or Python is useful.

Evaluate different deconvolution methods for x-ray scattering with edge-illumination

Supervisors: Dr. Peter Modregger and Fabio Vittoria

Student: (Project available)

Imaging the ultra-small angle x-ray scattering distribution with edge-illumination provides access to sub-pixel information, which implies the tantalizing opportunity to increase pixel sizes in diagnostic x-ray imaging and consequently to decrease dose significantly. In the post-detection processing the scattering signal is retrieved by deconvolution, which is a numerically challenging task. This project is aimed at comparing different methods for numerical deconvolution of the specific signals generated by x-ray imaging with edge-illumination. It is expected that the entirety of the project will consist of numerical simulations. Prior experience with either Matlab or Python as well as numerical mathematics is useful.

X-ray phase contrast imaging for detecting explosives: data collection and analysis

Supervisors: Dr. Alberto Astolfo and Prof. Alessandro Olivo

Student: (Project available)

UCL, in collaboration with Nikon, is developing an X-ray phase contrast imaging system to improve sensitivity and specificity in security scans by exploiting the unique advantages of the technique. The system will have a 15x25cm2 field of view that will be the larger available in the world for X-ray phase contrast imaging. This opens the possibility to test the technique in a new range of applications that can go beyond the security field (e.g. medical, pre-clinical, quality control). The project consists on acquiring images of threat and non-threat materials, as well as of other samples, using a new setup, and then performing some analysis on the collected data. The system will be available at UCL between Nov 2015 and Jan 2016. Prior knowledge of IDL/Matlab and some familiarity with the principles of x-ray imaging are advisable.

Exploring the use of iterative algorithms for x-ray phase contrast CT reconstructions

Supervisors: Dr. Charlotte Hagen and Anna Zamir

Student: (Project available)

X-ray Phase Contrast imaging (XPCi) stands for a class of radiographic imaging techniques, which, in addition to x-ray attenuation, are sensitive to phase and refraction effects. XPCi techniques are especially important for the imaging of weakly attenuating biological samples and are investigated by an increasing number of groups worldwide, including the phase contrast group at UCL. Edge Illumination (EI) XPCi - a novel method developed at UCL – can measure the refraction of x-rays as they pass an object. EI XPCi has recently been implemented as tomographic modality. By rotating the object over an angular range of at least 180 degrees and acquiring images at every rotation angle it is possible to reconstruct volumetric maps of the refractive index distribution within the object. While until now all tomographic reconstructions were carried out using filtered back projection, the next step is to explore the benefit of iterative algorithms for the reconstruction of these maps. The student would be given an experimental EI XPCi dataset on which different iterative reconstruction algorithms can be tested. The student would define metrics that can be used for a comparison and eventually decide which algorithm is most suited to the reconstruction problem at hand. Besides being involved in the development of a new imaging method, the student would get familiar with the basic concepts of computed tomography and image reconstruction. The project requires advanced mathematics and experience in Matlab programming. Existing software packages (e.g. the ASTRA toolbox) can be used.

Rigorous simulation of light focussed through layers of materials with differing refractive indices

Supervisors: Dr. Peter Munro and Dr. James Guggenheim

Student: (Project available)

The focussing of light through layers of materials with differing refractive indices is important in numerous biomedical imaging techniques, including optical microscopy, photoacoustic tomography and optical coherence tomography. The aim of this project is to develop a toolbox using Matlab that is easily used by researchers in a variety of fields. This project will require understanding of both optics and computer programming using Matlab. This project will suit students with an interest in the simulation of physical phenomena with minimal approximations.

Optimal simulation of X-ray propagation using wave optics

Supervisors: Dr. Peter Munro and Fabio Vittoria

Student: (Project available)

Wave optics is the most general way to model the interaction of X-rays with tissue. The problem is that wave optics can be computationally intensive, which is why a ray optical is often employed. This project will look at some ways in which a wave model of X-ray propagation can be made as computationally efficient as possible, using mathematical rather than programming optimisations. This project will underpin new approaches to image restoration and quantification in X-ray phase imaging.

GPU modelling of wave optics

Supervisors: Dr. Peter Munro and Fabio Vittoria

Student: (Project available)

The simulation of the propagation of optical waves (including X-rays) requires that a large number of very similar integrals be performed. This problem is thus highly suited to parallelisation using a graphics processing unit, which may be able to compute thousands of such integrals in parallel. This project will seek to establish framework upon which a toolbox will be build. The first part of the project will be to determine the most appropriate programming tool to use and the second part will be to implement a proof of principle demonstration.

Construction of phantoms which mimic both X-ray and optical scattering

Supervisors: Dr. Peter Munro and Dr. Peter Modregger

Student: (Project available)

Light scattering is one of the factors which limit the depth at which optical imaging may be performed in tissue. Techniques which rely on the propagation of light deep into tissue (e.g. diffuse optical tomography and photoacoustic tomography) benefit immensely from mapping of the strength of optical scattering throughout the tissue being imaged. This project is aimed at developing phantoms to demonstrate that optical scattering can be correlated with the scattering of X-rays, which has only recently been demonstrated to be possible in the laboratory. This project will require a research into suitable materials and the development of a protocol to construct the phantoms.

Clinical photoacoustic lymph node imaging: a simulation study

Supervisors: Dr. Thomas Allen, Dr. James Guggenheim and Prof. Paul Beard

Student: (Project available)

Lymph nodes are a common site of metastases in cancers, and determining whether or not cancer has spread to lymph nodes has a vital role in disease staging, prognosis and treatment planning. As a result, there is tremendous motivation for monitoring nodes in vivo. Photoacoustic (PA) imaging is an emerging modality based on the detection of ultrasound generated inside tissue by pulsed laser excitation. In vitro studies have demonstrated that PA imaging can provide striking images of lymph node structure, and it is suggested that the technique could find clinical utility in assessing cancer. The aim of this project is to make a realistic simulation of in vivo lymph node imaging using the open source software k-Wave developed at UCL. Key objectives are to examine optimal detection parameters and to assess potential in vivo imaging performance. This project is heavily computational and a good knowledge of MATLAB is essential.

Radioisotope mapping using RadICAL

Supervisors: Prof. Robert Speller and Dr. Dan O’Flynn

Student: (Project available)

RadICAL is a detector system designed for localising radioactive isotopes. Several versions have been designed and built and this project is to look at alternative approaches to the basic principle. This can be approached in several ways and will depend upon the skills of the student. A Monte Carlo modelling approach could be used or just experimental measurements. Different designs would need to be tested and this will require some building of equipment probably using the facilities available in Institute of Making. Testing would be undertaken in the Radiation Physics labs using radioactive isotopes.

Novel collimation for spatial discrimination in x-ray diffraction

Supervisors: Dr. Robert Moss and Dr. Francesco Iacoviello

Student: (Project available)

UCL has developed a new approach to X-ray diffraction which make use of a multi-element detector (a pixellated array). In the present setup the detector collects data for every point where X-rays are scattered from a sample. A real sample is likely to contain a region of interest surrounded by 'clutter'. A more meaningful result would be obtained if diffraction data could be collected for the region of interest only and the clutter could be ignored. The aim of this project is to design and build a collimator that can be used to mask the detector such that only data from a specific region within a sample are collected. The student will be encouraged to use a combination of modelling and CAD to develop a series of designs which can then be built using the rapid prototyping capability in the Make Space. The student will characterise the prototype designs using modelling and optical techniques.

Ray trace modelling of X-ray diffraction

Supervisors: Prof. Robert Speller and Dr. Francesco Iacoviello

Student: (Project available)

Tissue diffraction using X-rays can potentially play an important role in the diagnosis of disease. We are currently studying how this technique can best be applied in the detection of early breast cancer. However, to support our experimental studies we are developing modelling techniques. This project is to look at using Matlab or IDLto model different diffractometer designs. It requires an interest and some experience in computing. The eventual aim will be to see if we can reproduce our experimental results.

X-ray diffractometer design for tissue evaluation in breast cancer surgery

Supervisors: Dr. Rob Moss and Prof. Robert Speller

Student: (Project available)

Recurrence of breast cancer following removal of the primary tumour is still disappointingly high. It is thought to be due to inadequate removal of disease; particularly infiltrating and difficult to image strands of tumour cells. X-ray diffraction may hold the key to being able to identify tissue involvement that cannot be seen with normal techniques. This project is to look at different aspects of the design of a system that could be used to measure diffraction signals on tissue. The project will involve designing different collimators and making measurements of the sensitivity of the system. It is also hoped that the student will be able to evaluate the effect of the positioning of samples within the sensitivity volume and hence allow an optimised system to be developed. Experimental skills will be important and the ability to use Matlab (or similar) an advantage.

Comparison of different X-ray imaging techniques in breast cancer

Supervisors: Prof. Robert Speller and Dr. Rob Moss

Student: (Project available)

We have a database of ~100 X-ray images of breast cancer samples. These have been recorded in a variety of ways - conventional absorption imaging on a clinical system, absorption imaging on a laboratory system and using a laboratory phase contrast imaging system. We also have a sub-set of these images (~40) that have been ‘imaged’ using a novel X-ray diffraction technique. The aim of the project is to compare the results from all these techniques to identify which of the techniques provides the most information for the different stages of cancer development as seen in the 100 samples. For example, an initial stage in the project might look at finding features in the diffraction data that can be quantified. The student would then compare these metrics with the equivalent values obtained from the other imaging techniques on the same samples. The project requires some computing skills so that image analysis can be carried out and statistical tests developed.

Coupling acoustic and thermal models for high intensity focused ultrasound (HIFU)

Supervisors: Dr. Panayiotis Georgiou, Dr. Brad Treeby, and Dr. Elly Martin

Student: (Project available)

High intensity focused ultrasound (HIFU) is a novel approach for treating non-invasively various conditions, such as malignant tumours. Unlike diagnostic ultrasound, this approach utilises high intensity beams to induce intense localised heating, and as a result, destroy the tissue in the area where the beam is focused. At such high intensities, non-linear effects in the propagation of the ultrasound beam become significant and need to be accounted for in acoustic propagation models. Additionally, the acute increase in temperature changes the properties of the medium and thus, affects the propagation and focusing of the beam. Our group has developed accurate acoustic models and thermal models that independently describe these two effects. The aim of the project is to couple together the thermal and acoustic models. In other words, the acoustic model should use the thermal model in a feedback loop every few iterations of the simulation to calculate the updated properties of the medium due to the induced increase in temperature. Once the two models are coupled together, the student will initially test the system by simulating simple scenarios with medium data extracted from patient’s CT scans. The project will also consist of an experimental component during which the student will verify in the lab the validity of the coupled thermal-acoustic model. In particular, the student will compare the lesion volumes theoretically predicted by the model with the actual lesion volumes induced on a bovine liver phantom under the influence of HIFU of varying intensities. Good knowledge of MATLAB is required for this project.

Characterisation of a Fabry-Pérot fibre optic hydrophone

Supervisors: Dr. Elly Martin, Dr. Brad Treeby, and Dr. Ben Cox

Student: Stecia Fletcher

The use of high intensity focused ultrasound for therapy is growing. There is therefore an increasing need to characterise these therapeutic ultrasound fields for quality control and treatment planning. However, most measurements of acoustic pressure for ultrasound field characterisation are performed using miniature PVDF hydrophones which are unable to withstand the high pressures, temperatures and mechanical effects generated in clinical focused ultrasound fields. Fibre optic hydrophones provide an alternative that should be more resistant to damage, are cheaper and easier to replace if damage occurs, and provide an increased bandwidth and smaller sensor size. In this project, a Fabry-Pérot fibre optic hydrophone (developed at UCL and now commercially available), will be characterised in terms of its stability over time, linearity, and damage threshold, in order to ascertain its suitability for mapping of high intensity focused ultrasound fields and to aid optimisation of the device for this purpose.

Characterisation of acoustic properties of biologically relevant materials

Supervisors: Dr. Elly Martin, Dr. Brad Treeby, and Dr. Ben Cox

Student: Michael Ruddlesden

In high intensity focused ultrasound therapy, ultrasound is focused into the body to heat tissue to temperatures of 60 ºC or more in order to kill diseased cells. Modelling of the propagation of this ultrasound in the body can help in the planning of these treatments, to ensure targeting of the correct regions and to avoid damage to surrounding healthy tissue. To accurately model ultrasound propagation in tissues, the acoustic properties of the tissues (sound speed, attenuation coefficient and nonlinearity parameter) must be known under clinically relevant conditions – i.e. at body temperature and over the range of temperatures generated during treatment and over a frequency range of tens of MHz. The aim of the project is to design and assemble a system for measuring the acoustic properties of materials over a wide frequency range and as a function of temperature. The system will consist of a laser generated ultrasound source (to obtain a wide bandwidth signal), material sample holder and a broadband PVDF ultrasound sensor mounted in a water tank with temperature control.

Optimising the acquisition strategy for a miniature all-optical 3D ultrasound scanner

Supervisors: Dr. Erwin Alles and Dr. Adrien Desjardins

Student: (Project available)

Recent advances in laser-generated ultrasound have resulted in optical ultrasound sources constructed on optical fibres. These fibres are covered with an optically absorbing coating, which converts absorbed light into heat, resulting in a localised pressure increase which generates an acoustic wave. When such a fibre is combined with an optical ultrasound detector, an all-optical ultrasound sensor with a diameter below 1 mm is obtained that consists of just two optical fibres. Currently, a miniature all-optical ultrasound scanner is being developed as a step towards the first all-optical endoscopic probe. Instead of a single fibre, a coated fibre bundle with a diameter of a few millimetre is used, together with a single optical receiver. By steering a focussed light beam across the surface of this fibre bundle, different regions of the fibre bundle can be illuminated. This way, the source location can be manipulated and the tissue can be scanned from various angles, and by combining these scans three-dimensional images can be obtained. The aim of this project is to simulate and optimise the imaging process for such a probe, and to test the most promising schemes on real tissue. As this study will mainly be performed through simulations, some experience with programming languages (e.g. Matlab) would be advantageous.

Muscle activity during electrically stimulated exercise for people with spinal cord injury

Supervisors: Dr. Lynsey Duffell and Prof. Nick Donaldson

Student: Sarah Massey

Electrical stimulation has been used for many years as a treatment modality for patients with spinal cord injury. We have developed an exercise machine that combines electrical stimulation with voluntary effort during cycling, which aims to maximise recovery using the latent plasticity of the spinal cord. In order to verify the effects of the machine, we would like to measure activity of the working muscles using electromyography (EMG) during the electrical stimulation. We have developed a unique stimulator and EMG amplifier capable of blanking out stimulus artefacts, however the system still needs to be integrated with the exercise machine. The student will investigate ways to integrate the two systems, such that the stimulation is triggered by the exercise machine. The student will also collect EMG data on healthy volunteers while using the exercise machine.

The effects of transcutaneous spinal cord stimulation on corticospinal excitability

Supervisors: Dr. Lynsey Duffell, Dr. Karen Bunday and Dr. Ricci Hannah

Students: Francesca Lenham and Eden Atherton

Electrical stimulation applied to the spinal cord is an emerging technique that has demonstrated immediate recovery of function in patients with spinal cord injury. We intend to investigate the underlying mechanisms of the noted recovery in function with this intervention using transcranial magnetic stimulation (TMS). The student will work in the Institute of Neurology, Queens Square, and carry out neurophysiological experiments on healthy volunteers. Specifically, they will use electromyography and TMS before and after a 30-minute intervention of electrical stimulation, applied transcutaneously over the lumbar spine, to explore changes in the excitability of the central nervous system.

The development of hardware and software to provide feedback to physiotherapists on the progress of a spinal cord injury patient carrying out FES cycling

Supervisors: Dr. Lynsey Duffell and Prof. Nick Donaldson

Student: (Project available)

We are developing a new exercise machine for patients with spinal cord injury. To maximise recovery, we want to use the latent plasticity of the spinal cord by combining electrical stimulation of the paralysed muscles with a system that encourages voluntary effort to drive the pedals while cycling. The voluntary effort is encouraged by the patient participating in a virtual race in which their speed depends on the crank shaft torque without stimulation. For this system to be used by physiotherapists in hospitals, it is important that the data from the machine provides useful and clear feedback for the therapists to assess each patient’s progress. Additionally, this data should be easily accessible to the therapists. A 3G wireless data-transmitter has been developed by previous students for sending the exercise data to the therapist’s computer. The aims of this project are; i) to test the 3G data-transmitter with the exercise machine; (ii) to show that this complies with data protection standards and; iii) to design a software package that automatically accesses the data once it has arrived on the computer, analyses the signals, and displays the data in a useful format for physiotherapists. You will have access to physiotherapists at RNOH, who can provide feedback on your ideas.

Development of ultrasound phantoms with controlled acoustic properties for percutaneous procedures

Supervisors: Dr. Wenfeng Xia, Dr. Daniil Nikitichev, and Dr. Adrien Desjardins

Student: Joshua Wong

Ultrasound imaging is widely used to guide minimally invasive medical procedures such as nerve blocks. This imaging modality has many advantages, including being real-time and non-ionsing, but interpreting images and planning an optimal path to the procedure target can be challenging. There is an urgent need for better training tools for a wide range of patient anatomies. This project will be centered on the development of gel-wax based ultrasound phantoms for percutaneous (needle-based) procedures.  This project will include the investigation of the acoustic properties of gel-wax based materials, which promise to have tailorable acoustic properties to simulate a wide range of soft tissues. The project will be performed in close collaboration with a Consultant Anaesthetist at the University College Hospital. The student should have an interest in experimental studies, data analysis, and the application of physics and engineering concepts to medicine. Prior experience with ultrasound would be useful but it is not required. 

Optical analogue of X-Ray CT, for teaching the concepts

Supervisors: Dr. Jenny Griffiths and Dr. Rebecca Yerworth

Student: (Project available)

Investigative learning is beneficial for students trying to understand how medical imaging devices work, but it is impractical, and potentially dangerous to use commercial devices in a classroom or teaching lab. In addition, in clinical devices the physics/engineering is often hidden from view. During this project you will need to acquire a detailed understanding of the principles of clinical CT machines and image reconstruction so as to design and test a prototype classroom demonstration kit and test phantoms, using visible light in place of x-rays. This project will suit a student who is creative, and likes making and explaining things.

Optical analogue of gamma camera, for teaching the concepts

Supervisors: Dr. Rebecca Yerworth and Dr. Jenny Griffiths

Student: Nicola Wolff

Investigative learning is beneficial for students trying to understand how medical imaging devices work, but it is impractical, and potentially dangerous to use commercial devices in a classroom or teaching lab. In addition, in clinical devices the physics/engineering is often hidden from view. During this project you will need to acquire a detailed understanding of the principles of selective isotope uptake, clinical gamma cameras and image reconstruction so as to design and test a prototype classroom demonstration kit and test phantoms. It is envisaged commercially available fluorescent or coloured dyes will be used in place of radioisotopes. This project will suit a student who is creative, and likes making and explaining things.

Ultrasound scanner – teaching tool

Supervisors: Dr. Rebecca Yerworth and (To be decided)

Student: Adam Goldschneider

Medical physics and Biomedical Engineers need to understand how medical imaging devices work, and investigative learning is beneficial. However in clinical devices the physics/engineering is hidden from view. What is needed is a striped down device where the individual stages can be controlled by the students. During this project you will need to acquire a detailed understanding of the principles of clinical ultrasound machines so as to design, build and test a prototype classroom ultrasound demonstration kit and test phantoms, using low cost electrical components.

EIT perfusion imaging

Supervisors: Dr. Rebecca Yerworth and Prof. Adam Gibson

Student: (Project available)

Electrical Impedance Tomography (EIT) creates images of the internal impedance changes related to physiological function using a series of surface electrodes measurements placed on the surface of the body in real-time. It is increasingly being used as a bedside tool for monitoring regional lung ventilation. However surprisingly little is published on perfusion (blood distribution)/flow. This may be because most clinical systems use serial data collection which, if uncorrected, results in image distortion, and may be obscuring the cardiac signal. This project aim is to see if the application of a recently developed data correction technique enables the cardiac related signal to be visualised and would involve creating simulations and reanalysing previously collected data.

Reconstruction of CT images of the Antikythera mechanism

Supervisors: Prof. Adam Gibson, Prof. Robert Speller and Dr. Jenny Griffiths

Student: (Project available)

The Antikythera Mechanism is an analogue computer over 2000 years old which was used to predict astronomical events and the dates for the ancient Olympic Games. It was rediscovered in 1900 following a shipwreck and has been imaged by x-ray CT in an attempt to determine its internal structure and function. Unfortunately, one fragment moved during image acquisition and some projections were lost. In this project, you will analyse the existing projections to determine what problems occurred during imaging, and develop methods to correct for them. This project requires an understanding of CT image reconstruction, image processing and will involve computer programming.

Automated neonatal monitoring

Supervisors: Prof. Adam Gibson and Dr. Vinay Gangaharan

Student: (Project available)

We have recorded about 2 weeks of multichannel monitoring data on 9 babies in intensive case. We have already showed that intelligent analysis of this data can identify adverse events. In this project, you will carry out further analysis, to determine the analysis technique which maximises the sensitivity and specificity with which the system can identify adverse events. This project will require mathematics and computer programming.

Absolute measurements with MONSTIR

Supervisors: Prof. Adam Gibson and Laura Dempsey

Student: (Project available)

We have a new time-resolved optical imaging system which is designed to give accurate measurements of the time taken for photons to travel across a volume of tissue. It is equally important to know the intensity of light, but this is harder to measure. This project will involve building a tissue-equivalent phantom, measuring the intensity of light crossing it, and determining how accurately the intensity can be measured using different correction factors. It requires a student who is interested in experimental physics, and will involve a substantial proportion of data processing which will include computer programming.

Localisation of range mixing in proton radiography

Supervisors: Prof. Adam Gibson and Dr Paul Doolan

Student: (Project available)

Proton radiography, the use of protons to image the patient, could prove to be a useful tool in the planning process for proton therapy patients. The current planning procedure requires conversion of the patient’s anatomical dataset from X-ray attenuation to proton attenuation. This conversion is one of the largest uncertainties currently in proton therapy, but it could be eradicated completely if proton radiography could be relied upon.

Unfortunately, unlike X-rays, protons do not travel in straight lines. This means that there is a possibility that two protons could arrive at the same point on the detector having taken different paths. If these paths have different energy losses, the estimate of the material being imaged may be incorrect – which proton energy loss value is correct? This situation is known as ‘range mixing’ and it is crucial to identify areas of range mixing in proton radiographs so that reliable pixel values are identified.

The task of the student is to analyse some real proton radiographic data, acquired in the proton beam at Massachusetts General Hospital, and to develop a method to identify potentially range mixed signals.

The steps of the work include:

  • Analysis of the calibration data for homogeneous materials, forming a ‘ruler’ against which to compare the phantom data.
  • To develop and test a variety of metrics in their ability to identify range mixing.
  • To determine the most sensitive metric, with demonstration on a heterogeneous phantom.

The student for this project should be comfortable handling data in Matlab and with statistical measures of distributions.

Exploring the use of inexpensive optical photon-time-of-flight technology for characterizing the optical properties of tissue-simulating fluids

Supervisors: Prof. Jem Hebden and Dr. Danial Chitnis

Student: Ruchir Shah

New technology developed for the mobile phone market provides an inexpensive means of measuring the time it takes for photons to travel between an optical source and a detector. The objective of this project is to investigate whether these small devices can also be used to measure the optical properties of highly scattering fluids produced to simulate human tissues. The student will construct a probe based on one (or possibly two) of these devices which can be inserted into suitable homogenous fluids. Experiments will be performed on a range of fluids of different (but known) optical properties in an attempt to demonstrate that the time-of-flight measurements enable the absorbing and scattering properties of the fluid to be uniquely determined. This project is most suitable for a student who enjoys building mechanical and/or electrical devices and has very good manual skills.

Generating 3D-printed phantoms with optical properties matched to those of human tissue

Supervisors: Prof. Jem Hebden, Laura Dempsey, and Prash Ganeswaran

Student: Melissa Persad

The UCL Biomedical Optics Research Laboratory (BORL) have extensive expertise in the development of physical models of human tissue (known as “phantoms”) which have optical properties matched to those of real human organs. These are used to evaluate new optical techniques and instruments for diagnostic monitoring and imaging, and of the brain in particular. New 3D printing technology is enabling highly sophisticated plastic objects to be constructed, including those with anatomically-realistic structures derived directly from medical images (e.g. MRI scans). The objective of this project is to investigate whether scattering and absorbing substances can be added to the printed plastic in order to generate materials with optical properties closely matched to those of human tissues. The student will initially print a series of samples with different concentrations of added scatterer and absorber, and measure their optical properties using a sophisticated time-of-flight system in the laboratory. Then the student will attempt to print a phantom with a complex geometry and known tissue-like properties. If time allows, images of the phantom will be generated using a diffuse optical topography system.

Imaging matrix displacement and force development in 3D collagen gels to assess the role of GRAF1 in trachoma cell contraction

Supervisors: Dr. Maryse Bailly (Institute of Ophthalmology) and Prof. Jem Hebden

Student: Gabriel Lee

The aim of the project is to develop a new technique to image matrix displacement and force development in 3D collagen gels during tissue contraction. The protein GRAF1 is down-regulated in trachoma cells and re-introduction of GRAF1 in the cells leads to a decrease in their contraction potential. One of the possible explanations for that phenotype is that GRAF1 modulates the cell interactions with the matrix, and its absence results in the cells exerting more force on the matrix, leading to more tissue contraction. Once set up, this new technique could be used to determine whether GRAF1 is involved in force development by analysing forces generated by trachoma or control cells, or cells depleted for GRAF1.