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.

Deadlines

  • 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: 57
Number of projects still available: 38

Identification of biomarkers to guide management of adult acute brain injury

Supervisors: Prof. Clare Elwell and Phong Phan

Student: (Project available)

Management of critically ill brain injured patients is guided by multimodal brain monitoring, using patient-specific physiological data to individualise treatment and improve outcome. We have an on-going programme of research into brain monitoring on the neurocritical care unit which has yielded a large archive of multimodal clinical data. This project will involve using these data sets to establish relationships between the measured physiological variables to help us create biomarkers of brain injury. This project is suitable for a student with an interest in the analysis of clinical data.

Investigation of the eye colour in jaundiced newborn infants with digital photography

Supervisors: Dr. Terence Leung, Dr. Judith Meek, and Dr. Lindsay MacDonald

Student: (Project available)

Neonatal jaundice is a common condition among newborn infants, caused by an increased bilirubin level in the blood and tissues. Bilirubin is a yellow breakdown product of haemoglobin and jaundiced infants can therefore appear to have yellow colouration in their skin and sclera. The aim of this study is to establish the relationship between the sclera colour and the serum bilirubin level in newborn infants using a digital camera. The role of the student will be to participate in analysing data collected from the neonatal unit of UCL Hospitals and analyse them. The project is especially suitable for a medical student who is interested in neonatology and would like to have early clinical contacts with patients.

Assessment of nasal blockage with acoustic sensors

Supervisors: Dr. Terence Leung and Peter Andrews

Student: Rishi Gupta

Nasal blockage is a common condition which could indicate a range of pathologies from common cold to tumours. While a patient can describe nasal sensation, the information is often subjective, inaccurate and lacking in detail. There is also a growing need for quantifying nasal blockage severity as it is becoming increasingly important for clinicians to provide evidence for their medical/surgical interventions. The aim of this project is to develop a nasal blockage analyser to assess the degree of nose blockage. Acoustic sensors are used to measure the nasal airflow at the nostril opening through recording air turbulence sounds. The bio-acoustic signals provide a novel, accurate and yet simple way to characterize and quantify nasal airway conditions naturally and objectively. The role of the student will be to participate in analysing data collected from the Royal National Throat, Nose and Ear Hospital and analyse them. The project is especially suitable for a medical student who is interested in ENT and would like to have early clinical contacts with patients.

Clinical monitoring of cirrhosis patients

Supervisors: Dr. Terence Leung and Dr. Raj Mookerjee

Student: (Project available)

Liver disease is the 5th leading cause of death in Europe and there are currently more than 1.5 million advanced cirrhosis patients in need of regular monitoring, as currently the mortality stands at 170K deaths a year. The deterioration of cirrhosis (decompensation) often leads to a change in peripheral skin blood flow, variation of heart rate and development of jaundice. These physiological changes can be measured non-invasively using Doppler flowmetry, thermal imaging, ECG monitoring and spectral imaging. The aim of this project is to measure and integrate these physiological signals, image features and biomarkers measured from cirrhosis patients in order to provide an early warning of a declining condition so that timely intervention can be enacted. The role of the student will be to participate in analysing data collected from the UCL Institute for Liver and Digestive Health, at the Royal Free campus. The project is especially suitable for a medical student who is interested in hepatology and would like to have early clinical contacts with patients.

Optimising kidney haemodialysis treatment using bio-impedance and pulse oximetry

Supervisors: Dr. Terence Leung and Dr. Andrew Davenport

Student: (Project available)

More than a million people worldwide have chronic kidney disease and are treated by haemodialysis. Although life sustaining, haemodialysis patients have an increased risk of both cardiovascular and cerebrovascular disease, with a 5 year survival in the UK less than that for ovarian cancer. Hypotension is the commonest complication of outpatient haemodialysis treatments, occurring in around 20-30% of treatments. Repetitive hypotension accelerates cerebrovascular disease and causes cardiac arrhythmias and cardiac ischaemia. Non-invasive monitoring changes in central blood volume could potentially be used to develop feedback systems to the dialysis machine to prevent hypotension. The aim of this project is to investigate the use of two techniques, namely bio-impedance and pulse oximetry, to optimise the transfer rate of the dialysis machine and therefore improving the treatment. The role of the student will be to participate in analysing data collected from the UCL Centre for Nephrology at the Royal Free campus. The project is especially suitable for a medical student who is interested in nephrology and would like to have early clinical contacts with patients.

Characterization of head movement with and without commercial neck collars

Supervisors: Dr. Pilar Garcia Souto and Prof. Nick Donaldson

Student: Ajinkya Karmarkar

Amyotrophic Lateral Screrosis (ALS) is a neurodegenerative disorder characterized by weakness and atrophy of muscles as a result of the degeneration of upper and lower motor neurons. One of the most famous cases is Stephen Hawking. From early stages of the ALS, patients experience difficulties supporting the weight of their heads even if seated, which has a major effect in their autonomy. Therefore these patients would benefit from the design or identification of a suitable collar to support the weight of the head and give stability while facilitating side-to-side movements of the head. This project aims to characterize and quantify the capacity of head movement of healthy volunteers while wearing currently available neck collars. The study involves the collection of data using a motion capture system to characterize the motion of the head relative to the trunk while walking and seating, analysis of the data, and preparation of a report of publication quality and possible submission to a scientific journal. The projects builds on two previous studies that can be made available to the student undertaking this project.

Development and evaluation of material for an undergraduate lab practical on mechanical properties of materials

Supervisors: Dr. Pilar Garcia Souto and Prof. Alan Cottenden

Student: (Project available)

The understanding of the mechanical properties of materials is essential in many aspects of engineering, from construction of buildings and bridges to biomedical devices and implants. We need to know how strong a material is, how it reacts to applied forces under different conditions, and to be able to predict under which conditions it would fail. This is of essential to avoid serious personal or material consequences. Our department currently runs a 3-hour laboratory session for first-year biomedical engineering students (in term 2) where they analyze simple real data from compression and tension experiments. Data is acquired using an Instron E3000, a state-of-the-art linear-torsion dynamic test instrument that can perform a range of mechanical tests, such as compression, stretching, and bending. This allows our first-year students to relate experimental data with the theoretical behavior of the materials they are taught about in lectures. The aim of this project to refine, support, and assess the pedagogical efficiency of the laboratory session. Extra material needs to be developed, data collected, and evaluation methods established to accommodate an increased number of students in the lab. The student undertaking this project will learn how to use the Instron E3000, learn about mechanical properties of materials and gain experience of teaching, and trial the developed material with a group of students. The student needs to be able to perform data collection and analysis and have some knowledge of Matlab.

Mechanical characterization of collagen-rich gels towards the modeling of cancerous cells growth

Supervisors: Dr. Peter Wijeratne, Dr. Pilar Garcia Souto, and Prof. Alan Cottenden

Student: (Project available)

It is well established that cancerous growth is dependent on both biochemical and biomechanical factors. Recently, remodelling of the collagen-rich extracellular matrix has been implicated in cancerous growth and progression. This project aims to quantitatively measure the mechanical properties of collagen gels used as embedding material for in vitro cancer mass experiments at the Royal Free hospital. Given appropriate consideration for COSHH regulations, tests will also be performed on the cancer masses themselves. The student will perform precision experiments using an Instron materials testing machine and analyse the resulting data, which will be used to inform a biomechanical model of tumour growth. Such a model can be used to quantify the effect of both intra- and extra-tumoural collagen properties on cancerous growth and invasion.

Identification of core temperature using infrared imaging: comparison of manually and automatically extracted data

Supervisors: Dr. Pilar Garcia Souto and (to be confirmed)

Student: (Project available)

During the outbreak of infectious diseases (e.g. SARS in 2003, the Influenza A pandemic in 2009, and Ebola in 2014) core temperature screening was used to detect individuals with fever with the aim of isolating infected individuals, which could help to contain the spread of such infectious diseases. In high transit places such as airports and hospitals, infrared (IR) thermometry has been used for screening as it is relatively easy to use, quick, and non-invasive. This method estimates the core temperature from measurements of heat (in form of IR radiation) emitted from the skin. However IR devices are prone to significant error due to incorrect use by personnel who have had insufficient training. Typical mistakes are the incorrect identification of the area of interest within the body, or the erroneous interpretation of the measurements. The student undertaking this project will compare the manual and the automatic approach to region-of-interest identification and the application of models. Front and/or side views of human heads with an IR camera will be provided. The aims of the project are: 1) Generate appropriate models using the automatically extracted data; 2) Compare the efficiency of models using manually and automatically extracted data; 3) prepare a report of publication quality for possible submission to a journal. The project builds on two previous studies that can be made available to the student undertaking this project. Prior knowledge of computer programming and statistics would be useful.

Human thermal sensation identification from infrared images – a step towards the personalization of general thermal comfort models

Supervisors: Dr. Pilar Garcia Souto and Dr. David Shipworth (UCL Institute of Energy)

Student: (Project available)

How many times have you argued with others over opening a window because you were feeling hot or increasing the heating because you were feeling cold? Over the years, researchers have been looking for a model that predicts how hot or how cold a person will feel in a given environment, but this is very difficult as it strongly depends on individual circumstances. Models tend to work for an "average" person, but will not work for all. In order to make these models more accurate and reliable, a component dependent on an individual's conditions and present circumstances should be included. Infrared (IR) thermometry allows local temperatures to be monitored non-invasively, and is easily applied to a wide variety of real-life situations. The aims of this study are: 1) Review the current literature on thermal comfort models; 2) Design and perform experiments where front and upper body IR images of people can be related to their thermal sensation and thermal comfort level or equivalent; 3) Derive a model relating skin temperature as measured in the IR images of the subjects and their thermal sensation; and (4) Compare the new model with a traditional thermal comfort model.

Using SQUID magnetometry to validate MRI tissue magnetic susceptibility measurements

Supervisors: Dr. Karin Shmueli and Dr. Paul Southern

Student: David Adams

There has been a recent explosion in the use of magnetic resonance imaging (MRI) techniques to map tissue magnetic susceptibility. Susceptibility is a property of tissue that determines how easily and strongly it can be magnetised by the very high magnetic field found inside an MRI scanner. Susceptibility maps are useful because they reveal new information about tissue composition such as its iron and myelin content. Therefore these images show promise for investigating diseases involving iron accumulation (e.g. Parkinson’s and Alzheimer’s) and demyelination (e.g. Multiple Sclerosis). One drawback of MRI-based susceptibility mapping is that the required image-processing steps affect the resulting susceptibility values so that we can only map relative tissue susceptibilities. This means it is important to compare MRI-based susceptibility values with independent measures of tissue magnetic susceptibility if the MRI susceptibility values are to be truly quantitative. One of the most accurate susceptometry techniques uses a highly sensitive magnetometer built from a superconducting quantum interference device (SQUID). SQUID magnetometers measure small changes in sample magnetisation as the magnetic field is varied so that accurate absolute susceptibility values can be calculated. Previous measurements of tissue magnetic susceptibilities made with SQUID magnetometry and MRI gave highly discrepant results. The aim of this project is to make samples of known magnetic susceptibility and use both SQUID magnetometry and MRI to investigate and compare the accuracy of both susceptibility measurement techniques. You will identify an appropriate gel material and dope it with different concentrations of a paramagnetic salt (e.g. MnCl2) and carry out SQUID and MRI susceptibility measurements on these samples. Comparing the results will give insight into the true accuracy and precision of SQUID magnetometry and MRI susceptibility mapping techniques.

Electrical Impedance Tomography in acute stroke: literature review and modelling study

Supervisors: Nir Goren, Dr. D. Werring and Prof. David Holder

Student: Tobin Joseph

Electrical impedance tomography (EIT) is a novel medical imaging method, which can produce images of the electrical impedance of the head using a box about the size of a paperback book, laptop, and EEG electrodes placed on the head. It is portable, safe, fast and inexpensive. The supervisors’ research has been to develop its use in imaging functional activity in the brain. One application lies in imaging in acute stroke. EIT could be used in an ambulance to provide early imaging which would discriminate whether stroke was due to a haemorrhage or blockage of an artery and so allow early use of a clot-dissolving agent. It could also be used in hospital to image after a stroke had occurred. It could provide early warning of bleeding into the stroke and so allow rapid surgery to relieve pressure. This project concerns monitoring after stroke. The challenge for this application is that there is natural drift in the impedance measurements. In this project, the student will investigate whether it is possible to image changes due to haemorrhage despite this drift. The underlying principle is whether the time course of the haemorrhagic change differs from that of the drift. The student will review the literature on the time course and natural history of haemorrhagic transformation in stroke and head injury, and generate some typical exemplars of time course and size. These will be inserted into a computer model of the head to produce simulated data recorded during EIT in haemorrhagic transformation in stroke. These will be reconstructed to explore if EIT imaging is feasible. Skills to be acquired: review of literature on stroke and head injury; programming in Matlab; data analysis; computer modelling. The project is suitable for a medical student with an interest in programming. Previous programming experience is desirable but not essential as full training and engineering support will be given. The project is suitable for a single student or two working as a pair.

Developing 3D-printed multishell head phantoms for Electrical Impedance Tomography

Supervisors: Dr. James Avery, Dr. Rebecca Yerworth, and Prof. David Holder

Student: (Project available)

Electrical impedance tomography (EIT) is a novel medical imaging method, which can produce images of the electrical impedance of the head using a box about the size of a paperback book, laptop, and EEG electrodes placed on the head. It is portable, safe, fast and inexpensive. The supervisors’ research has been to develop its use in imaging functional activity in the brain. For research purposes, systems are tested in head-shaped liquid-filled tanks which emulate the electrical properties of human tissue. Construction of a head tank is particularly challenging, and often is a compromise between representing the shape accurately and matching the properties of different tissue layers This is commonly achieved by using different concentrations of saline or saline infused agar gel. These are made to be anatomically accurate by the use of 3D-printing. It is desirable to construct tanks with four separate layers : Scalp, Skull, cerebrospinal fluid (CSF) and Grey/White brain matter but, until now, it has only been possible to make an outer shell and simulated skull. When filled with saline, this only simulates scalp, skull and brain but not grey/white matter in the brain or the CSF. The aim of this project is to improve upon the existing 3D printed tank through the use of Volume Conductive Film (VCF), which prevents diffusion of ions between layers of different concentrations, whilst allowing current flow. Initial work will include the construction of samples validating the stability of phantoms using VCF, before moving on to construction of a phantom with a complex geometry using 3D printing, and comparing EIT measurements to simulations. Skills to be acquired : 3D printing, use of CAD (computer-aided design) software for this, Electrical Impedance Tomography, medical imaging. The project is suitable for a student with a background in physics, engineering or computing, or a medical student with an interest in programming.

Imaging of neonatal brain pathology using Electrical Impedance Tomography: a tank study

Supervisors: Dr. James Avery, Dr. Rebecca Yerworth, and Prof. David Holder

Student: (Project available)

Electrical impedance tomography (EIT) is a novel medical imaging method, which can produce images of the electrical impedance of the head using a box about the size of a paperback book, laptop, and EEG electrodes placed on the head. It is portable, safe, fast and inexpensive.  The supervisors’ research has been to develop its use in imaging functional activity in the brain. Previous work both in simulation and physical models (“phantoms”), has demonstrated the potential of imaging impedance changes resulting from epileptic activity or bleeding into the brain (intraventricular haemorrhage, IVH). This could provide a valuable new cotside imaging method in new-born babies who are at risk of these conditions. The aim of this project is to further the understanding of the feasibility of imaging these pathologies in neonates through experiments using an existing 3D printed anatomical head phantom. Currently the minimum volume and magnitude of the physiologically induced change which can be successfully imaged is not well understood. The purpose of this project is to evaluate whether the use of EIT for these applications appears feasible. The study will employ the UCH ScouseTom or commercial SwissTom EIT systems in an anatomically realistic head-shaped tank. The student will design test objects to simulate epilepsy or haemorrhage using biologically representative materials such as vegetables or sponge. These will be imaged in the head phantom. Images will be evaluated for The clinical relevance of this application of EIT will then be assessed based on the minimum change which can be imaged successfully. Experimental skills are important for this project, as well as some knowledge of Matlab (or similar). Skills to be acquired : Experimental design, bioimpedance, use of EIT systems, data analysis and statistics, medical imaging. The project is suitable for a student with a background in physics, engineering or computing, or a medical student with an interest in programming and methods in biophysics.

Comparing the use of custom and generic finite element meshes for imaging with Electrical Impedance Tomography: a computer modelling study

Supervisors: Dr. Thomas Dowrick and Prof. David Holder

Student: (Project available)

Electrical impedance tomography (EIT) is a novel medical imaging method, which can produce images of the electrical impedance of the head using a box about the size of a paperback book, laptop, and EEG electrodes placed on the head.  It is portable, safe, fast and inexpensive.  The supervisors’ research has been to develop its use in imaging functional activity in the brain in conditions such as epilepsy or stroke as well as normal functional activity. In order to produce reconstructed, an anatomically accurate computer model of the head is needed. This is achieved using Finite Element Model (FEM) meshes, which resemble ad wire-frame model with about 10 million tiny tetrahedral elements. These can be generated from CT and MRI images of the subject. However, these are time consuming to produce. For hospital use, it would be easier to use a stock FEM mesh for all subjects. However, the difference between a stock mesh and the subject’s real head geometry may introduce unacceptable errors in the reconstructed images.The purpose of this project is to evaluate, using computer modelling, if acceptable accuracy can be obtained by using a stock FEM mesh. The student will undertake the following steps: CT/MRI image segmentation to generate 3D meshes, reconstruction of EIT images using human and animal data and objective evaluation of image quality for different mesh types. Skills to be acquired : Electrical Impedance Tomography, programming using Matlab, EIT image reconstruction, image segmentation, data analysis and statistics, medical imaging. The project is suitable for a student with a background in physics, engineering or computing, or a medical student with an interest in programming.

Imaging the internal structure of autonomic nerves in the body using Electrical Impedance Tomography: a literature review

Supervisors: Ilya Tarotin and Prof. David Holder

Student: (Project available)

Electrical impedance tomography (EIT) is a novel medical imaging method, which can produce images of the electrical impedance of the head using a box about the size of a paperback book, laptop, and EEG electrodes placed on the head.  It has the unique potential to produce images of activity in nerve cells over milliseconds. It is portable, safe, fast and inexpensive.  The supervisors’ research has mainly been to develop its use in imaging functional activity in the brain. However, it can also be used to image nerve activity inside nerves, using a flexible rubber cuff surgically inserted around the nerve. One such application, funded by a major drug company, is to use this in imaging inside autonomic nerves. A particular candidate is the vagus nerve in the neck. This is known to contain component nerve pathways contributions from about ten different organs in the body such as the bowel, heart and lungs. However, the internal organisation of the vagus nerve is not well known. In order to determine if EIT is likely to be useful in imaging activity within this nerve, it is necessary to know if the contributions from different organs are well localised. Imaging studies to establish proof of concept are currently being undertaken in the cervical vagus nerve in the anaesthetised rat.The purpose of this project is to review all known information on this topic and establish the pattern of localisation of contributions from different organs. The student will undertake a literature review physiology, anatomy and histology of the vagus nerve in the rat. The outcome of the project will include answers to the following questions : What is internal organization of the vagus nerve of the rat (anatomy and histology)? Which organs does it supply? Which fascicles of the vagus and what percentage of them are responsible for supplying particular organs? Is there some internal organization of fascicles supplying particular organs? What are the implications of this for the likely success of EIT in imaging within the nerve? The reviewed data will be consolidated into a computerised model which will then be used to establish the feasibility of EIT for imaging activity within the nerve. Skills to be acquired : The project is suitable for a medical student with an interest in neuroscience, biophysics and programming. Previous programming experience is not essential as training will be given.

Investigating the mechanisms of cancer calcification using state-of-the-art physical chemistry characterisation

Supervisors: Dr. Sergio Bertazzo and Prof. Alessandro Olivo

Student: (Project available)

Breast cancer is the commonest cancer in women in the UK. The calcified material found in breast cancer has never been thoroughly characterized and there is no study in the literature comparing its characteristics with bone and with regard to calcification degree, site of origin and type of cancer. In this project, we will use for the first time cutting-edge physical-chemistry characterisation techniques such as focused ion beam (FIB) and electron microscopy (SEM-EDX and TEM) to determine crucial variations in the nature of the calcified material found in cancer, and then fully compare this material with bone. This innovative research will build on the comprehensive skill set of the applicant and take it in a new and exciting direction that focuses on truly medically important breakthroughs, such as the mechanisms for cancer calcification.

Integrating bio-imaging methods: a single non-toxic sample preparation protocol for electron, fluorescence, bio-Raman microscopy and macroscopic imaging methods

Supervisors: Dr. Sergio Bertazzo and Dr. Adrien Desjardins

Student: (Project available)

The wide array of bio-physical requirements for biological imaging using different methods (such as electron and fluorescence microscopy, photoacoustics, among others) inadvertently creates obstacles to a full integration and correlation of all bioimaging methods. In this way, a synergistic and holistic characterization of bio-medical systems cannot be achieved., We propose to develop in this project a single novel protocol whereby we will be using non-toxic reagents and inorganic polymers to prepare biological samples to be imaged sequentially by all major bio-imaging methods, from the nano to the macro (meter) scale. The possibility to use a single non-toxic protocol for sample preparation will allow us to select macroscopic regions of interest within a sample and then further investigate each region by different methods, consolidating the information of biochemical composition and structure, including ultrastructure. This new protocol, which we discovered by serendipity, is a truly exciting way to prepare biological samples for imaging. It will open unforeseen opportunities to integrate the information provided by different imaging methods into a single comprehensive overview of biological systems, leading to unprecedented advances in biomedical research.     

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: Sophie Schauman

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.

Ultrasound phantom for minimally invasive intra-cardiac procedures

Supervisors: Dr. Adrien Desjardins, Dr. Wenfeng Xia, and Dr. Malcolm Finlay (Barts Heart  Centre)

Student: Ragav Manimaran

Description: Ultrasound imaging can be valuable to guide minimally invasive intra-cardiac procedures. These procedures include treatment of atrial  fibrillation by ablation of pulmonary veins, which can be guided by intra-cardiac echocardiography (ICE) using a needle or catheter probe. Interpreting ultrasound images can be challenging, particularly for trainees. This project is focused on the development  of a training phantom for electrophysiology procedures with realistic ultrasonic properties and a modular design to allow for replacement of the inter-atrial septum. Time permitting, vascular access phantoms will also be created using a similar approach. The  project will involve 3D design, data acquisition and processing, and a hands-on approach to phantom construction. There will be close involvement with clinicians at all stages of the project.

Ultrasound imaging of perfused placentas

Supervisors: Dr. Wenfeng Xia, Dr. Tom Vercauteren, and Dr. Adrien Desjardins

Student: Batol Daher

Visualisation of the placenta with ultrasound imaging is important to identify and treat pathologies. Recently-developed ultrasound probes provide unprecedented image quality, so that there is strong potential to improve patient outcomes. This project will be set within the context of the “Guided Instrumentation for Fetal Therapy and Surgery” (GIFT-Surg) project, which is focused on developing advanced surgical tools and novel imaging techniques for fetal medicine. It will have two main foci: a) 3D imaging of fetal ultrasound phantoms with a state-of-the-art ultrasound imaging system, to optimise quality by tuning acquisition parameters; b) perfusion and ultrasound imaging of human placentas obtained from University College Hospital. Support with perfusion and ultrasound imaging will be available from Gift-SURG Staff and PhD students. Throughout the project there will be close collaboration with clinicians.

Improved cycling exercise machines

Supervisors: Prof. Nick Donaldson and Dr. Pilar Garcia Souto

Student: Jeevan Ubhi

Cycling has long been used for neurological rehabilitation: it is easier to arrange and generally safer for the patient than walking because there is no risk of falling over. It is used for exercise of the leg muscles, strengthening bones, cardio-vascular fitness, and, we are investigating its use as a therapy to reduce paralysis after spinal cord injury. However, cycling machines for disabled people have foot-rests instead of pedals which prevent ankle plantarflexion and therefore (theoretically) all the power is produced by muscles of the hip and knee joints, none from the ankle muscles. It would better if that mechanism included ankle motion and this might be done with a mechanism that couples the angle of the foot-rest to the crank angle. The aims of this project are: (i) to set up a recumbent tricycle with a motion-capture system and learn to record leg motion and plot the results; (ii) to test a group of able-bodied people to find out how the hip, knee and ankle motions are related; (iii) to design a mechanism which rotates the footplates appropriately during rotation of the crankshaft to give plantarflexion with flexion and extension of the hips and knees.

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: Muneeb Muhammad

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 Prof. Jem Hebden

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.