UCL DEPARTMENT OF MEDICAL PHYSICS AND BIOENGINEERING

MSc Projects 2009-10

Here is a list of projects being offered for MSc students in the Department. For details of deadlines and for registering submissions, see the Moodle page. Full instructions are available here.

Dose optimisation in lateral cephalometry

Supervisors: Dr Adam Gibson and Dr Jenny Griffiths

Student: MSc, particularly Radiation Physics

A standard imaging protocol in orthodontics is to take a lateral x-ray image of the head. From this image, certain landmarks are identified and some standardised measurements are made. This allows facial deformities to be identified and characterised as well as informing the surgical treatment. The patients are usually children and we want to reduce the radiation dose.

In this project, you will simulate the effect of reducing the radiation dose and examine the effect of dose reduction on image quality. You should be able to recommend a new protocol and predict the subsequent dose reduction.

This project will be carried out in collaboration with Kidderminster Hospital and you may be expected to travel there on occasion; expenses will be covered.

Medical Physics forum website.

Supervisors: Dr. Nick Everdell and Prof. Jem Hebden

Student: UG or MSc.

This project is to design and build a ‘proof of concept’ website that could be a very useful resource for the department and possibly the Engineering faculty as well. The idea is that the website would be a ‘resource centre’ for the department. It would have 3 main strands:

1. a discussion forum where staff and students could post their technical problems and questions

2. a database of departmental expertise. The idea here is that anyone within the department could consult this to find out who the best person would be to talk to about a particular problem

3. a database of departmental resources and facilities

These 3 elements would link together in some way to enhance the site’s usefulness. The purpose is to promote the free exchange of ideas, skills and resources between staff members (and students), something that does not always happen that well at the moment. Part of the project would involve the preparation and distribution of questionnaires around the department, to gather information for the database. This project will obviously require some interest and/or knowledge of web programming. If the concept can be shown to work well for the Medical Physics department, it could then be implemented faculty wide (the ‘faculty forum’), where we envisage it being a very useful resource.

Designing and constructing a cylindrical tissue-equivalent phantom for evaluating simultaneous EEG and optical imaging.

Supervisors: Prof. Jem Hebden and Rob Cooper

Student: Robin Eames

Researchers within the UCL Biomedical Optics Research Laboratory (BORL) are attempting to simultaneously display the electrical and haemodynamic changes associated with brain activity. This work uses an optical imaging system which has an array of optical fibres placed in contact with the head, combined with an array of EEG electrodes. The project will initially involve designing and building a hollow cylinder (based on a combination of polyester resin and thin conducting wires) through which light and electrical currents can pass. The cylinder will then be filled with an optical-scattering / electrically-conducting liquid. Measurements will be made using optical fibres and electrodes placed on the surface of the cylinder as appropriate targets/electrical sources are moved within the liquid. Data will be analysed and images will be generated. This project is most suitable for a student who enjoys building mechanical and/or electrical devices and has good manual skills.

Maximising sensitivity and specificity of optical mammography.

Supervisors: Dr. Adam Gibson and Dr. Danny Alexander

Student: MSc. (probably MIC)

We have imaged about 50 women using optical mammography. For each woman, we record images of blood volume, blood oxygenation and optical scatter. These gave us a sensitivity of 85.8% and a specificity of 66.8%. In this project, you will determine the combination of these images which maximises the sensitivity and specificity with which the system can distinguish between healthy tissue and tumour. One method which will be examined will be support vector machines.

Obtaining initial estimate of optical parameters.

Supervisors: Dr. Adam Gibson and Prof. Jem Hebden

Student: UG or MSc.

A time-resolved optical imaging experiment yields up to 1024 distinct histograms of photon arrival times (click here for technical details). These are measurements correspond to different lines-of-sight across the same object, using different source-detector combinations. The purpose of this project is to model the data analytically and obtain a fast estimate of the mean optical properties throughout the whole object. This project would be suitable for a student with an interest in computer programming and will involve some mathematics.

Measurement of optode locations using mean flight-time and intensity.

Supervisors: Dr. Adam Gibson and Prof Jem Hebden

Student: UG or MSc.

Our optical imaging works by shining light from each connector in turn and measuring light from other connectors. The time taken for the light to travel across the body depends on the distance travelled and the optical properties of the body. If we assume the optical properties to be constant, it should be possible to use the measurements of photon transit time to calculate the separation between the connectors, and hence their locations. This project will determine whether such a method can work, and the likely errors. This project would be suitable for a student with an interest in computer programming and will involve some mathematics.

A feasibility study for a very low cost optical topography system using just LEDs.

Supervisors: Dr. Nick Everdell and Dr. Salavat Magazov

Student: Abdulla Ghaly, Muhammad Saif

An LED (light emitting diode) can also be used as a light detector (Stojanovic et al., Physiological Measurement 2007). With this in mind this project will investigate the feasibility of building a very simple, low cost optical topography system that uses LEDs as both sources and detectors. This project would suit someone with an interest in electronics and will involve some circuit design and construction. Further details of our optical topography work can be found at: www.medphys.ucl.ac.uk/research/borl/research/topography.

Imaging the auditory cortex using the UCL optical topography system.

Supervisors: Dr. Nick Everdell and either Anna Blasi / Teresa Correia / Rob Cooper

Student: MSc.

This project involves optical imaging of the adult auditory cortex, attempting to map it’s response to various auditory stimuli. The student will design a new optical array to be used with the UCL optical topography system, which fully exploits the system’s ability to produce three dimensional images of the cortex. This project will involve some practical work so would suit someone who is happy to spend a fair amount of time in the workshop. Further details of our optical topography work can be found at: www.medphys.ucl.ac.uk/research/borl/research/topography.

Pulse plethysmography using an optical mouse

Supervisors: Dr Adam Gibson and Dr Nick Everdell

Student: Amena Noorani

An optical mouse consists of an LED and a photodetector. It is possible to modify certain types of mouse so that the detector can be read out using a serial port. This project will involve selecting a mouse and making appropriate modifications so that it can be used to detect pulsatile blood in the finger. This project is intended to lead to a demonstration of medical optics which can be used in school practical classes.

Maximising sensitivity and specificity of Terahertz images

Supervisors: Dr. Adam Gibson and Dr. Caroline Reid

Student: MSc. (probably MIC)

We have Terahertz images from cancer and healthy tissue. The data can be processed to give many different datatypes. In this project, we will examine these datatypes and determine which combinations of datatypes maximise the difference between healthy and cancerous tissue. One method which will be examined will be support vector machines.

Comparison of optical mammography of the compressed and uncompressed breast.

Supervisors: Dr Louise Enfield and Dr Adam Gibson

Student: Bahareh Gholipour

Optical imaging techniques are being developed at UCL as a means of imaging the adult female breast to detect breast cancer. There are two main approaches to optical mammography: imaging the compressed breast or the uncompressed breast. In this project, the student will construct a compressible anatomically-realistic optical  phantom containing features of known size and contrast. This will then be imaged using our optical tomography system in compressed and uncompressed geometries, and then the images will be analysed to compare the two methods.

Near infrared stethoscope: listening to body sounds with light

Supervisors: Dr. Terence Leung and Dr Ben Cox

Student: MSc

Internal organs are noisy. These noises are caused by the movements of the internal organs and can aid doctors to check their health, e.g. heart and lung sounds. A simple device long used by doctors to listen to body sounds is the stethoscope. Its principle is based on channelling sound waves from the surface of the patient’s skin to the examiner’s ears. The aim of this project is to investigate a different transduction mechanism to measure body sounds, in which near infrared light is used to pick up sounds. The new “near infrared stethoscope” may provide a better sensitivity than the conventional acoustic stethoscope. The project involves computer simulation and experiments. It will suit a student who has computer programming experience, preferably Matlab, and likes experimental work.

Simulation of Rapid Magnetic Resonance Spectroscopy (MRS) Studies

Supervisors: Prof. Roger Ordidge and Dr. David Carmichael

Student: MSc

Based on the Echo Planar Imaging method, several MRS signal acquisition schemes will be tested by computer simulation for sensitivity and accuracy. Speedy measurements are required to accuratley measure tissue physiology and metabolism within reasonable measurement times.
Skills required (to be learned): MATLAB simulation and reasonable mathematical skills.

Simulation of MRI of magnetically-labelled contrast agents

Supervisors: Prof. Roger Ordidge and Dr. David Carmichael

Student: MSc

The aim is to produce positive contrast images of drugs and cells labelled with iron particles. The method requires simulation of the selection abilities of modified amplitude-modulated radiofrequency pulses that will be used to select the water surrounding such iron particles without affecting water in normal environments.
Skills required (to be learned): MATLAB simulation and reasonable mathematical skills.

Using infrared light to investigation the absorption properties of nonwoven felts used in medical applications

Supervisors: Prof Alan Cottenden, Raquel Santamarta and Prof Jem Hebden

Student: Emily Krimholtz

Absorbent nonwoven felts are used in a number of medical applications, notably incontinence pads and wound dressings. It is a major objective of the Continence and Skin Technology Group to establish a better understanding of how fluids interact with absorbent materials and build mathematical models which will enable the development of more effective medical products. This project will use an infrared device to investigate the absorption properties of nonwoven felts by mapping the distribution of fluid in them under a number of equilibrium (e.g. retention under gravity) and dynamic (e.g. horizontal and vertical wicking) experimental configurations. Data from the new device will be compared with both experimental data using other techniques and predictions based on existing mathematical models. The project will be primarily experimental and based at the UCL Archway campus (by Archway tube station).

Measuring the permeability of superabsorbent polymers

Supervisors: Prof Alan Cottenden and David Cottenden

Student: UG or MSc

Superabsorbent polymers (SAP) are remarkable materials capable of absorbing more than 100 times their dry weight in water. They are much used in absorbent medical and hygiene products, as well as in food packaging (for example, to absorb meat juices) and spill sorbents. To exploit their properties optimally we need to measure their permeability when hydrated (how easily fluid flows through them under pressure) but this is difficult to measure. This project will involve developing a method - using a simple, recently built flow cell - to measure the permeability of four SAPs supplied by BASF (the world’s biggest supplier, with whom we are working). Time permitting, the data will be used to test theoretical models for SAP performance. The project will be primarily experimental and based at the UCL Archway campus (by Archway tube station).

Development of a new laboratory method for characterising the leakage performance of experimental absorbent materials

Supervisors: Prof Alan Cottenden and Raquel Santamarta

Student: Maria Gkika

The Continence and Skin Technology Group is currently collaborating with two other universities and five companies to develop a new washable absorbent pant for lightly incontinent women. As part of the project, we have developed a test rig for measuring how much fluid a pad will hold under standard conditions before it leaks. Currently, we simply apply fluid at 2 ml/s until leakage occurs. The proposed project will involve investigating the impact on pad performance of using different flow rates and intermittent dosing patterns which may better reflect real use. The methodology developed in the project will be used to evaluate experimental fabrics provided by Leeds University and the data will be fed into our ongoing product development work. The project will be a mix of experiment and theory and based at the UCL Archway campus (by Archway tube station).

Investigation of a new device for measuring water vapour flux density from skin

Supervisors: Prof Alan Cottenden and Rob Heggie

Student: UG or MSc

In the last couple of years students and staff at the Continence and Skin Technology Group have characterised the performance of a range of devices for measuring the water vapour flux density from skin, an important measure of how wet skin is – for example, having been wearing an incontinence pad. This work has involved comparing various devices inter alia and calibrating them to reveal their accuracy and limitations. Recently, a new device has become available and this project will involve investigating and quantifying its performance to see if it is any better than earlier devices. The project will be primarily experimental with the possibility of some mathematical modelling, and it will be based at the UCL Archway campus (by Archway tube station).

Investigation of a device for measuring the volume of urine loss in incontinent people

Supervisors: Dr. Martin Fry, Prof. Alan Cottenden and Rob Heggie

Student: Hassan King

The Urilos nappy is a diagnostic device which comprises a pad with a capacitive sensor imbedded in it. When the pad becomes wet the capacitance of the sensor changes (the dielectric constant for wet and dry pad differ) and it is claimed that, once calibrated, it is possible to estimate the volume of urine in the pad from the change in capacitance. However, anecdotal evidence suggests that the readings are heavily dependent on where in the pad the fluid arrives; the flow rate at which it arrives and the shape of the worn pad. This project will involve a controlled laboratory investigation in which the output of the device is studied for various volumes, flow rates, points of fluid application and pad geometries. We would also like to investigate the potential for estimating leakage flow rates by differentiating the capacitance change with respect to time. The project will be primarily experimental with the possibility of some mathematical modelling, and it will be based at the UCL Archway campus (by Archway tube station).

Development of a MATLAB based FES cycling model

Supervisors: Prof. Nick Donaldson and Kylie De Jager

Student: MSc

FES (Functional Electrical Stimulation) has been successfully used to enable SCI (Spinal Cord Injured) patients to stand in clinical trials. However, this is a complicated process that is not popular for home use. FES cycling is an alternative that has generated a considerable amount of research over the last decade or so as it is relatively simple to use at home, outside of the clinical environment. Nonetheless, the recreational use of the technology still has limitations, predominantly due to the low efficiency and power output generated by SCI persons, as compared to that of AB (Able Bodied) cyclists. The goal of this project is to develop a biomechanical model for FES cycling. Such a model would ultimately serve as a tool to investigate the relationship between muscle activation and the final output power generated. A model, developed by Riener and Fuhr1 , for FES standing, will be adapted to build the cycling model. The current model, implemented in MATALB and Simulink, consists of a three-segmental model (shanks, thighs and upper body) and 9 mono- and bi-articular muscle groups. A combination of functional blocks, each block describing some aspect of the FES process, are used to simulate movement. The blocks can be grouped as follows:
• Electrical stimulation
• Muscle activation
• Muscle force
• Generation of joint moments
• Resultant movement
You will have to adapt the model from that of a seated subject standing up, to a recumbent cycling position where the legs pedal against a variable load. An interface is also required that allows the model parameters to be set, such as the selection of which muscle groups to stimulate and the pedal position at which the stimulation starts and stops. The simulated muscle force and joint moments can then be used to determine output power generated. Graphics depicting the resultant movement will also be required.
Please note that previous experience with both MATLAB and Simulink is essential for this project.

History of Electrotherapy

Supervisors: Prof. Nick Donaldson and Dr. Anne Vanhoest

Student: UG or MSc

A recent book from a Cambridge historian (Fara P., An Enlightenment for Angels, Icon Books, 2002) shows that electrotherapy, treating illnesses by the application of electricity to the body, started immediately following the invention of the Leyden Jar in the 1740s. It seems to have been a thriving business during the remainder of the 18th century and continued in the 19th century. As recently as the 1920s, text books on the subject were appearing with recommendations for treating all manner of complaints. However, in Britain, by the 1970s, the methods had been abandoned except perhaps by some physiotherapists. Nowadays, the treatment of motor disorders by exploiting neural plasticity with electrical or magnetic stimulation is a hot research topic: we may wonder whether some methods that were in use for some 200 years will be rediscovered but now with some scientific understanding of the therapeutic mechanisms.

It would be interesting to know how widely electrotherapy was used and why it fell out of use early in the 20th century. We propose that an interesting project would be to investigate these questions using the resources of the Wellcome Library of the History of Medicine (on Euston Road). The study should aim to understand the treatments used, described in modern scientific terms, but also critically appraise the methods, at least concerning the physics involved (but not necessarily the neurophysiology).

An Implantable Movement Sensor

Supervisors: Prof. Nick Donaldson and Dr. Anne Vanhoest

Student: Jorge Chacon Caldera

A closed silicone rubber tube, filled with isotonic saline and implanted in the body, will be in osmotic equilibrium, neither gaining nor losing volume. If electrodes are placed at the ends of the tube, the impedance through the saline can be measured and this may change as the tube is stretched or bent. A thin tube could therefore make movement sensor: we want such devices to detect changes in the shape of the bladder (as part of a system to prevent incontinence). What is needed is a simple method to measure the tube resistance through the skin. One possibility, using radio-frequency induction, is to arrange two resonant circuits (inductor-capacitors pairs) coupled through the variable resistance. If one resonant circuit is excited by a short burst of radio-frequency energy from an external transmitter, can we use the time course of the magnetic field generated by the second resonant circuit to show the resistance? The advantage of such a system is that it uses components that can easily be protected from body fluid, and should be independent of the magnetic coupling from the external transmitter.

The project will be to develop such a system on the bench (if possible). Prior experience of electronics will be helpful but not mandatory.

Understanding the effect of surface roughness on electrode impedance

Supervisors: Prof. Nick Donaldson and Dr. Anne Vanhoest

Student: UG or MSc

A polarisable electrode like platinum has an impedance that has both capacitance and resistance but these are not combined in a simple way. Over a range of frequency that is useful to recording nerve activity, such an electrode may have a nearly constant phase angle of about 70 degrees. Part of the reason for this strange behaviour is thought to be due to the roughness of the surface. The interface itself may be perfectly capacitive but the roughness means that some of the surface capacitance is accessed through the resistance in tissue within the crevices. The electrode then has a distributed structure which may have the measurable constant-phase characteristic. In this project, the effect of different types of roughness will be explored using models made from resistors and capacitors in 2D arrays. Models will be made with crevices of different depths and different profiles (convex and concave). The impedance of these models will be measured on an Impedance Analyser that plots impedance over the chosen range of frequency.. One aim will be to see what type of roughness can give a phase-behaviour like platinum, assuming that the platinum-saline interface itself is purely capacitive.
An enjoyment of model-making and mathematics will be helpful in this project.

Wind Turbines in the Jet Stream: a feasibility study

Supervisors: Prof. Nick Donaldson and Dr. Anne Vanhoest

Student: UG or MSc

The power from wind turbines rises as the cube of the wind speed. The speed of the jet stream is sometimes 200 miles per hour. Obviously the power that might be extracted could be enormous. However the course of the jet stream moves over the earth’s surface and is high in the atmosphere. Might turbines be placed in the jet stream to extract some of this power? One idea is to fly a large kite, which lifts the turbine, from a ship that moves about the ocean under the jet stream. Electricity from the generator could electrolyse sea water and the hydrogen could be stored in the ship.

This is a project for two students who should come up with one concept and then write two reports about its feasibility, One should report on the engineering aspects; the other on the meteorological and economic aspects of this concept. Good reports should use stated principles of engineering; use data from references; and be generally quantitative rather than merely descriptive. Of course it is essential that none of the possible difficulties (for example: the weight of the wire going to the kite) is neglected.

Electrical nerve stimulation: designing, producing and testing a portable stimulator

Supervisors: Dr. Anne Vanhoest and Prof. Nick Donaldson

Student: UG or MSc

Computer models are increasingly replacing real nerves to test new stimulation concepts. While this is necessary at the early stages of development, the simplifications intrinsic to the model limit its usefulness as it is not a true representation of in vivo electrical stimulation. To avoid setbacks during chronic experiments it is important to keep controlling the efficacy of new stimulators and electrodes against real nerve in vitro. At the Implanted Devices Group we have used xenopus sciatic nerves to improve our understanding of stimulation due to current spread and compare proposed stimulation methods against our experimental stimulator. This project, for one or two students, is to build and test a new experimental stimulator based on the current one. The project involves designing, making, populating and testing the pcbs for the new stimulator as well as packaging it in a convenient and robust manner. Depending on the qualifications of the student(s), parts of the current circuits will be re-designed and the finished stimulator will be used in tests on explanted xenopus sciatic nerves.

The project is open to one or 2 students, whether at B.Sc. or M.Sc. level, with a basic understanding of electronics (resistor, capacitor, comparator and integrator) and a willingness to get away from the pc and “make things” (pcb, box). If 2 students are interested but only one of them has the electronics knowledge while the other has some understanding of nerve physiology, the experimental part of the project could be expended. It will then be important for both of them to demonstrate their ability to work as a team, supporting and complementing one another.

Optimal techniques for modeling x-ray phase contrast imaging systems

Supervisors: Dr. Peter Munro and Prof. Robert Speller

Student: Chrameh Mbah

The bulk of current day x-ray imaging systems image an object's x-ray absorption profile. Most objects of interest in medicine and biology are, however, predominantly phase objects which delay incident x-rays in accordance their composition. Our group is currently building a novel system for performing phase contrast imaging and need to model a variety of phenomena to aid in the design of the system.

Models of our and related systems employ scalar diffraction theory in the Fresnel regime. The application of such theory is still in its infancy in x-ray imaging. We currently use a reasonably direct application of scalar diffraction to model our system however we are proposing a project in which a student would consider a number of techniques which may be employed to efficiently model phase contrast imaging systems. In particular, the student would be encouraged to consider how the chirp z transform, Wigner distributions and the method of stationary phase can be used to complement or replace our existing modeling techniques. The student may then apply the developed techniques in the study of important phenomena which arise in x-ray phase contrast imaging systems such as Talbot self imaging.

The student will need to have good mathematical and computer programming skills. Skills in developing and testing models will be acquired as well as a good understanding of x-ray phase contrast imaging systems.

Deconvolution of experimental phase contrast patterns to simulate acquisitions with higher spatial resolution devices

Supervisors: Dr. Sandro Olivo and Prof. Robert Speller

Student: Thomas Heslin

Background - X-ray phase contrast imaging is a new, exciting imaging modality with the potential of revolutionizing the world of diagnostic radiology over the next years. It generates image contrast from the phase changes of x-rays instead of x-ray absorption, and as a consequence it solves the main problem of diagnostic radiology i.e. poor image contrast due to low absorption differences. Fields like mammography were demonstrated to benefit enormously from this approach.

Deconvolution is a classic method of increasing image quality, especially in terms of resolution. The student would be provided with a dataset of phase contrast images, open-source deconvolution and phase contrast modeling software, and would have the accomplish the following tasks: - process phase contrast images acquired with a given spatial resolution; - simulate phase contrast images with a finer resolution; - match processed experimental and simulated images. This project would allow the student to acquire fundamental skills in data analysis and simulation methods. Some basic degree of computing skills is required. For students at MSc level, some degree of interaction/modification/improvement of the open source code provided would be required.

Implementation of de-blurring routines

Supervisors: Dr. Caroline Reid and Prof. Robert Speller

Student: MSc or UG

Conventional projection radiography is the most widely implemented method of x-ray screening methods, be it mammography, security screening of passenger luggage or quality control of industrial products. This method can be limited, firstly, through effective ‘stacking’ of objects in a projection image resulting in flattened images from which it is difficult to discriminate objects and, secondly, distortion of image information due to variations in x-ray absorption properties of imaged structures, for example, difficulty in distinguish between a thin sheet of strong absorber and a thick slab of weak absorber. These effects can lead to important information from the screening process being overlooked. It is proposed that this may be overcome through the use of digital x-ray tomosynthesis, an imaging technique currently attracting much attention in the medical imaging field. Tomosynthesis is a refinement of conventional geometric tomography methods where a finite number of projection images are acquired at varying orientations of the x-ray tube around the imaged object, from which a 3D image of the object is created. From these 3D images retrospective reconstruction is used to create focussed 2D slice images of an arbitrary number of planes through the object. It is proposed this method will be performed on objects moving on a conveyor system, leading to the name ‘On-belt Tomosynthesis’ (ObT).

Typically in tomosynthesis, a set of slice images are generated from the summation of a set of shifted projection images acquired at different orientations of the tube. This is referred to as the Shift-and-add (SAA) reconstruction. This SAA reconstruction takes into consideration the fact that the projection of objects at different heights above the detector will be dependent on the relative heights of the objects above the imaging plane. While one benefit of the SAA image reconstruction method is the small computing power required to run the algorithms, the resulting images are heavily affected by blurring as they contain images from every plane of the imaged object; one plane in focus and all the others smeared on top. Code for the SAA image reconstruction method has been developed. This project aims to implement a number of de-blurring routines, implemented on top of the SAA image reconstruction method, have been developed to remove artefacts and improve the reconstructed image quality. Test procedures will then be developed to assess the relative image quality of the reconstructed images. This project would be suitable for a student with an interest in computer programming and will involve mathematics.

Intelligent CT

Supervisors: Prof. Robert Speller and Dr. Peter Munro

Student: Caroline A Magrath

X-ray and gamma ray imaging are still the most frequently carried out examinations despite the concern for radiation burden. Recently the UCL Radiation Physics Group developed a technique capable of reducing dose without a loss of image quality – the technique is called I-ImaS. This technique adjust the imaging conditions on-the-fly to suit each local region in the object being imaged. The technique was designed for planar imaging but now we wish to extend this to CT.

A project to investigate the I-ImaS_CT concept. Last year a student demonstrated that the concept is viable for dose reduction but did not really study the steering algorithm that should be used to control exposure. Furthermore only one type of imaging task was studied. The project requires phantoms to be built, software to be written and many experiments carried out using the X-Tek CT system. This is an u/g merging into an MSc project.

The Bazooka: an ultra-high resolution gamma imaging camera for nuclear medicine

Supervisors: Dr. Gary Royle and Dr. Ian Cullum

Students : Kiran Easwaran and Berta Darakchieva

Nuclear medicine images distributions of radioactively labeled pharmaceuticals in the patient for diagnostic purposes. Image quality is generally poor in comparison with techniques such as CT or MRI due to the imaging cameras employed. Generally this is acceptable because the clinician is looking for functional information rather than anatomical detail, but there are situations when very high spatial resolution images are required. This project will construct and evaluate a nuclear medicine camera capable of achieving very high spatial resolution images.

It is based on a highly sensitive CCD camera coupled via an optics system to a coded aperture collimator. The project will involve instrument development, experimental measurement and development of computer codes for controlling the camera and processing the images. The aim of the project will be to determine the spatial resolution that can be achieved and the minimum level of radioactive pharmaceutical that can be used to generate an acceptable image.

Reprogramming and Improving our Optical Topography System

Supervisors: Dr Nick Everdell and Rob Cooper

Student: MSc

Our optical topography system is designed to acquire images of functional activation in the human brain cortex. It does this by shining infrared light onto the scalp, and measuring the amount of light reflected back. From these measurements, the changes in concentration of oxy- and deoxyhaemoglobin in the cortex can be deduced.

Our topography system is able to obtain cortical images at the relatively fast rate of 10 frames per second because it uses a system of source frequency encoding – this allows all the light sources to be illuminated simultaneously. Each one is modulated at a slightly different frequency from all the others. A fourier transform of the detected signal allows the sources to be distinguished from one another. The disadvantage of this system is that it can result in data with a low signal to noise ratio. A time encoded system, i.e. where each source is illuminated in turn, gives a higher signal to noise ratio but a slower frame rate. We want to reprogram the system to be a hybrid of the 2 methods, so that we can utilise the advantages of both methods.

This project would suit someone with some experience of computer programming.

Comparison of Two-Point Fat-Water Separation Techniques

Supervisors: Dr Maria A Schmidt, Cancer Research UK Magnetic Resonance Unit

Student: Nadra Musa

In MRI, chemical shift causes fat and water signals to have different frequencies. Phase-sensitive methods (Dixon methods) exploit this difference to produce separate MRI images for fat and water. This requires a minimum of two images (with fat and water signals in phase and out of phase) and involves processing the phase of MRI images to separate phase changes associated with chemical shift from those associated with magnetic field inhomogeneity. The objective of this project is to compare the performance of different two-point fat-water separation algorithms in the presence of noise and magnetic field inhomogeneity, identifying the most robust techniques. This involves modelling the main sources of error in computer simulations and designing appropriate test objects to test the conclusions with actual MRI data.

This project involves basic knowledge of MRI, basic maths (complex numbers) and some programming skills.

Development of an interactive teaching aid to demonstrate the principle of magnetic resonance imaging (MRI)

Supervisors: Prof. Roger Ordidge and Dr. Terence Leung

Student: MSc

Equations can be quite confusing sometimes. Students often love the stories behind the equations but feel totally lost when they see the mathematical symbols. To untrained eyes, it may be difficult to appreciate how the variables in the equation can influence the final result, especially when non-linearity is involved. Students can gain enormous insight if they can interact with the equations and see the impact instantly. The latest version of Mathematica (a popular computational software) has made the implementation of interactivity, e.g. slider, easier than ever before. The aim of this project is to develop an interactive teaching aid based on Mathematica to demonstrate the principle of magnetic resonance imaging. This project will suit someone who has computer programming experience, and is willing to take up the challenge of revealing the secrets of equations!

Development of breast density measurement technique for cancer screening

Supervisors: Prof. Robert Speller and Ben Price

Student: Dastan Khalid

Recent studies have shown that the radiographic density of breast tissue is linked to a woman possibly developing breast cancer in the future. However, to measure the radiographic density requires a mammogram being taken. For screening the population it would be much better to use alternative techniques. This project is to look towards a method to obtain the same, or related information, without the use of ionising radiation. Radiographic density can be related to physical density (under certain assumptions) and hence to estimate radiographic density in vivo requires a method for estimating the physical density of breast tissue in-vivo. During this project different techniques will be considered for estimating both the volume and mass but, for practical experiments, all of them require a phantom to be built of materials that are mechanically, radiographically and physically tissue equivalent. Therefore, the first task will be to build different phantoms and then develop techniques for estimating their density under ‘in-vivo’ conditions. The work will require a student interested in a project requiring practical skills and it is likely that the project may take different directions during the development stages of the phantom. The project is equally suited to undergraduate and MSc students.

Monitoring tissue oxygenation and energy metabolism in muscle and brain using novel optical instrumentation

Supervisors: Dr. Ilias Tachtsidis and Prof. Clare Elwell

Student: Tingting Zhu

Monitoring the tight balance of brain blood flow, oxygen delivery and brain tissue metabolic rate is a major aim in patient diagnosis and care. For several years our group has pioneered the development and use of non-invasive methods and instrumentation that are based on near-infrared spectroscopy (NIRS) to provide information on the status of the brain tissue. NIRS is an optical technique that uses harmless low light levels that can penetrate the skull and reach the brain tissue; from the detected reflected light we can resolve the major tissue chromophores. While typically NIRS measurements are based on two light wavelength systems, therefore able to resolve only for the concentrations of oxygenated and deoxygenated haemoglobin; we have recently acquired a multi-wavelength (7 wavelengths) instrument that allow the measurements of additional molecules and hence provide measurements on the distribution of oxygen and blood in the brain and how oxygen is being utilised by the brain. The students will set up the 7 wavelength NIRS spectrometer and design experimental protocols that will allow testing the system and collecting data from volunteers and patients. In particular the experimental protocols will involve a combination of: (1) measuring muscle oxygenation during exercise, (2) monitoring the brain during task activations such as anagram solving and video gaming and (3) monitoring anaesthetised patients before, during and after brain surgery. Experiments will be conducted both in our labs in Medical Physics and/or National Hospital for Neurology and Neurosurgery. This project will divided between two students each of whom will concentrate on different experimental protocols and appropriate analysis method. This project would be suitable for students with an interest in experimentation, data collection, and human physiology; and will involve data processing and some statistical analysis.

Initial Assessment of a High Resolution In-Vivo Radioisotope Imager

Supervisors: Dr. Ian Cullum and Dr. Kjell Erlandsson (ian.cullum@uclh.nhs.uk; kjell.erlandsson@uclh.nhs.uk)

Student: MSc

A new type of emission imaging device, consisting of collimator, scintillator, image intensifier and CCD camera has been in use in the Institute of Nuclear Medicine since late 2008. The device is capable of obtaining high reolution planar and tomographic data. Initial measurements with the device have proved promising. The project is aimed at accurately characterising the system and making simple hardware and software modifications to improve its performance If these results are satisfactory then images of tissue samples will be obtained.
Major activities involved: Some minor hardware and software development of the system may be necessary, at present this is uncertain. Images will be acquired and analysed. Some computer programming may well be involved.

Investigation into Methods of Obtaining Data on Patient Motion During Radioisotope Imaging Investigations

Supervisors: Dr. Kjell Erlandsson and Dr. Ian Cullum (kjell.erlandsson@uclh.nhs.uk; ian.cullum@uclh.nhs.uk)

Student: Sara Muddei

The quality of radioisotope images can be severely degraded during data acquisition due to patient movement. The movement may be the patient as a whole or organs within the patient, for instance due to breathing. This project aims to: a) Compare two instruments that record respiratory motion to allow correction of SPECT and PET/CT acquisitions b) Use one of the instruments to develop a technique that can be applied to the PET/CT scanner at UCL. One of the devices to be tested is a commercially available system, the second one is a system built at UCL. If time allows a novel method of measuring head motion in brain imaging using a ‘gaming’ computer will also be investigated.
Major activities involved: Some minor hardware development of the UCL respiratory motion system. Acquiring respiratory traces from the two systems from volunteers and analysing the results. Extracting image data from a PET scanner and modifying it based on the respiratory trace obtained at the time of acquisition. Analysing differences between corrected and uncorrected data.

Monte Carlo Simulations of High Resolution Emission Imaging

Supervisors: Dr. Ian Cullum and Dr. Kjell Erlandsson (ian.cullum@uclh.nhs.uk; kjell.erlandsson@uclh.nhs.uk)

Student: Hrir Mahdi

Monte Carlo simulations allow accurate predictions of the performance of imaging devices to be made prior to building any equipment. The aim of this project is to investigate the potential performance of single and multi pinhole (or coded aperture) devices for planar and tomographic emission imaging. Monte Carlo codes using the GATE simulation suite have been designed and tested in a previous project . These will be built upon to obtain predictions of system performance in measuring gamma rays and positrons from small animals and tissue samples with an aim to produce images with sub millimetre resolution. Some results will be tested by confirming them with measurements using an existing imaging device
Major activities involved: Running existing computer simulations. Analysis of results. Modifying the simulation codes to extract more information.

Development of an Imaging System for Use in Radiopharmaceutical Quality Control

Supervisors: Dr. Ian Cullum and Dr. Jennifer Wootten (ian.cullum@uclh.nhs.uk)

Student: Maria Hadjicosti

Before being injected into patients, radiopharmaceuticals must undergo strict quality assurance tests to check they are safe. One of these tests is to determine if the radionuclide has been properly bonded to the pharmaceutical. This is most often performed by paper chromotography, where the different chemicals move a different distance across a paper when a solvent is applied. By determining how much activity is at each part of the paper the percentage of the radionuclide that has been properly bound to the pharmaceutical can be determined. Traditionally this has been determined by cutting the paper into sections and counting each part in a detector. Commercial systems that do not involve cutting are available but are expensive and have low sensitivity. Previous projects have determined the imaging characteristics required and possible designs for a new detector to carry out this work. In this project an instrument based on a small scintillation crystal, optical fibres and a CCD will be built and tested. Initial results will be compared with those obtained from the existing (cutting) method and the images of the strips acquired by a traditional gamma camera.
Major activities involved: Building the Imaging System from Existing Components. Testing the System. Comparision of Results with those from the existing technique.

Automated data logging and temperature control for thick-film process analysis

Supervisors: Dr. Anne Vanhoest and Kylie De Jager

Student: Alexander Messenger

Many manufacturing processes carried out in the IDG cleanroom require controlled temperature and humidity level. For example, thick film printed electrical resistors are fired at temperatures above 600C and the exact temperature profile determines the final resistance of the printed tracks. The aim of this project is to conduct an analysis of the thick-film printing process as implemented in the IDG cleanroom. First an automated recording system will be developed that stores measurements at regular intervals, with emphasis on easy communication with PC. The input to the device has to be standardised to accept measurements from either a thermometer, a humidity sensor or a profilometer. The analysis of a thick-film printing stage will then be undertaken in our DEK840 belt-furnace. Depending on the results of this analysis and on the level of advancement of the project, a second, optional, stage, will be to assess the feasibility of adding a temperature controller (type eurotherm) in one of our 1100C furnaces. The pre-requisites for this project are to show a practical disposition, some knowledge of data storage and a willingness to "build things" and get away from the pc.

Improving the resolution of radiographic images using deconvolution techniques

Supervisors: Dr. Gary Royle and Dr. Sandro Olivo

Student: MSc or UG

The spatial resolution of an x-ray image is dependent upon a number of geometric factors within the imaging system, such as x-ray spot size, imaging pixel size and the geometry of the system. In a typical imaging system these will add significant blurring to the image, making it difficult to see fine details. It is possible to reduce these effects using deconvolution techniques to try to retrieve the `true' image. This project will investigate these techniques and develop a code to try to improve the quality of x-ray images.

Development of a cone beam optical imaging system for gel dosimetry

Supervisors: Dr. Gary Royle and Dr. Jenny Griffiths

Student:Teressa Ramsay

Modern radiotherapy equipment is capable of treating complex 3D volumes within the patient. In order to verify the quality of the treatment it is necessary to check that the delivered treatment is the same as the one planned. One approach is to use a chemical gel that changes colour / opacity upon irradiation. A 3D volume within the gel can be irradiated and then compared with the treatment plan. To do this it is necessary to produce a 3D image of the gel. This project will design and build a simple optical imaging system to capture image projections of objects and reconstruct a 3D image.

Reliable quantification of aortic dilation

Supervisors: Dr. David Atkinson, 2nd supervisor TBA

Student: MSc

The aorta is an elastic blood vessel transporting blood pumped from the heart to the body. The mechanical characteristics of the aortic wall are important to its function and in disease the aortic wall may weaken and dilate. It is important to be able to quantify the aorta diameter at multiple, repeatable places along its length and compare diameters with subjects of a similar age. In this project, pre-segmented aortas will be registered to the patient data. The student will investigate the optimum way of performing the registration and transforming the planes used to compute diameters so that meaningful comparisons across patients can be made. The student may also look at the range of variability expected in children at different ages.

Suitable for an MSc student with an interest in real clinical problems and image registration. Project in collaboration with the cardiothoracic unit at the UCL Institute of Child Health.

Investigating the ability of autofocus motion correction to work on local image regions

Supervisors: Dr. David Atkinson, 2nd supervisor TBA

Student: Hao Wu

Motion during an MRI scan causes image blurring and ghosting that can degrade the diagnostic potential of a scan. Autofocus is an algorithm that assesses image quality using a focus criterion such as image entropy and seeks to optimise this by iteratively applying correction for motion. Previously the entropy has been calculated over the whole image but there may be benefits to computing it only near a region of interest. The benefits may be a more accurate correction of motion.

This will suit a student with an interest in MR physics and image/signal processing.

Registration of High Resolution low SNR, diffusion weighted images

Supervisors: Dr. David Atkinson, 2nd supervisor TBA

Student: Stian Johnsen

High resolution imaging can reveal small structures but comes at the price of worsened signal to noise ratios and increased scan times. The lengthy scan times increase the chance of subject motion which then degrades the analysis of images. This project is concerned with the registration of poor signal to noise ratio images with the application being high resolution diffusion images of the hippocampus and deep brain structures.

This will suit a student with an interest in MR physics and image registration.

Electrical Impedance Tomography of evoked physiological activity

Supervisors: Prof. David Holder, 2nd supervisor TBA

Student: MSc

Background:
EIT is a novel medical imaging method, with which images of the electrical impedance of the head can be produced with a box about the size of a paperback book, laptop and EEG electrodes on the head. It is portable, safe, fast and inexpensive. The supervisor’s research has been to develop its use in imaging functional activity in the brain. One possible use could be to image increases in blood volume which occur over some tens of seconds during normal brain activity, such as during the standard clinical techniques of stimulation of the visual system by flashing lights or the somatosensory system by mild electrical stimulation at the wrist. Such imaging can already be performed by fMRI (functional MRI); the advantages of EIT are that similar images could be acquired with portable much less expensive technology which would increase its availability. EIT data has been collected in these situations before and led to a landmark publication in which reliable single channel data were observed but, unfortunately, the data was too noisy to form into reliable images. Since then, the electronics and imaging software have been improved – for example, we can now collect images at multiple frequencies whereas before they were only collected at one. This gives greater opportunities to reduce noise. Students will work together to collect EIT data during repeated evoked activity in about 10 healthy volunteers, and then will help produce images using Matlab code written for this purpose. Digital photos will be taken around the head, and then photogrammetric software will be used to localise their positions. Images will be reconstructed using an MRI of the patient’s head, which needs to be converted to a Finite Element model with software for segmenting medical images and meshing them. The accuracy of these images will be compared with similar studies using fMRI.

Skills to be acquired:
Students will spend time in the lab in Medical Physics at UCL learning relevant methods and analysing the data, and some time in Prof Holder’s department at UCH, learning how to collect evoked responses using scalp electrodes. Skills to be acquired will include one or more of: Medical image reconstruction, Photogrammetric software use, Medical image segmentation and meshing software, EEG electrode placement and use, Experimental design and data analysis. The project would be suitable for a single student or more than one working in a team.

Suitable backgrounds:
Would suit students with a background in Medical Physics, Engineering, Computing or Medicine.

Development of a novel flexible disposable headnet for EEG and Electrical Impedance Tomography of brain function

Supervisors: Dr. Anne Vanhoest and Prof. David Holder

Student: MSc

Background:
In EEG, about 20 silver cup electrodes, each about 1 cm in diameter, are placed on the scalp, usually by hand and after manual abrasion of the skin. Various commercial headnet designs are available, but they are generally expensive and require manual skin abrasion, or do not abrade the skin and so may suffer from poor skin electrode contact. We are interested in developing a new approach in which technologies from thick film printing onto printed circuit boards is applied to a flexible backing such as silicone rubber. The project will be to learn about existing EEG electrode designs and undertake a review of methods available for printing onto flexible substrates. The student will then design and manufacture simple electrode strips according to the optimal design and assess which method is the best. If time permits, they will then develop this into a full headnet. Skills to be acquired. The student will be based in Prof Holder’s laboratory where they will have a desk and undertake the literature review. Practical work will be spent in Prof. N. Donaldson’s laboratory, supervised by Dr. A. Vanhoest, which has a clean room and several methods for production of flexible electrodes, such as thick film printing, etching flexible laminates and a laser cutting device.

Skills to be acquired:
- experimental design -clinical EEG - methods of printed circuit board and other electrode design and manufacture.

Suitable backgrounds:
This will suit a student or students working in a team with material science, physics, engineering or medical backgrounds.

Electrical Impedance Tomography (EIT) of acute stroke

Supervisors: Prof. David Holder and Dr. TongIn Oh

Students: Anthea Kwan, Francesca Leek

Background:
EIT is a new medical imaging method which could be used as a portable and non-invasive way to image in acute stroke. It physically comprises a box of electronics about the size of a paperback book, laptop computer and use of ECG type electrodes placed around the body part of interest. New clot-busting drugs are available for the treatment of stroke but can only be given after a head scan as it is only safe when the stroke is due to blockage of an artery by a thrombus; it cannot be given if there is a haemorrhage. This can be undertaken by urgent CT but this is often not available. EIT could provide a method for imaging in an ambulance or in casualty departments at low cost, using a system, which is similar to an EEG machine, and 30 electrodes on the head. A state of the art EIT system has been developed which is ready for clinical testing in patients with acute stroke at UCH. In the project, suitable patients will need to be identified on the same day as arrival in the hospital. Electrodes will be applied to their head and a recording lasting about 20 minutes will be made with the EIT system. Digital photos will be taken around the head, and then photogrammetric software will be used to localise their positions. Images will be reconstructed using an MRI of the patient’s head, which needs to be converted to a Finite Element model with software for segmenting medical images and meshing them. The accuracy of these images will be compared with “gold standard” images of diffusion weighted MRI taken at UCH.

Skills to be acquired:
Students will spend time in the hospital helping identify suitable patients and making the recording, and in the lab in Medical Physics at UCL analysing the data. Skills to be acquired will include one or more of: Medical image reconstruction, Photogrammetric software use, Medical image segmentation and meshing software, EEG electrode placement and use, Experimental design and data analysis. The project would be suitable for a single student or more than one working in a team.

Suitable backgrounds:
Would suit students with a background in Medical Physics, Engineering, Computing or Medicine.

Assessment of a novel method for automated EEG analysis

Supervisors: Prof. David Holder and Dr. T. Tidswell

Student: MSc

Background : In Electroencephalography (EEG), about 20 voltages are recorded from the scalp, over about 20 minutes. These are subsequently analyzed, to see if there are abnormalities in conditions such as epilepsy. The analysis is currently undertaken by a Clinical Physiologist and medically qualified Consultant. Methods have been developed to analyse records by computer, in order to quantify the information and save time. These employ the power of modern computers and are intended to speed up the laborious process of visual analysis of many pages of EEG. In the supervisor’s group, a novel method for automated analysis of the EEG has been developed, which employs independent component analysis and a quadratic classifier. It is written in Matlab. The purpose of this project is to assess the accuracy of this new method on a group of about 30 EEG recordings in normal subjects. The outcome will be a comparison of its accuracy compared to visual identification by an expert and should lead to a peer reviewed publication in a scientific journal.

Skills to be acquired:
Students will spend some at UCH in the supervisor’s department learning the basic of EEG collection and analysis, and learn how to use the newly developed Matlab based EEG analysis software. They will then run it on the EEG records and use statistics to compare the results with the “gold standard” of visual inspection. Skills to be acquired will include one or more of: Matlab programming, Simple medical statistical analysis, EEG use, Experimental design and data analysis.

Suitable backgrounds:
Would suit students with a background in Medical Physics, Engineering, Computing or Medicine. Some experience in programming, ideally with Matlab, would be desirable.

Development of a web server for Telemedicine in Clinical Neurophysiology

Supervisors: Prof. David Holder and Mr. Dave Plummer

Student: MSc

Background:
In Electroencephalography (EEG), about 20 voltages are recorded from the scalp, over about 20 minutes. These are subsequently analyzed, to see if there are abnormalities in conditions such as epilepsy. This is widely used as a routine test in hospitals. In the past decade, the machines for acquiring EEG have all become computer based and digital but much of the clinical practice is inherited from the previous customs of reviewing paper records. The supervisor is interested in using the power of the internet and modern PC based processing to improve the practice of reviewing and reporting EEGs – he has a joint position with a research group in Medical Physics but also practices as a Consultant at UCH. The purpose of this project is to develop and evaluate a web based system for reviewing and sharing EEG records. Each record is about 20 Mb and requires special software for review – an expert observer will page through the 100 or os pages of each record and observe any abnormalities. The supervisor has already developed a Java based program which permits EEG review over a web browser and another program written in Matlab which enables automated analysis. The student will design and implement a web site based within Medical Physics at UCL or UCH which will allow clinical EEG records to be uploaded from around the country from other hospitals and then reviewed as needed. The review may either be for urgent clinical reasons or for education and training. A system for robust and secure tracking of clinical reports will need to be developed, and a bulletin board for discussion of any difficult cases. Once implemented, a small pilot user survey will be undertaken to assess its effectiveness.

Skills to be acquired:
Web design, Java programming, Exposure to clinical working practices in EEG Conduct and evaluation of a user survey, EEG use.

Suitable backgrounds:
Would suit students with a background in Computer Science, Medical Physics, Engineering, or Medicine. Experience in programming is required.

PACS network optimization

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Picture Archiving and Communication Systems (PACS) are networks of various sizes from 10 to 100s of workstations where images of a few Megabytes of size are transmitted between archives and workstations. The archive has several components, a fast response archive, a slower response archive and an 'offline' archive. The performance of the network is dependent on the architecture and performance of various components. This can be studied by simulation and or queuing theory. Different network designs can be investigated: loop, star interconnected loops etc. A useful tool is a graphical demonstrator of the performance of the network, which can be modified so that a user can study performance subject to changes in design. This project is to build such a tool and investigate various techniques to enhance network performance such as so-called pre-fetch as opposed to use of a very fast central file server.
[Note this is probably quite difficult to code although background is straightforward]

Design of an object orientated multimedia patient report

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

This could be either an architecture study, or a (considerably) simplified implementation. The concept is that a 'cast' of objects of various types represent the raw data, for example text, graphs and video need to be lined together into a report. These are insubstantiated into playable objects associated with a 'score', or the way in which a report can be read. They are associated with objects containing information about layout, for example, where on the screen they are to be placed, colour, etc. [This needs to be linked to an understanding of so called DICOM hanging protocols. The 'score' can be played from beginning to end, or navigated. Thus concepts of navigation 'goto','if' etc, need to be incorporated. The concept is based on the draft report of the CEN standardization committee on multi-media records. Two phases needs to be considered: creation, replay. A particular problem is that is synchronisation of different objects for example video sequences for which a tool such as SMIL could be employed.
[Requires knowledge to be acquired of standards]

Image data compression using a neural net

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Description: Data compression by a method such as Digital Pulse Code Modulation (DPCM) involves matching the value of a pixel against its value predicted from a series of weights and previous pixel values. The set of weights effectively form a model. Their values are often image specific and depend on the form of the image data: the covariance matrix etc. It is suggested that using a small neural net might be an efficient manner for generating such model/ sets of weights, which are image specific. The project involved coding a DPCM data compression routine with variable weights and then implementing a neural net to attempt to optimise the set of weights for different types of images. The programming environment can be C or C++ on either a Sun or PC based platforms.

Registration of images (in medicine), improving robustness and testing for accuracy

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Several algorithms exist (and have been developed) for registering similar images in medicine, for example variance minimisation and mutual information maximization, for rigid registration, optic flow and thin plate spline for non-rigid registration. The aim of this project is to pursue this work with the view of evaluating the performance of these types of algorithms, in particular when working with relatively different types of image data, for example images from MRI and Nuclear Medicine, and for different applications, for example images of the heart or liver as opposed to the more conventional images of the head. In general these algorithms are slow (if they are robust) and in any case perform more poorly as the difference between the types of image increases. Part of this project will be analytical, that is studying the performance of the algorithms for example for different parameters of the optimization. For non-rigid registration, the process of evaluation requires the assessment of the accuracy of registration at every point in the field of view, although not necessarily with equal weighting. The process can be tested by deforming an object in a know manner, and then re-registering it back, both of which can be represented as a vector field. The main part of this method will be to devise a method for evaluating the difference between these two vector fields (for example by fitting an active shape model) and investigating parameters to intercompare different non-rigid registration methods. An extension of this which is novel is to look at the vector deformation field, to decompose it into divergence and curl components and to use these to look at the local field (for example to decide if the local field can be expressed as a rigid transformation.
[Important part is evaluation methods]

Deformation of images (in medicine) based on constrained models

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Deformable images are required for matching to atlases and for other special purposes such as image subtraction in angiography. Several models for deformation exist, polynomial, thin plate spline and diffusion based. For the example of brain images, it is clear that the constraints should be position (and possibly shape) dependent, for example much greater weight being applied at the centre than at edges. This project will investigate and test the accuracy of several model based deformable models with the aim of find the most appropriate for use in generating a brain atlas including various moments (mean, variance) about the expected values and their positional reliability. Again a critical parameter is that of validation and overall measures of the vector displacement field provide tools for assessing local and overall accuracy. Part of the project, since simulated data would be required to provide a suitable testbed and gold standard is to investigate methods for creating images of a different type from real acquired images for example PET like imaged from MR raw data.
An associate task is to develop a Finite Element soft tissue deformation model (cf Schnabel IPMI 2001) for an organ such as the liver or the heart.

Motion correction of in vivo or in vitro images

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

An important source of error is that of motion of the patient in various types of studies where the acquisition time is not negligible with respect to patient motion, an example being in nuclear medicine and CT. Markers can be placed to identify position on the surface of the patient, radioactive sources in the case of NM and 'wires' in the case of CT. The problem arises that the restoration of the data is not completely analytical: in NM the data are acquired as projection, in CT as slices where missing data can occur (e.g. between slices). The project involved determining the best algorithms for correcting such motion, simulation to establish the limits of error and real data collection on patient to validate the results. An alternative source of images is that of sequences of images of cells which can move and indeed undergo modification for example cell division
As an example: when renograms (dynamic kidney function studies) are acquired, a problem occurs with respect to patient motion. This project involves writing a program to translate successive images of such a study to re-register the kidneys. It would also be interesting to compare: registering both kidneys together, registering individual kidneys separately, using an external marker. Three algorithms are possible, the first (more complex) uses the stochastic sign change method, the second involved detecting increase in counts from within a 'guard ring', and thirdly, computing the autocorrelation function.

Quantitation of electrophoresis images

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Description: Electrophoresis images are generated by placing samples of proteins etc on a plate where the sample is 'drifted' across the plate for example by the presence of an electrical potential. Images are then created which contain a track for each sample, where concentrations of material may be observed along these tracks corresponding to different constituents in the sample. These images are captured using a CCD camera, and then available for quantitative analysis, that is estimation of the amount of material at different places along each track after calibration with respect to a set of reference tracks. Artefact exist in that the tracks may curve, frequently have different widths at different positions, are may be disturbed by 'smiling' artefact, or the presence of noise. In order to quantitate these tracks, a spatial distortion correction must be performed, and the tracks segmented. The analysis proceeds by generating a curve as a function of distance along the track correcting for the width of the tracks, and then calibrating this curve, for example ensuring that distance corresponds to molecular weight. The images are available is matrices of size 256x256 up to 640x480, but the segmentation and calibration algorithms need to be written in C under an existing general analysis framework, on a PC. Programming environment Java, C++ etc as desired
[This project needs to be extended into the area of calibration and interpretation of results]

Image Processing for quantitation of vocal folds

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Data is acquired of vocal folds (chords) of patients using a CCD camera and fibre light guide system, while being illuminated for example by a stroboscope. The aim is to identify (segment out) the vocal chords on these images, and then to perform various measurements of them: separation, bending, length, areas between, etc, with the aim of providing a good clinical classifier for different conditions, and as a measure of therapy when treated. An additional task is to correct for fisheye distortion that occur in such images, assuming a projected test pattern of known form. A suggested method for characterising the shape and motion patterns of the vocal folds it to use an active shape contour (snake) or better an active shape model so as to represent different motion patterns in the form of their characteristic changes in shape. Normal and abnormal data should be included to test the sensitivity of such analysis to the clinical condition. The use of an active shape model would be a very useful extension.
[Motion analysis is interesting part]

Texture analysis of radiographic data

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: Iona L Doble

Images such as mammograms and liver CT and MR images contain features which it appears may associate texture as an indication of the clinical type and stage of different tumours. The aim would be to extend (and devise new parameters) being local texture estimates, such as local spatial frequency and fractal order, as an aim to provide a good texture estimate. An alternative target would be to investigate the classification of MR bone image by the use of texture to investigate its accuracy with respect to identification of Osteoporosis. Considerable amounts of data are available and a suitable programming environment could be either PC or Sun. A particular aim would be to compare several different texture analysis methods on one of the available datasets. A sub-aim would be to investigate optimal window size over which texture should be evaluated in such images, a good example of which is the use of wavelet for classification.
An alternative approach would be to implement and test the Pattern Fed Objects (PAFO) algorithm as an alternative method for texture analysis and segmentation.

Lesion detection and classification in lung CT scans

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: Igor Stanisic

It is proposed to use lung CT scans for screening for lung cancer. Early indications of lung cancer are the presents of small lesions (2-8mm diameter) in the lung field, but the problem is complicated by the present of considerable numbers of other structures such as blood vessels etc. The first task is to develop a method for removing confounding information for example filtering out linear structures. The second is to develop a sensitive detector for the presence of small lesions (which are not always circular/ spherical) One method which could be applied is the use of a neural net after suitable preprocessing. The final task (if there is time) is to look at classification methods of which the most promising is likely to be a fuzzy texture evaluation (although the neural net might be extended to perform the same process). The difference between objects detected which are normal and those corresponding to possible tumours is typically the variation of shape of the variation of pixel values within the object. The use of a fuzzy method is suggested since the exact localisation of the lesions is difficult. Several methods exist (for example radial profiles, matched filters, neural nets etc) which should be intercompared.
An interesting extensionn of this is the extraction of arterial (venous) and bronchial trees with the aim of improving detection of nodules.
[This project could use liver scan images as an alternative]

Shape description and segmentation of bones in a projection image

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: Deshal De Silva

Conventional x-rays are projections where groups of objects are superimposed. This project which has important implications in the automated analysis of image of infants suffering from different bone dysplasia syndromes (in collaborations with Great Ormond St. Hosp. for Sick Children) is concerned with taking the image of a skeleton, identifying different bones (e.g. vertebrae, ribs, tibia, fibula, femur etc, and segmenting them in such as way that individual shape outline of the different bones can be identified (with the possibility of overlapping structures being the major problem) and then characterizing the shapes into short, long, straight, bent, deformed and various other more specialized categories with the aim of eventually linking into an expert system being developed independently. Data would be acquired on a laser digitized and be (initially) of high resolution - 2000x2500 pixels.
A previous project used snakes to segment such images which proved to be not very robust. An alternative techniques which could be employed is the use of active appearance models where the image is decomposed into images of different modes of variation and placement of nodes can be optimised. An alternative problem of considerable interest other than that of segmentation is that of the robust extraction of symbolic (or textual) descriptions. An active shape model is a useful extension.
[This project needs extending into analysis methods]

Classification of microcalcifications in mammograms

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

Work has already been undertaken in the detection of individual and groups of microcalcifications on mammograms. Simple parameters such as size, roundness, linear arrangement etc can assist in the classification of the mammogram into malignant or benign. However, so far, no information from other structures in the breast, for example presence of a lesion, segmental distribution etc has been implement in order to use other than purely local parameters. This project would extend the classification and description of clusters of microcalcificaion by including other descriptive parameters associated with other detected structures in the mammographic images.
[An interesting extension would be into defining and ‘detecting’ asymmetry]

Segmentation of White and Grey matter to classify abnormal lobes in brain images

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: Juan Zheng

MR Brain image segmentation for example into white and grey matter is complication by several factors: non-uniform signal response, partial volume effects, difficulty in identification of individual lobes etc. Good simulated data is available form Montreal Inst. Of Neurology which can be used as a test bed. So far quantitative assessment of the ratio of grey to white matter has not be validated in the no gold standard data is available. This project would use existing tools to investigate the accuracy of such classification measure and to investigate their sensitivity with respect to the several sources of error. The use of a 3D clustering algorithm such as proposed by Udupa could be of considerable interest.
An associate project is that of the detection, classification of tracking of the sizes, shapes and ‘intensities’ of multiple sclerosis lesions over time to investigate if such temporal information can be of prognostic value; e.g. is the condition essential stable or is it deteriorating rapidly. The distribution of plaques is different regions of the brain seem to be of considerable significance.
An associated problem with respect to MS lesions is to develop a robust method to define spatial localisation (above below left right) between such different rather fuzzy objects, which requires notions of fuzzy logic to be employed.

Expert Aiding System for Image Analysis and Reporting (EASIER)

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

An architecture for associating an image processing system with an expert (symbol based) system has been proposed. A suitable implementation would be using agents. One demonstrator of such an architecture would be ‘EASIER’. The interface between these two different types of system is difficult and the question of the types of messages exchanged and the granularity of the system control is critical. While this project would be based on several previous studies, the main task is to go beyond and architecture design so as to implement a prototype system as a test bed to evaluate different strategies and to permit eventual implementation of a real system.
An associate problem is the of investigating how uncertainly can be handled is such a system and particular to investigate the idea of associating individual pixels and structure with multiple higher level structures with associate probabilities and incorporating this structure into appropriate classification tools.
[Needs knowledge of Artificial Intelligence methods]

Pre-processing radiographic images (signal to noise ratio in digitized images)

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

When digitizing images from film using a laser digitizer, a problem exists in the signal to noise ration achieved as a function of spot size of the laser, and the dynamic range as a function of grey scale. These effects need to be investigated, and a good overall measure of image quality, in particular of overall dynamic range, need to be established. In particular when used as the input for a mammographic analysis system (for example CADMIUM), considerable sensitivity has been found with respect to the pre-processing and handling of the histogram of grey scale values. This can be assessed by simulation such that a optimal (or better) method for acquiring the data can be proposed and methods for assessing the quality of the data acquired investigated.
An associated project would to be implement the pre-processing technique suggested by Brady et al (HINT) and to investigate the noise properties with respect to microcalcifications in mammograms.

Tomographic Uniformity in SPECT

Supervisors: Prof. Andrew Todd-Pokropek and Dr. Tryphon Lambrou

Student: MSc

A method for assessing tomographic uniformity has been established but need to be validated. The effect of non-uniformity is to create circular artefacts in the reconstructed data. However, these artefacts vary in importance depending on their distance from the axis of rotation, their size, the reconstruction filter etc. The problem can be studied by simulation and physical measurement. The aim of the project is to determine a simple protocol for indicating the importance of an observed circular artefact. An alternative approach would be to measure and predict the resolution and Signal to Noise ratio in a simulated Jaszczak phantom. A previous project involved the generation by computer simulation of a Jaszczak phantom. The next stage in the development of this phantom is to determine physical measurements, in particular of resolution and signal to noise ratio, determined from the reconstructions of this phantom, and compared with theoretical predictions. The importance of these measurements is to be able to compare different reconstruction algorithms. The work would be carried out on any suitable microcomputer. A proposal has been made to the international standards body, which needs to be backed up with more extensive testing and validation. A further extension is proposed for evaluation the effectiveness of attenuation correction is SPECT which required the technique to be extended to non-circular objects which in a preliminary study seems to be possible.
[This is based on 2 papers which have been published, but results need to be validated and made more robust]

Non-rigid registration of sliding motion using a spatially adaptive regularization term

Supervisors: Dr. Andrew Melbourne and Dr. Jamie McClelland

Student: MSc

A crucial component of any registration algorithm is the deformation field regularisation term. Many methods find the solution of a corresponding PDE to smooth the deformation field; more recently, spatially adaptive regularisers have been proposed. This project will investigate the choice of optimal regularisation for particular images. The application will be the regularisation of sliding motions in lung X-ray CT images.
This project will require good mathematical and programming skills.

Vessel based image registration and motion modeling of liver images

Supervisors: Dr. Dean Barratt and Dr. Erik Rijkhorst

Student: Valentin Hamy

Image registration is an important area of medical image analysis. The general aim of registration is to align one or more images by transforming them into a common co-ordinate system. This is useful in many applications including, for example, quantifying changes in tissue due to disease progression or organ motion.
In case of large organs like the liver, blood vessels (arteries and veins) are clearly identifiable in ultrasound, MR and CT images, and this makes them a very useful feature for driving image registration algorithms. However, physical deformations, for example due to breathing motion, and variations in grey-level brightness of blood vessels that occur between different imaging modalities, make accurate and automatic vessel-based registration a challenging problem in practice.
Several techniques for segmentation and registration of vascular structures of the liver are currently under active development within our group. This MSc project aims to further develop and extend these techniques, and apply them to clinically relevant cases. The starting point of the project will be to obtain reliable segmentation of liver vasculature using an available Hessian filtering technique. To make this work for the different imaging modalities - ultrasound, MR and CT - several pre- and post-processing steps will be implemented and tested using either ITK or Matlab. Thereafter, a number of different non-rigid intensity and feature based registration techniques will be applied for aligning the vascular structures. Upon successful registration, a motion model for simulating the breathing motion of the liver vasculature and surrounding tissue will be computed.
The methods developed will also be evaluated using images acquired during the course of the project, giving the student the opportunity to get hands-on experience with imaging techniques, in particular abdominal ultrasound. Clinical applications relevant to this project include minimally and non-invasive image-guided interventions for liver cancer, such as radio-frequency (RF) ablation and high-intensity focused ultrasound (HIFU).
The UCL Centre for Medical Image Computing (CMIC) is a large, international research group comprising about 50 staff and students. Research in the laboratory focuses on all aspects of medical imaging, image processing and image analysis, and is world leading in a number of areas. CMIC has strong links with the major teaching hospitals in London, industry, and similar research groups throughout the world. CMIC has access to state-of-the-art computing and imaging facilities and runs a comprehensive lecture and seminar program.

Imaging soft tissues using the vibration potential

Supervisors: Prof. Paul Beard and Dr. Edward Zhang

Student: MSc

The aim of this project is to investigate whether it is possible to generate a voltage in tissue by the passage of ultrasound waves and exploit this phenomenon to image biological tissue. The method is based on the notion that a potential difference can be produced by the differential acoustically-induced motion between the charged particles and surrounding fluid in a colloidal suspension or a ionic solution. When applied to tissue imaging, the technique is most likely to be suited to imaging blood vessels. This is because blood is both colloidal (due to red blood cells) and ionic (due to dissolved electrolytes) and should provide a relatively large signal compared to other tissue constituents such as collegen or fat. To obtain images with this approach, a focussed ultrasound beam is scanned over the sample and the induced voltage recorded at each point. The objective of the project is to design and build an experimental set-up using a focussed ultrasound transducer and sample cell equipped with a pair of electrodes to measure the vibration potential of colloidal and ionic solutions and different tissue types. A simple scanning arrangement will then be developed to obtain images of tissue mimicking phantoms and ex-vivo tissues.

Segmentation of Dynamic Contrast Enhanced MRI

Supervisors: Dr. Andrew Melbourne and Dr. John Hipwell

Student: MSc

Accurate segmentation of breast tissue into multiple tissue types is a challenging task. In non-contrast enhanced images, segmentation often proceeds with an initial segmentation of the breast from the pectoral muscle and background; a second classification then separates fat and fibro-glandular tissue. The inclusion of contrast enhancement information, following an injection of contrast agent, allows for additional analysis of vascular properties and the potential for a more sophisticated segmentation method. This project will develop a breast MRI segmentation method including contrast-enhancement information and investigate the advantages (or otherwise) of this additional information.

This project will require good mathematical and programming skills.