MPHY3000/MPHY3002/MPHYM000: Projects 2016/17

Below is a list of Medical Physics and Biomedical Engineering projects being offered for final-year undergraduate and intercalated 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.

Note that intercalated students and third-year BSc and BEng students are required to attend a series of Research Skills lectures during the first term, covering important aspects of conducting a research project, including guidance on how to perform a literature search, how to write a research report or scientific paper, and how to give an effective oral presentation. This component of the project will include a coursework assignment worth 10% of the overall project mark. For fourth-year MSci and MEng students the Research Skills lectures are optional and the coursework is not part of the assessment of this module. Click here for more details.


  • A Project Outline is due on Monday October 10, 2016. 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 Millie Abraham 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 16, 2017. Two copies should be handed to Millie Abraham or James Vallerine in the Medical Physics Departmental Office.
  • Project talks will be held on Wednesday March 15, 2017 in Rooms 1.19 and 2.14 of the Malet Place Engineering Building.
  • Final Reports are due by Friday March 24, 2017. Please hand in two copies to James Vallerine in the Medical Physics Departmental Office.

Project information

Total number of projects listed below: 61
Number of projects still available: 43

Designing a dynamic optical phantom to characterise the ability of a multi-wavelength time resolved near-infrared spectroscopy system to quantify metabolic activity

Supervisors: Frederic Lange and Dr. Ilias Tachtsidis

Student: (Project available)

Near Infrared Spectroscopy (NIRS) is an optical measurement technique that uses low light levels to quantify changes in tissue oxygenation and metabolism. Our team is especially interested in monitoring the brain, in both normal and pathological conditions, with that technic. Infrared light is directed into the head and light that is reflected back to the surface will be attenuated by different chromophores (light absorbing molecules) according to their concentration. To retrieve information about the oxygenation, one can monitor the oxygenated and deoxygenated haemoglobin. To retrieve information about metabolism one can monitor the cytochrome-c-oxidase. The investigation of this last chromophore is quite challenging since its concentration is ten times lower than the one of the haemoglobin, and that its spectrum is broad in the near infrared range. Another challenge is to retrieve the absolute concentration of those chromophores, current system retrieving just the changes in concentrations. Recently, we have developed a multi-wavelength time resolved NIRS system that has the potential to retrieve absolute information about oxygenation and metabolism. In order to properly characterise the system, and test its limits, we need to develop a realistic phantom that we can control. Phantoms that simulate the optical characteristics of tissues are commonly used to mimic light distributions in living tissue. The student will be designing and manufacturing an optical phantom that will be used to quantitatively characterise our system. The basic material for the development of such a phantom is intralipid, to control the scattering coefficient, fresh blood, to control the oxygenation level, and bovine cytochrome-c-oxidase batch, to control the metabolic activity.The first step will be to design a static phantom, to test the ability of the system to retrieve background properties. The second step will be to develop a dynamic phantom, using pumps and tubes, in order to mimic the blood circulation, to test the ability to retrieve functional information. Once the system properly characterised, their is also scope to conduct experimentation in-vivo, on healthy volunteers.

Monitoring brain metabolism and oxygenation at multiple depths in the healthy adult using functional near-infrared spectroscopy

Supervisors: Isabel de Roever and Dr. Ilias Tachtsidis

Student: (Project available)

Functional near-infrared spectroscopy (fNIRS) is a non-invasive, neuromonitoring technique used to monitor brain activity via measurements of the haemodynamic response of the brain to a stimulus. It relies on the concept of neurovascular coupling, where a local change in neural activity is correlated with a local change in cerebral blood flow. Hence, by monitoring changes in concentration of oxygenated- (HbO2) and deoxygenated-haemoglobin (HHb) with NIRS, we can monitor neural activity indirectly. Using a broadband NIRS system, we can additionally monitor changes in concentration of the oxidation state of cytochrome-c-oxidase, a marker of tissue metabolism, thus providing additional information about the brain response. Our group has built a broadband NIRS system consisting of 8 detectors able to monitor multiple regions of the head simultaneously; recently, this has been expanded to 16 detectors. The project will involve using this new system to collect and analyse data from healthy adult volunteers during brain stimulation; the main aims include devising a protocol for a functional task (such as auditory or visual), experimental data collection from different regions of the head, and analysis of the optical data collected, including extraction of the functional response. Of particular interest will be the spatial distribution of the metabolic and haemodynamic response in the presence of a stimulus. This project would be suitable for a student with an interest in optical technologies and neuromonitoring techniques, and will require working with Matlab.

Monitoring brain oxygenation in real-world scenarios by means of wireless fNIRS systems: development of new tools and methods for the analysis of real-world fNIRS data

Supervisors: Paola Pinti and Dr. Ilias Tachtsidis

Student: (Project available)

The recent advancement and availability of functional neuroimaging methodologies have opened the way to several studies in the field of neuroscience research. Previous studies demonstrated that, for the investigation of some mental abilities, more ecologically valid situations are highly recommended, such as those involving social interactions or free bodily movements, especially in case of neurological conditions. However, monitoring the neural substrates of brain activity in more naturalistic settings can be extremely difficult in a typical neuroimaging environment. This is because most of the modern functional neuroimaging techniques (e.g., functional magnetic resonance, electroencephalograpy/magnetoencephalography, positron emission tomography) are highly susceptible to bodily movements and impose significant physical constraints on subjects as they are required e.g. to lying in a scanner in an unnatural environment. By contrast, the new generation of portable, wearable and wireless functional Near Infrared Spectroscopy (fNIRS) devices can represent an innovative solution to monitor brain activity in more ecological situations as they impose fewer physical constraints and allow free movement and walking in a more naturalistic environment. fNIRS is non-invasive technique that optically estimates cortical activity. It measures the relative changes in concentration of oxygenated (HbO2) and deoxygenated (HHb) haemoglobin secondary to neuronal activity through the evaluation of the absorption of the near infrared light by the biological tissue. However, monitoring brain activity through wireless fNIRS in naturalistic settings can present different challenges (e.g., detectors saturation, movements, unstructured experimental designs, systemic changes). Our group have previously demonstrated the feasibility of such devices in the real-world in a preliminary study, developing new analysis methods and tools, but additional improvements, validations and experiments are needed.The project will involve (i) the acquisition of new real-world fNIRS data on mobile participants using the Wearable Optical Topography system developed by Hitachi, (ii) the improvement and validation of the existing methods and (iii) the development of new signal processing tools for the analysis of real-world fNIRS data. It will require programming skills (Matlab or similar) and enthusiasm to work on a multidisciplinary project. The student will learn how to operate with fNIRS in ecological settings and will become familiar with fNIRS data processing and statistical analysis.

Comparing two optical methods to monitor cerebral blood flow in a pre-clinical model of hypoxic-ischaemic brain injury

Supervisors: Dr. Gemma Bale and Dr. Ilias Tachtsidis

Student: (Project available)

Neonatal brain injury, in particular hypoxic-ischaemic encephalopathy, occurs in 1 in 1000 births and can lead to severe neurodevelopmental impairment or even death. There is an urgent need to monitor the changes in cerebral oxygenation in the first days of life to assess the injury, detect those infants at risk and help direct treatment. To address this challenge our group is focussed on developing instruments and methods to monitor cerebral changes at the cotside. Near-infrared spectroscopy (NIRS) is an optical technique that can monitor changes in brain tissue oxygen levels non-invasively. Infrared light is directed into the head and light that is reflected back to the surface will be attenuated by different chromophores (light absorbing molecules) such as oxygenated and deoxygenated haemoglobin according to their concentration. From these measurements, it is possible to calculate cerebral blood flow (CBF) when there is a large change in cerebral oxygenation. CBF is an important indicator of brain health. Another optical technique, diffuse correlation spectroscopy (DCS), can measure CBF continuously. This project will focus on implementing both techniques to monitor CBF and comparing the results. We have a preclinical model of neonatal brain injury which we have monitored with broadband NIRS and DCS during hypoxic-ischaemic injury. Oxygen challenges are performed before and after the injury so CBF can be measured and assessed in both the healthy and injured brain. This project will involve implementing algorithms to measure CBF with both NIRS and DCS data, testing the robustness and reproducibility of the methods, comparing their results and using the results to assess their potential to identify the severity of brain injury. It will require programming skills (preferably Matlab or similar) and enthusiasm to work in a multidisciplinary environment. The project is a collaboration between the Biomedical Optics Research Laboratory (BORL) at UCL and the Lawson Health Research Institute in London, Ontario, Canada.

The effect of transcutaneous electrical stimulation of the upper limb on local blood flow

Supervisors: Dr. Gemma Bale and Dr. Anne Vanhoest

Student: Stamatina Ioakim

There are many reports in the literature on the use of electrical stimulation to promote wounds healing, especially for patients with impaired arterial blood flow.  In this project, the student will use a set of sensors to assess the impact of electrical stimulation on physiological parameters associated with blood circulation. The student will use a NIRO, Near InfraRed Oxygenation monitor and a pulse oximeter, to assess the impact of the electrical stimulation on blood oxygenation, and temperature sensors to evaluate another aspect of the metabolic response. The student will review the literature, propose a study protocol and conduct a study of healthy volunteers.

Development of an impedance meter

Supervisors: Prof. Nick Donaldson and Dr. Anne Vanhoest

Student: (Project available)

An impedance-measuring device is often useful in clinical situations, such as when recording biopotentials like EEG: the impedance between the electrode and the head must be low enough that the brain signals are not spoilt by noise or interference. In a student project a few years ago, a portable Impedance Meter was developed that was meant to be suitable for use on people (it passed a very small current). The student claimed that it gave good measurements but left no circuit diagram, no validation test results, and no device ready for us to use. However, we do have a device which looks more-or-less finished. We want to complete this development. I envisage the project having the following phases: (i) working out the schematic diagram and seeing how the device should work; (ii) doing bench tests and perhaps making minor improvements; (iii) properly documenting the design and its performance; (iv) perhaps designing a new printed circuit board and enclosure; (v) making the new device; (vi) making exemplary measurements on people.

Monitoring muscle oxygen consumption in marathon runners with optical spectroscopy

Supervisors: Dr. Gemma Bale and Prof. Alun Hughes (Institute of Cardiovascular Science)

Student: Matt Kinsella

An important part in achieving a positive response to exercise training depends on improving muscle oxidative function. Measuring oxidative processes in human skeletal muscle is often done using a tissue sample collected with a large needle. Therefore, developing non-invasive methods that allow muscle to be examined during exercise is an exciting scientific challenge. The Marathon Study provides a platform for examining muscle physiology pre and post training. The overall objective is to understand the changes that occur in the cardiovascular and metabolic profile of first time marathon runners throughout training. In the Biomedical Optics Research Laboratory (BORL) we have built a miniature broadband near-infrared spectroscopy (NIRS) device, called mini-CYRIL, which can monitor oxygenation and metabolism in tissue. NIRS is non-invasive and non-ionising technique that uses the absorption of light by specific molecules within tissue to monitor changes in their concentration. The most physiologically important absorbers in the near-infrared are haemoglobin and cytochrome-c-oxidase (CCO), an enzyme involved in metabolism. Both molecules have different absorption spectra depending on their oxidation state; therefore it is possible to monitor changes in oxygenation and metabolism via changes in light attenuation in tissue. The mini-CYRIL system has been trialled in a pilot study to monitor muscle metabolism on marathon runners during a maximal oxygen consumption (VO2max) fitness test with promising results. This project will build on this work, first by analysing this preliminary data and then conducting a new study on marathon runners both before and after the marathon. This project will involve monitoring volunteers with mini-CYRIL during exercise tests, and designing and implementing methods to analyse the data, from both physics and physiology perspectives. It will require programming skills (preferably Matlab or similar) and an enthusiasm to work in a multidisciplinary environment. This project is a collaboration between BORL and the Cardiometabolic Phenotyping Group, Institute of Cardiovascular Science.

Design and construction of headgear for fNIRS brain imaging in infants during the first two years of life

Supervisors: Prof. Clare Elwell and Dr. Anna Blasi

Student: Simon Scott

There is an increasing interest in using functional near infrared spectroscopy (fNIRS) techniques to image the developing brain, especially over the first two years of life. This project will involve designing and constructing age appropriate methods to fix multiple optical sources and detectors to the infant head to enable a range of cortical brain regions to be measured.

Probe-based confocal laser endomicroscopy (pCLE) for visualisation of brain tumour

Supervisors: Dr. Yijing Xie and Dr. Tom Vercauteren

Student: (Project available)

Endomicroscopy has been developed for in vivo and in situ pathology in various clinical applications. In brain tumour detection in particular, certain fluorescent agents (e.g. fluorescein, indocyanine green, and 5-ALA-PpIX) that accumulate preferably in cancerous tissue can be applied to provide imaging contrast between normal and cancerous tissue. The current reported pCLE systems lack the specificity and sensitivity necessary for 5-ALAPpIX detection especially in low grade brain tumour. We are developing a system dedicated to 5-ALA-PpIX that can provide the required sensitivity and specificity for low-grade glioma. In this project, the student will design experimental protocols to assess the image quality in terms of spatial resolution and image contrast under different illumination schemes and will develop/apply image processing algorithms for contrast enhancement. During the placement, the student will be provided opportunities to work with our research partner neurosurgeons from the National Hospital of Neurology & Neurosurgery.

Characterisation of a brain-tumour-mimicking fluorescence phantom

Supervisors: Dr. Yijing Xie and Dr. Tom Vercauteren

Student: (Project available)

It has been demonstrated that fluorescence-guided brain tumour resection can achieve enhanced extent of resection and thus improved patient prognosis compared with conventional white-light guided surgery. The exogenous fluorescent agent 5-ALA-PpIX is in routine human use for this indication in Europe. However, the confounding effects of tissue layers, light scattering, and blood absorption make the interpretation of fluorescence signal challenging. We are developing a spectrally-resolved fluorescence imaging system to help neurosurgeons reliably differentiate between brain tumour and normal tissue. To evaluate this imaging system, we are developing fluorescence phantoms which simulates brain tumour tissue and brain healthy tissue in terms of their intrinsic optical properties and PpIX fluorescent properties. The phantom overcomes the limits of the current existing fluorescence phantom model which lack of consistency in its optical scattering coefficient, as well as stability with respect to photo-bleaching. In this project, the student will design and implement an experimental protocol to determine the optical properties (absorption coefficient and scattering coefficient) of phantoms with various compositions and various material properties. Using 3D printing in combination with adequate tissue-mimicking materials will allow for the creation of realistic phantoms for neurosurgery.

Evaluation of online and interactive resources for educational purposes 

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

Student: (Project available)

Prompt feedback is a key element of the learning process; it reinforces students when they are doing things well and also indicates when there is a knowledge area that is lacking or their problem solving approach is incorrect. However it is very difficult for academics to provide prompt feedback at all times, as for instance during holidays, weekends, nights, etc. while students might appreciate to have an answer right away. Also, in part due to the increase of student numbers, the time available to have face-to-face discussions per student is highly limited. Online and interactive resources present a compromised alternative. It is available at any time of the day and year, hence catering for all kinds of study patterns, students’ timetables and responsibilities. It also provides immediate feedback, allowing students to solve their questions and continue with their learning right away. Finally students can use it for any number of times, and focusing on the desired areas, allowing students to study at their own pace. This project aims to review current online and interactive educational systems, their scope, benefits and limitations. Then the student will work with (a) lecturer(s) who are using a series of resources newly developed within the UCL Medical Physics and Biomedical Engineering to support the teaching of various modules (e.g. Mathematical Modelling and Analysis II; Materials and Mechanics; and Research skills course). The project student shall evaluate its effectiveness and user-friendliness as perceived by students by analyzing anonymous questionnaires completed by students, look into how these resources are being used by the students, and the academic perception. The project student should then be able to make an informed recommendation for future use and/or development of the system. Some data is currently available, e.g. a trial within a module with over 500 students, however additional data can be collected over the current academic year, including student interviews. If you want to see a sample of our online interactive resources, please contact Pilar and we will give you temporal access to the Moodle site.

Mechanical characterization of dental cements under exposure to sugar drinks

Supervisors: Dr. Pilar Garcia Souto, Dr. Erica Di Federico and Prof. Alan Cottenden

Student: Niels Holdhof

Current life style and eating habits lead to a significant amount of teeth damage and visits to the dentist. Dental damage is believed to be related with the sugar intake, but dental erosion also takes place with the exposure to diet sodas and other sugar free drinks, as well as citrus fruit juices. Cavities are commonly treated, and dental fillings put in place in the hope that they shall last long. This is an experimental project aiming to study the mechanical properties of at least two types of dental cement commonly used for cavity filling, with particular focus on the influence that exposure to various elements might have, e.g. frizzy drinks, citrus juices or mouthwashes containing alcohol. The effect of different exposure times shall be investigated. Experiments will be done using a state-of-the-art mechanical testing machine (Instron E3000), for which training will be provided.

Evolution of core temperature, skin temperature and thermal sensation under ambient transient conditions

Supervisors: Dr. Pilar Garcia Souto and Prof. Jem Hebden

Student: (Project available)

Human thermoregulation and thermal comfort have been subjects of study for quite a few decades, yet their prediction is still difficult because of the large number of parameters that affect both human physiological and psychological responses. A good understanding of the thermoregulation and thermal conform is necessary for instance to identify when a given person might be at high risk and so intervention is needed, e.g. some runners during a marathon, miners exposed to poor ventilation and high temperature, etc.. It is also highly desirable for the development of suitable and efficient climate control systems for indoor spaces, which would enhance working efficiency of the occupants and reduce the energy consumption within the building. This project focuses on the effect of ambient transient conditions (e.g. changes in room temperature over time) both on physiological (core and skin temperature) and psychological (thermal sensation, thermal comfort) parameters. These have been selected as to represent a range of parameters, e.g. core temperature is mainly kept constant while skin temperature is more variable with the environmental conditions. An important finding would be to understand how, and in which order, these parameters change under transient conditions. Data from 16 volunteers collected in a climate chamber and with infrared technology is already available. Additional data might be collected if the student deems it necessary.

Skin temperature detection for mass-screening systems: manual vs automatically extracted data

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

Student: Samantha Devine

Temperature monitoring systems are becoming more popular, especially after the latest infectious diseases outbreaks (e.g. SARS in 2003, the Influenza A pandemic in 2009, and Ebola in 2014) when temperature screening was used to detect individuals with fever with the aim of isolating infected individuals and therefore 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 skin temperature measurement as it is relatively easy to use, quick, and non-invasive. There are some known skin areas that provide relevant information for fever screening, i.e. forehead, ear canal and temple. Currently these are manually identified by personnel from the airport, which can lead to significant human error and the erroneous interpretation of the measurements. The student undertaking this project will develop a detector of the temple area by means of image processing. Ear canal and forehead detectors are already available. S/he shall then compare the information and quality of the data obtained for the three areas of interest by (a) the automatic system, and (b) the manual data extraction, and discuss the benefits and disadvantages of either method. This project can lead to a journal publication if the report is presented to high quality. Prior knowledge of computer programming and statistics would be useful.

Detection of radiotherapy-induced damage of lung radiotherapy patients using serial CT imaging

Supervisors: Catarina Veiga and Dr. Jamie McClelland

Student: Jared White

Radiation induced lung damage is an unwanted side effect of curative radiotherapy. Radiological findings can be used as indicators of lung damage, which is identifiable as changes in the CT imaging features (e.g., anatomy shape, intensity and texture). This project will be inserted in a larger project that aims to develop a standardized method to characterize radiotherapy induced lung toxicities, and implementing automatic methods for its detection. Different aspects of the work could be taken by the student: 1) Investigate strategies to use deformable image registration to align lung CT scans acquired 1 year apart; 2) Develop automatic/semi-automatic methods to detect mass/shape/volume changes in the lung anatomy, such as changes in airways tree, vesselness, fissures and lobes; 3) Automatize a data collection process to create a patient database that can be used on a larger data study. The specific topic of research is flexible and can be chosen by the student.

Electrical Impedance Tomography (EIT) of brain function using a warm blood bolus

Supervisors: Dr. Kirill Aristovich and Prof. David Holder.

Student: (Project available)

EIT is a technique which can be used to image activity in in the brain and nervous system, using EEG type electrodes on the scalp. It is currently being investigated for the real time imaging of epileptic activity in the brain, and of nerve activity for bioelectronics medicine applications. One possible application lies in imaging blood flow in the brain using a bolus of saline of different conductivity to the blood; the bolus produces an impedance contrast over several seconds which can be imaged. However, this is invasive, as it requires insertion of an arterial cannula which is advanced up to the aortic root. An alternative approach could be to use a Peltier device, which is an electronic pad which can heat or cool substances in contact with it with a response times of seconds. This would be placed over the carotid artery in the neck and used to create a bolus of arterial blood with altered temperature, which may be detectable with EIT with scalp electrodes as it enters the brain. The purpose of the project will be to determine the feasibility of this idea. Initial studies will be in computer simulation, then in saline filled tanks and, if successful, some human studies. The project will suit one student with a background in physics, medicine, or engineering, or two working together. Skills to be acquired: computer modelling using Matlab; electronics and use of a Peltier device; some breadboard or printed circuit board construction; Electrical Impedance Tomography; experimental design for tank and human studies.

Building phantoms for experimental testing of fast neural Electrical Impedance Tomography (EIT)

Supervisors: Dr. Tom Dowrick and Prof. David Holder

Student: (Project available)

EIT is a technique which can be used to image fast neural signals in the brain and nervous system, with resolution down to several milliseconds. These capabilities are currently being investigated for the real time imaging of epileptic activity in the brain, and of nerve activity for bioelectronics medicine applications.  EIT is able to image tiny impedance changes which last millseconds, which are due to the opening of ion channels in nerve or brain during activity. EIT systems may be tested in saline filled tanks, termed “phantoms”, with static test objects such as sponges immersed in saline. These existing test phantoms for EIT are not able to model these fast changes, as the test objects are static and do not vary over time. The purpose of this project is to develop new EIT phantoms, in which the test object varies its electrical conductivity over milliseconds and so simulates the changes seen during nervous activity. This could be accomplished using photoconductive materials in which the conductivity is varied using flashes of light or an electronic switch network. The project will involve: background study of fast neural EIT and relevant physiological principles; examination of existing electrical and mechanical test phantoms; identification of novel materials/electronic components to replicate fast neural impedance changes; PCB Design/3D printing of new phantoms; testing and evaluation. The project will suit one student with a background in physics, medicine, or engineering, or two working together as a pair. Skills to be acquired: electronic design/PCB design, including use of CAD software; bioelectronics; Electrical Impedance Tomography; experimental design.

Rapid prototyping of ultrasound transducers

Supervisors: Dr. Bradley Treeby and Louis Robertson

Student: Samuel Searles-Bryant

Ultrasound, well known for its applications in diagnostic imaging, is increasingly being used for therapeutic purposes. Some examples include high-intensity focused ultrasound (HIFU), which is used to destroy tissue in a highly localised manner through thermal ablation, and ultrasonic neuromodulation and stimulation (US-NMS), which is used to mechanically stimulate neural tissue in the brain. These applications of ultrasound require custom transducers, often containing many hundreds of elements arranged in a bowl-shaped or hemispherical geometry. This makes manufacturing using conventional techniques both time consuming and very expensive. The aim of this project is to use recent advances in rapid prototyping techniques (such as 3D printing) to design, construct, and characterise a range of single-element focused ultrasound transducers. The transducers will comprise a 3D printed housing including a lens, a matching layer, air-backed piezoelectric element, and an impedance matching network. The parameters for these components will be designed based on standard formula. The 3D printed housing will be drawn using CAD software and then printed using Vero materials. Characterisation of the transducers (including the beam profile and frequency response) will be performed using a precision scanning tank and a needle hydrophone. If time permits, a multi-element array will also be designed and constructed. The transducers will have a wide range of possible applications, including for HIFU and US-NMS. The designed transducers will also directly contribute to the experimental work performed by other members of the Biomedical Ultrasound Group, for example, for validating computational models, and characterising the acoustic properties of tissue and other materials. The project will be largely experimental in nature, and give significant insight and training into the basic physics of ultrasound and piezoelectric transducers, as well as the rapidly growing applications of therapeutic ultrasound.

Is there more than one kind of bone?

Supervisors: Dr. Sergio Bertazzo and Dr. Mehran Moazen (Mech. Engineering)

Student: Kate Ryan

Biomineralization is a fundamental biological process present in several animals and plants. The structures produced by this process surround us and are clearly recognized in the form of shells, bone and teeth. The most common biomineralized structures are composed of silica (found in diatoms), calcium carbonate (found mainly in shells) and calcium phosphate (mainly present in teeth and bone). The nanostructure of bones from some mammals and birds presents a well-defined distribution of collagen fibres and calcium phosphate crystals. This nanostructure, visible through electron microscopy, provides a clear fingerprint of bone and is today well-known. Interestingly, the same methods currently applied to the study of bone in mammals have not yet been extensively transferred to the study of other species, such as the majority of birds, lizards and fish. In this project, we will use state-of-the-art electron microscopy techniques to study and characterize the nanostructure of bone from several different species and compare them with mammalian bones. The new information about these systems will not only improve our understanding of how a wide variety of organisms produce hard tissues, but could also lead to the design and development of new materials bioinspired by this novel data. The student will participate in the development of the project, sample collection and preparation, experimental measurements, analysis and interpretation of the data. Initially the project will make extensive use of electron microscopes, with new techniques potentially added as the research work progresses. This is an experimental research project where laboratory experience is a plus but not a requirement. 

A closer look at blood cells from vertebrates

Supervisors: Dr. Sergio Bertazzo and (to be decided)

Student: (Project available)

Most of what is now an extensive collection of studies on blood and the cells that it contains have been, as expected, done on mammalian blood. When compared to all other animals, however, mammals present by and large the most unusual cells in their blood,. We therefore have identified an important potential gap in our knowledge about cellular structures and how these vary among different species. In this project, we will use state-of-the-art electron microscopy techniques to study and characterize the cells obtained from blood taken from different species and compare these with cells contained in regular mammalian blood. The new information we acquire about these systems will not only improve our understanding of how a wide variety of blood cells are present in different species, but will also be the first step towards a better understanding of several diseases where blood plays a fundamental role. The student will participate in the development of the project, sample collection and preparation, experimental measurements, analysis of the data and interpretation. Initially, the project will make extensive use of electron microscopes, with new techniques potentially added as the research work progresses. This is an experimental research project where laboratory experience is a plus but not a requirement.

Phantoms for tissue diffraction studies

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

Student: (Project available)

X-ray diffraction studies of tissue are transforming how X-ray images will be taken in the future. Correctly used the technique could provide both detection and characterisation of lesions in tissue that would cause a step change in medical diagnosis. At UCL we have developed a number of promising approaches to this technique that are now undergoing evaluation. A recurring problem is the development of phantoms for this new technique so that realistic assessments can be made of its performance. This project is to look at developing phantoms. Firstly suitable tissue equivalent materials will need to sourced and evaluated. This will then be followed by a period of phantom design and building. Finally measurements will be made on the diffractometers in the Department to assess their performance. Skills required are mainly experimental with an interest in using the Institute of Making.

Mapping radioactive isotope distributions using RadICAL

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

Student: (Project available)

Understanding where radioactive materials are distributed has many applications in medicine, industry and security. At UCL we have developed a new detector concept (called RadICAL) that uses the shape of a detector to provide directionality. This has the potential to have a major impact in many areas and there are a number of possible projects available to either help develop improvements or to look at different applications of the technology. Current examples are:

1. Development of a low cost version;

2. Looking at applications where extended source distributions need to be mapped;

3. Development of a high-speed version for rapid assessment of changing radio-isotope distributions.

All of these projects require good experimental skills and some will require the development of computer code to control the detector and acquire the data.

Coded aperture scatter imaging

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

Student: (Project available)

Scattered radiation fields contain vast amounts of information about the materials that the photons have interacted with. In the case of X-ray scattered fields, coherent scatter is preeminent in the specificity of the information it provides and has the possibility to transform the examination of materials. One technique that has been suggested for making tomographic images from coherent scattered radiation is the use of coded apertures. These devices are introduced into the diffraction system and allow multiple estimates of the diffraction signal to be recorded at the same time and hence increasing efficiency. The difficult part is recovering the individual signals from the recorded data. This project is to set up a simple system to evaluate its potential in the study of breast cancer. This is a challenging project and will require good experimental skills and an ability to write computer code to reconstruct the measured data.

Bone quality assessment using microCT

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

Student: (Project available)

Diseases such as osteoporosis are often assessed by looking at the density of bone tissue in the skeleton. However, there are many examples where the density is low but the bone strength is high and vice-versa. Alternative indicators of bone quality have been sought and one contender is the Ca/P ratio and, in particular, the distribution of the Ca/P ratio. This project is to look at different aspects of this problem. The following areas could contribute towards understanding the Ca/P ratio and any one would make a suitable project:

1.Development of a dual energy microCT approach for tissue analysis;

2.Understanding how bone ‘works’ by using microCT;

3.Developing phantoms for studying the Ca/P ratio.

Each project is experimental and involves the collection and analysis of sets of data. Most projects would require the ability to develop simple computer code and the ability to make components using the Institute of Making.

Estimating neutron dose in proton therapy

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

Student: (Project available)

Proton therapy is particularly good at protecting organs at risk due to the dose deposition characteristics of charged particles. However, the use of high energy proton beams means that neutrons are also produced. The effect neutrons have upon tissue is significantly greater than many other forms of radiation so it is important to estimate the radiation dose due to neutrons during a proton therapy treatment. One technique that has been suggested is to use a similar approach used to estimate doses during nuclear medicine imaging, i.e., the MIRD approach. This project is to investigate if this approach could be used to estimate the dose due to neutrons in proton therapy. The project will involve significant amounts of computing using Monte Carlo methods. It will involve setting up models of the patient and a proton beam to study where energy is deposited. Using these levels of deposited energy calculations of MIRD correction factors will need to be made. A high level of computing experience will be needed for this project.

Positive margin analysis using X-ray diffraction

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

Student: (Project available)

Management of breast cancer usually involves surgery to remove the primary tumour. It is important that no cancer cells are left behind in this process to avoid recurrent disease and hence the margins of the removed tissue need to be investigated. This is usually carried out by taking thin sections of the tissue, staining them and then visually inspecting them under a microscope. We wish to improve this by carrying out an assessment of the surface of the removed tissue at the time of surgery using X-ray diffraction. We have already shown that X-ray diffraction can tell the difference between normal and diseased tissue and we now need to design a system that will accept the tissue sample and present it to the X-ray beam in an appropriate manner. This project is to build a prototype of this tissue support system. Different approaches will be investigated and built using the facilities in the Institute of Making. This is a challenging project suited to somebody with good experimental and constructional skills.

Evaluation of Biosensing IC for a low cost pocket bioimpedance analyser

Supervisors: Dr. James Avery and Dr. Rebecca Yerworth

Student: (Project available)

Electrical Impedance Tomography (EIT) generates images of physiologically induced impedance changes within a subject through measurements using EEG type electrodes. Ensuring good quality electrode contact is vital both for good EIT measurements, as well as for conventional electroencephalogram (EEG) recordings. The ability to measure the electrode impedance in the field quickly and accurately is often limited given the features available on commercial EEG amplifiers, and the specific requirements for EIT. The aim of this project is to evaluate the accuracy of the AFE4300, an Integrated Circuit (IC) originally designed for body composition impedance measurements, for in-situ impedance measurements during EEG and EIT recordings. Initially the focus will be on single channel spectroscopy measurements, before potentially moving to full multi-channel recordings. Should the accuracy of the device prove sufficient, these measurements could be used for full EIT conductivity reconstructions. Further, a successful device could be incorporated into a system to automatically platinise electrodes for cortical recordings, and would thus be a useful tool for in a research laboratory. This project requires experimental skill, with some previous knowledge of programming in Matlab and the Arduino environment beneficial but not essential.

Developing dynamic phantoms for Electrical Impedance Tomography

Supervisors: Dr. James Avery and Dr. Rebecca Yerworth

Student: (Project available)

Electrical Impedance Tomography (EIT) generates images of physiologically induced impedance changes within a subject through multiple surface measurements. For research purposes, experiments are performed in liquid filled tanks or “phantoms” which emulate the electrical properties of human tissue. Commonly, perturbations of agar gel or sponge are used to mimic the impedance changes arising from the pathology of interest e.g. stroke. However, difficulties arise when imaging perturbations which move over time, such as epilepsy, as artefacts resulting from the displacement of the background saline can obscure the impedance changes of interest. The aim of this project is to develop a novel dynamic phantom for EIT using dialysis tubing and Arduino controlled peristaltic pumps. Using the pumps, liquid of varying properties can be fed through the tubing, without altering its volume. Thus is may it possible to create a transient perturbation without disturbing the background. EIT Images of the resultant impedance can then be reconstructed and compared to both simulations and existing phantoms. A successful phantom would prove a valuable research tool. This project has an experimental focus, and would suit a student with prior knowledge (or at least an interest) in programming.

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

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

Students: Meda Brett and Tobi Odeyemi

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. Interested students are encouraged to get in touch with Dr. Leung sooner rather later because of the need to apply for research passport.

Assessment of nasal blockage with acoustic sensors

Supervisors: Dr. Terence Leung and Peter Andrews

Student: Martin Fan Min Tan

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. Interested students are encouraged to get in touch with Dr. Leung sooner rather later because of the need to apply for research passport.

A multispectral flat-panel illuminator

Supervisors: Prof Adam Gibson and Prash Ganeswaran

Student: (Project available)

We have a need for a device which provides uniform illumination at a number of discrete wavelengths from UV to near infrared. Such a device has a number of uses, but our application is transillumination of historical manuscripts. You will build the device, which will require mechanical manufacturing in the Institute of Making and design and assembly of the electronics. You will then characterise the device in terms of the wavelength, intensity and uniformity of the different illumination sources. Finally, you will test the device for transillumination of a range of samples.

Multispectral imaging of skin reddening

Supervisors: Prof Adam Gibson and Cerys Jones

Student: (Project available)

Sunburn and radiotherapy both cause reddening of the skin. We have a multispectral imaging system which acquires photographs at a range of wavelengths which is designed to image historical manuscripts. We propose to use the same system to characterise skin colour before and after insults such as warm water, cold water and Deep Heat cream (used for muscle pains). This project requires experimental skills and image processing, and will involve some computer programming.

Reconstruction of CT images of the Antikythera mechanism

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

Student: Ashkan Pakzad

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.

Development of a dynamic phantom for diffuse optical imaging based on smart film technology

Supervisors: Prof. Jem Hebden, Laura Dempsey, and Dr. Danial Chitnis

Student: Jonathan Saye

The UCL Biomedical Optics Research Laboratory (BORL) has 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. For example, optical imaging techniques are commonly used to observe localised changes occurring in the brain, due to variation in blood flow and oxygenation. The objective of this project is to develop a “dynamic” phantom which can mimic a rapid change in localised optical properties within the brain. The change will be produced by a layer of “smart film” whose optical transparency changes when an electrical voltage is applied. The student will experiment with samples of smart film, and measure the change in transparency as a function of the applied voltage. She/he will then develop a means of activating the smart film when embedded within a solid block of polyester resin. Pigments will be added to the resin to mimic the scattering and absorbing properties of biological tissues. Finally, images of the dynamic phantom will be generated using the UCL NTS diffuse optical topography system, and its optical properties will be fully characterised.

Development of clinical ultrasound training phantoms for minimally invasive spinal procedures

Supervisors: Dr. Wenfeng Xia, Efthymios Maneas, and Dr. Adrien Desjardins

Student: (Project available)

Ultrasound imaging is widely used to guide needle insertions in regional anaesthesia and interventional pain management. It is increasingly being used to guide needle insertions in the spinal region such as central neuraxial and paravertebral blocks, particularly in patients with complex anatomies. Imaging phantoms have been shown to be valuable training tools for improving visual-spatial awareness in ultrasound-guided procedures, and several have been constructed for training in spinal ultrasound. Commercially available ultrasound phantoms provide tactile feedback that is similar to that encountered in clinical practice, but they are typically based on generic models of sonoanatomy, they are expensive, and they have limited lifetimes because of the formation of needle tracks in the tissue-mimicking materials. This project will involve 3D printing and the development of a novel soft-tissue mimicking material to generate an ultrasound phantom of the spine with detailed patient anatomy. The student will work closely with clinical collaborators at the University College Hospital.

A miniature all-optical therapeutic ultrasound probe

Supervisors: Dr. Erwin Alles, Dr. Malcolm Finlay, and Dr. Adrien Desjardins

Student: (Project available)

Recent advances in all-optical ultrasound imaging have resulted in miniature probes that can yield high quality pulse-echo ultrasound images of ex vivo tissue. Current probes comprise two optical fibres, one for ultrasound generation and one for detection, and hence are readily miniaturised for interventional biomedical applications. In such a probe, ultrasound is generated photoacoustically: optical energy is absorbed in an optically absorbing coating, which heats up and locally increases the pressure. Recently a miniature probe (diameter: 2 mm) was developed that generates a tightly focussed acoustic beam, generating a high acoustic pressure (around 1 MPa) in its geometrical focus. However, there are indications that the sound-generating coating can withstand much higher optical pulse energies (30-50x) than used so far, and hence can generate much higher pressures still. This would enable therapeutic clinical use of the probe. The aim of this project is to experimentally determine the damage threshold of the applied coatings, and to numerically predict what pressures might be achievable.

Using SQUID magnetometry to validate MRI tissue magnetic susceptibility measurements

Supervisors: Dr. Karin Shmueli and Dr. Paul Southern

Student: Becky Hopkins

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 make liquid samples doped 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.

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

Supervisors: Dr. Marco Endrizzi and Prof. Sandro Olivo

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 through this analysis will enable the quantitative interpretation of retrieved phase information and the inclusion of the realistic detector performance into simulation software. Some familiarity with the basics of data acquisition and analysis (e.g. Matlab or 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 discarded. 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.

Analytical simulation of edge-illumination x-ray phase-contrast imaging

Supervisors: Dr. Marco Endrizzi and Prof. Sandro Olivo

Student: (Project available)

Numerical simulations are an invaluable tool for the design and understanding of experiments. This project focuses on the development of a new simulation framework for the edge-illumination X-ray phase imaging technique, where a geometrical optics approximation is used. While introducing significant approximations, this is expected to simplify considerably the required numerical calculations, with corresponding advantages on the demand of computing power. The student will develop both computer programming data analysis skills, for testing the new simulation framework and benchmarking against the results provided by established simulation softwares.

Parallelised phase retrieval for edge-illumination x-ray phase-contrast imaging

Supervisors: Dr. Marco Endrizzi and Prof. Sandro Olivo

Student: (Project available)

One possible way to deal with a real and imperfect imaging system is that of including the known defects into the algorithms that we use to interpret data. In edge-illumination X-ray phase-contrast imaging this requires a pixel-by-pixel evaluation of the system response. This approach delivers high quality data but is extremely time consuming, preventing its use in time-constrained situations. Parallelisation of this algorithm is attractive, with the potential of speeding up the whole process by at least two orders of magnitude. This project aims at the development of a dedicated retrieval algorithm, ultimately capable of delivering the retrieved images in real time. Heavily based on computing during its first part, the project will involve also some experimental data analysis for the test and comparison of the results achieved.

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 Endrizzi

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 Dr. 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.

Parameter optimisation for x-ray phase contrast CT of excised breast tissue

Supervisors: Dr. Charlotte Hagen and Anna Zamir

Student: (Project available)

X-ray phase contrast computed tomography (PC-CT) stands for a class of radiographic imaging techniques, which, in addition to x-ray attenuation, are sensitive to phase shifts. This is especially beneficial for the imaging of weakly attenuating biological tissues. PC-CT techniques are investigated by an increasing number of groups worldwide, including the Advanced X-Ray Imaging (AXIM) group at UCL. AXIM currently investigates the use of PC-CT for in-theatre scanning of breast tissue specimens excised during surgery, and aims to demonstrate that it provides improved delineation between tumour and healthy tissue. The student on this project will work alongside the AXIM team and explore the effect of different scan parameters, with the aim of determining those which maximize contrast between tumour and healthy tissue. The work will be based on simulations (a simulation code implemented in Matlab will be provided), with a possibility of verifying results experimentally. Skills required: Imaging with ionising radiation, basic Matlab.

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 Dr. 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.

Imaging deeper in tissue using photoacoustic tomography

Supervisors: Dr. Peter Munro and Dr. James Guggenheim

Student: (Project available)

One of the keys to performing photoacoustic tomography deeper in tissue, and thus addressing numerous clinical problems, is to develop more sensitive ultrasound detectors. The photoacoustic imaging group at UCL has developed the most sensitive detectors in the world and they use light to detect the ultrasound waves. There is currently a need to develop a numerical model of the optical characteristics of the sensor, both for the design of the next generation of sensor, and also to guide the everyday use of the sensors currently used in the lab. This project will suit students with an interest in the simulation of physical phenomena with minimal approximations and who enjoy matching theory and experiment.

Understanding x-ray scattering: a new contrast mechanism for medical imaging

Supervisors: Dr. Peter Munro and Dr. Fabio Vittoria

Student: (Project available)

The absorption and refraction of X-rays is now well understood and applied in the clinic. X-rays are, however, also scattered, due to tissue having features which are smaller than the resolution of the imaging system. The X-ray scattering signal is thus a measure of statistical properties of tissue. We have a research program currently focussed on this and have projects available in a range of areas including theory, development of computational models, implementing algorithms on GPUs, phantom construction and tissue imaging. This project can thus be adapted to the interest of the student. Feel free to come and chat with us if you’re interested in working on the development of a new imaging modality.

Elastography: imaging the mechanical properties of tissue

Supervisors: Dr. Peter Munro and Dr. Lai Bun Lok

Student: (Project available)

The mechanical properties of tissue have long been known to be integral to its structure and function. Indeed, manual palpation has long been part of routine clinical practise. Elastography is a rapidly developing field which acquires images of tissue stiffness. We are part of a collaboration developing optical coherence elastography, which maps tissue stiffness on a microscopic scale. It has so been shown to be clinically relevant in the detection of tumour margins in breast conserving surgery, however, efforts are ongoing applying this technique in a variety of other clinical applications. There is currently an important need to develop optical signal processing techniques to extract stiffness measurements from optical signals. This project represents an excellent opportunity for a student interested in applying mathematical algorithms for extracting clinically relevant information.

Making phantoms for elastography

Supervisors: Dr. Peter Munro and Prof. Alessandro Olivo

Student: Liam Collins Jones

A project is underway within the advanced X-ray imaging group to perform elastography using X-ray phase imaging. Elastrography obtains images of the mechanical properties of tissue and is performed by imaging how tissue deforms in response to a mechanical load. Part of this project requires the development of phantoms with controllable mechanical properties. This project entails the construction of such phantoms along with their characterisation using an instron machine which provides gold standard characterisation of the mechanical properties of materials. This project is largely experimental, though an elementary understanding of continuum mechanics will be beneficial.

Comparison of different phase-retrieval algorithm for beam tracking phase-contrast and dark-field imaging

Supervisors: Dr. Fabio Vittoria and Dr. Peter Munro

Student: (Project available)

X-ray imaging through a beam tracking approach is an innovative technique which exploits high resolution detectors, and dedicated retrieval algorithms, to track the local displacement and broadening of a reference beam caused by a sample. The aim of the project is to compare the performance of different retrieval algorithms and establish their relative benefits and disadvantages in terms of accuracy, noise transfer, etc. The comparison will be mainly performed on simulated data and, on a later stage, benchmarked against experimental data. During the project, the student will acquire an understanding of numerical simulation, the physics of image formation, data analysis and image quality assessment. Familiarity with data analysis and programming (e.g. Matlab) will be useful.

Mechanical characterization of collagen-embedded cancerous cells towards the modelling of cancerous growth

Supervisors: Dr. Peter Wijeratne and Dr. Pilar Garcia Souto

Student: Robert Shaw

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-embedded cancerous cells designed at the Royal Free hospital. The student will build on previous work, which established a rigorous protocol for measuring the properties of thin film collagen gels, and apply this protocol to cancer cells. Depending on preference, the interested student will also either i) extend the protocol into a detailed analysis of measurement effects; or ii) use in-house finite element software to perform tumour growth experiments using the acquired data.

Imaging structure and function in the in vitro tumour microenvironment

Supervisors: Dr. Peter Wijeratne and Dr. Simon Walker-Samuel

Student: William McLean

Recently the tumour microenvironment has been shown to play an important role in the inception, growth and invasion of cancerous cells. Here we propose to use in vitro cancer cells embedded in collageneous material, designed at the Royal Free Hospital, to image the change in the structure and function of the tumour microenvironment at the Centre for Advanced Biomedical Imaging (CABI). High-Resolution Episcopic Microscopy (HREM) allows large tissue samples to be optically imaged in three-dimensions, and at high resolution (up to 1 micron, isotropic). Following fixation, sample volumes of up to 2cm3 are embedded in resin. Within the microscope, an automated sectioning blade removes thin slices from the face of the sample. Images of fluorophores embedded within the sample are acquired with a microscope focussed on the exposed block face and, after each image acquisition, an automated stage raises the sample to allow the next section to be removed. This generates perfectly-aligned, three-dimensional image stacks. The interested student would perform this work using tumouroids, with potential for their work to contribute to a journal paper.

The effect of body position on ventilation distribution, as measured by Electrical Impedance Tomography (EIT)

Supervisors: Dr. Rebecca Yerworth and Prof. Richard Bayford

Student: (Project available)

Previous studies into this did not correct for systematic errors in the data collection - are their conclusions valid? In this project you will use Matlab to correct for the systematic errors and  re-analyse existing data from EIT studies. While of the Matlab code is already written, some familiarity with Matlab  is require to run. This project would suit a student taking MPHY3B27/MPHYMB27: Computing in Medicine.

The effect of shape handling on lung volume estimates in Electrical Impedance Tomography

Supervisors: Dr. Rebecca Yerworth and Prof. Richard Bayford

Student: (Project available)

Electrical Impedance Tomography (EIT) has the potential to fill a urgent clinical need in the management of Acute Respiratory Syndrome as it can provide real-time, long term, bedside monitoring  of the spatial distribution of respiration, without the use of ionising radiation. However, estimates of lung volume may be affected by assumptions within the image reconstruction process, specifically  those related to the chest shape. The aim of this project is to assess the impact of shape assumptions/compensating techniques, with respect to the resulting  lung volume estimations. The project will involve, mathematical simulations and re-analysing previously collected clinical data, using Matlab. It will suit a student who has selected MPHY3B27 Computing in Medicine or the M-level variant, MPHYMB27, or has equivalent previous experience.

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

Supervisors: Dr. Jenny Griffiths and Dr. Rebecca Yerworth

Student: (Project available)

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

Ultrasound scanner – teaching tool

Supervisors: Dr. Rebecca Yerworth and Prof. Jem Hebden

Student: Cameron Starling

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.

Intraoperative cellular-level imaging of the eye for precision surgery

Supervisors: Dr. Christos Bergeles and Dr. Tom Vercauteren

Student: Shweta Lahiri

Novel fibre optics tools passing through sub-millimetre instruments enable cellular level imaging of tissue. This project is about investigating the use of such endomicroscopes within the human eye. Is it possible to visualise the human photoreceptors intraoperatively, so that we can guide a dexterous robot towards cellular-level retinal biopsies? What algorithms do we need to develop to stich such high-resolution (but tiny!) images together for a larger field of view? How can we improve the quality of the images to assist the clinician?

Optical Coherence Tomography - transparent tools for eye surgery

Supervisors: Dr. Christos Bergeles and Dr. Manish Tiwari (Dept. of Mechanical Engineering)

Student: (Project available)

In order to save the sight of patients suffering with Age-Related Macular Degeneration, the clinicians need to be able to target tissue layers with the dimensions of the human hair. To visualise these retinal layers, new microscopes that are equipped with Intraoperative Optical Coherence Tomographs (OCT) can be employed, allowing images of unprecedented detail. The surgical tools, however, are opaque to OCT, meaning that anything below the tools cannot be visualised. This makes the manipulation of tissue extremely risky. This project is about creating tools from OCT-transparent materials, and experimenting with the application ex vivo.

Endoscopy through the eyes of a fly

Supervisors: Dr. Christos Bergeles and Sotirios Nousias

Student: (Project available)

Images acquired during endoscopic surgery may suffer from lack of focus, motion blur, and abundance of specular reflections. Existing imaging systems based around conventional cameras can only algorithmically bypass these limitations, and most often, with limited success. Inspired by the eyes of the fly, which can see multiple viewpoints at once, we are developing an endoscope that has microlenses which deliver many perspectives of the same scene. The goal of this project is, based on this technology, to develop a methodology to remove specular reflections from endoscopic images as a tool towards improved image quality in surgery.