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.

Deadlines

  • 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: 29
Number of projects still available: 29

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: (Project available)

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

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: (Project available)

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. 

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.

Fibre-optic fluid flow sensing

Supervisors: Dr. Erwin Alles, Dr. Simeon West, and Dr. Adrien Desjardins

Student: (Project available)

Through simple dip-coating, low-finesse interferometric sensors can be fabricated on the tip of an optical fibre. The thickness of this sensor varies with the pressure and temperature of the surrounding medium, and hence by optically tracking the sensor thickness, the pressure and temperature at the tip of the fibre can be recorded. Due to its small dimensions (diameter: 200 um), such a sensor is ideally suited to intravascular biomedical use, potentially enabling in vivo and in situ monitoring of blood pressure and temperature. In addition, the employed lasers can locally heat up the surrounding fluid, and by tracking the fluid temperature as a function of time a measure of fluid flow can be obtained. The aim of this project is to experimentally explore several methods of fluid flow measurements, either using a single fibre or using multiple fibres positioned in different locations, and attempt to obtain calibrated flow measurements. The project will involve the development of an experimental flow setup, as well as the design of excitation schemes and analysis methods, with the aim to move to clinical applications.

Using SQUID magnetometry to validate MRI tissue magnetic susceptibility measurements

Supervisors: Dr. Karin Shmueli and Dr. Paul Southern

Student: (Project available)

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.

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: (Project available)

It is well established that cancerous growth is dependent on both biochemical and biomechanical factors. Recently, remodelling of the collagen-rich extracellular matrix has been implicated in cancerous growth and progression. This project aims to quantitatively measure the mechanical properties of collagen-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.

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: (Project available)

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: (Project available)

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.