2015 CDT ISM Student Cohort

Callum MacArthur

University of Edinburgh

Early Detection of Multiple Sclerosis

Due to a large range of symptoms – and an unknown cause – Multiple Sclerosis (MS) and other demyelinating diseases are difficult to diagnose, and even more so to predict. MS causes permanent, seemingly irreparable damage to the myelin sheath of nerve cells (axons) in the central nervous system. Thus, the early detection of this disease is imperative to slow the monotonic downward progression that is characteristic of demyelinating disease.

For years now, clinicians and researchers have used the eye as a gateway to the body’s vasculature and nervous system. Eye-related difficulties are one of the most common presenting symptoms in MS, such as Optic Neuritis. However, many other eye abnormalities that are specific to demyelination occur long before MS is clinically confirmed.

My PhD. project is to investigate and facilitate the early detection of MS through the creation of a device that can test for multiple different symptoms of myelin scarring in the optic nerve.

Chiara Garbellotto

University of Glasgow

Computational Imaging in Fluorescence Microscopy

My project will combine computational imaging and compressive sensing techniques with SPIM microscopy, with the aim of increasing the speed, quality and field of view of imaging inside living tissue. The focus will be on the development of new imaging and sensing techniques for fluorescence microscopy, with the ultimate aim of improving microscope imaging capabilities for biologists studying living animals such as the zebrafish.  Starting with my background in physics and astronomy, an interest in optics, a good dose of passion for science in general and the desire of never stop learning, I will face the challenge of designing and building new optical imaging systems and  being able to recover high quality 3D image from the acquired  measurements.

Gianluca Melino

University of Glasgow

The Sonopill: CMOS Sensor Technology 

Our vision is of a capsule that can be swallowed comfortably, incorporating diagnostic and therapeutic ultrasound along with optical imaging. This will be complemented by other sensors, e.g. for pH measurement and autofluorescence imaging (AFI) for multimodal diagnosis. The capsule will allow autonomous positioning and will have multiple deployment modes: from an endoscope or swallowed directly, and tethered or with full autonomy. When a patient presents with a GI complaint, the use of such a capsule will be an early diagnostic choice rather than the current relatively late choice of conventional endoscopy (Fleischer, 2010). It may be deployed by a general practitioner, nursing staff, or a consultant. The capsule will provide information on the condition of the GI tract, both superficially and beneath the surface, and the same device or a different one will allow localised treatment, e.g. of cancer, haemorrhage or IBD. In the longer term, we foresee for GI conditions a family of diagnostic and therapeutic capsules no larger than paracetamol caplets, with the patient pathway defined according to diagnostic information assembled as different modalities, visual, ultrasonic, chemical and photonic, are utilised. In this project Gianluca Melino is focusing on design and optimisation of miniaturised optics for an autofluoresence pill. He will characterise the device using artificial phantoms and neonate rats prior to collaboration with Dr Mark Potter at Edinburgh Western General who will provide access to resected human gut tissue.

Jennifer Dodoo

University of Edinburgh

Bioelectronic Methods for Sensors Based on Engineered Bacterial Growth Responses

Whole cell biosensors are living cells, usually bacteria, which have been genetically modified to produce a detectable response to a specific analyte. The response is most commonly luminescence or fluorescence, and with the GM nature of the organisms, this largely restricts such systems to laboratory use. For field use it would be advantageous to use non-transgenic organisms and cheap, rapid electrical/electronic detection systems. We propose a novel class of systems in which bacteria are engineered, without transgenesis, to respond to specific analytes by growing only in their presence. This will be combined with electrochemical transduction for sensitive detection of this growth, which can occur on a rapid time scale. Such systems may be suitable for point-of-care diagnostics as well as detection of environmentally significant analytes in the field. This is a multidisciplinary project involving both biological aspects (genetic modification) and engineering (fabrication of test devices). It is of considerable potential interest in biomedical, environmental and other sectors, and could also potentially be modified for rapid detection of pathogens, including antibiotic resistant bacteria. It will take advantage of the resources of the School of Engineering for the design and fabrication of microfluidic devices, micro/nanoelectrodes and integrated systems. The combination of this capability with the expertise in the development of bacterial biosensing systems in the School of Biological Sciences represents a great opportunity for multidisciplinary collaboration.

Martin Sinclair

University of Glasgow

Optical Rotation Sensor In An Integrated Photonics Circuit

This project aims to develop an interferometric optical rotation sensor with silicon nitride on silicon on-chip optics.  This would utilise techniques pioneered in MEMS fabrication and could potentially provide feedforward noise isolation for the MEMS gravimeter developed at the University of Glasgow.  Due to rapid progress made in integrated optics based telecommunications, it is now possible to envisage the miniaturisation of an optical rotation sensor based on the Sagnac effect.  If realised, this sensor could supplant the ring laser gyroscope and MEMS gyroscope as the dominant methods of rotation sensing in aeronautical navigation systems and mobile devices, respectively.  With smaller and smaller sensor systems, featuring at the same time increased sensitivity, it is not hard to imagine that in the mid-term future we will be limited by readout noise and back-action noise of our optical sensors. This project will develop new optical readout strategies for readout systems evading back-action noise using so-called quantum non-demolition techniques, such as the application of squeezed light states.

Matthew Donora

University of Edinburgh

Smart Contact Lenses: A Non-Invasive, Continuous Sensor

Some of the most significant advances in medical technology over the past century have induced a shift from hospital-based to home diagnostics, monitoring and care. This focus on patient welfare and access in turn leads to increased uptake and efficacy of treatment. In the past decade, wearable and point-of-care technology has emerged as a prolific research focus, both in academic and commercial circles. My project considers the promising, fairly new field of smart contact lenses.

Lachrymal fluid, containing an ultrafiltrate of blood, can in many cases act as a sensing analogue in place of blood tests. Additionally, a contact lens sensing system can act continuously throughout the day, giving information about the ebb and flow of a biomarker, in contrast with the snapshot that a single blood test would provide. The most prominent direction of current research is working to develop a non-invasive glucose sensor for diabetes management. However, research into the role of various chemical species in the lachrymal fluid with regard to indication of disease and physical health is in its early stages, and there are numerous potential applications for a contact lens-based sensor.

During my PhD I aim to develop an array of electrochemical sensors suitable for simultaneous sensing of different biomarkers in the tear film, such that the continuous and parallel data may be used to monitor and diagnose various diseases, as well as providing a platform for further research into the role and nature of lachrymal fluid.

Paul Sullivan

University of Edinburgh

Implanted Optical Sensors for pH and Hypoxia

This project aims to develop support electronics and an integration platform for novel biosensors developed in Edinburgh (School of Chemistry). The sensors are ground-breaking examples of new ways to “interrogate” biology and the work will therefore be at the cutting edge of sensor technology. The student involved will:- • Build an understanding of the principles and practice in a new biosensor form • Work with chemists to develop an integration strategy for these unique sensors. • Construct and fabricate elements of the integration platform, working in collaboration with the team on the IMPACT (Implanted Microsystems for Personalised Cancer Care) project Further Information: Cancer kills over a million per annum in Europe alone. A malignant tumour is an uncontrolled growth of cells that can spread (metastasise) to distant organs. The microenvironment of a tumour is key to this spread and to the tumour’s resistance to radiotherapy. Implanted biosensors will allow a tumour’s biology to be monitored continuously and without further intervention. This project will develop novel in vivo biosensors of hypoxia and other key parameters of cancer biology. Subject to preclinical “proof in principle”, these biological data will be exploited therapeutically in treating cancers with RT in veterinary animal models. This project aims to explore the use of pH-sensitive polymers developed by the Bradley group in the School of Chemistry, Edinburgh, in combination with CMOS photodiode/SPAD sensors. These sensors require support electronics and possible post-processing fabrication techniques. Initially, the project will explore and evaluate the performance and support needs of a range of biosensors, selecting a target type at the end of year#2 of the CDT programme. Years 3-4 will be spent designing, fabricating and testing the necessary integration platform (on CMOS) for the chosen sensor type. Testing will be performed in vitro and in vivo via collaboration with the School of Veterinary medicine. Biosensors in radiation treatment for cancer.

Ross Drysdale

University of Glasgow

Quantitative Optical Imaging in the Eye

The Imaging Concepts Group pioneers new techniques for quantitative imaging within the eye including multispectral imaging of retinal and scleral blood oxygenation, computational scanning laser ophthalmoscopy, optical coherence tomography and imaging of retinopathy of prematurity. In this project the student will develop and apply new techniques for quantitative retinal imaging including using structured light and snapshot spectral imaging to quantify retinal chromophors, metabolism and to characterise systemic vasculature. That is, imaging of the retina will be used as a window on systemic health. The student will use and apply the principles of optics, imaging and mathematics at a deep level and will develop a working understanding of the relevant biology through specialist courses and through collaboration with clinicians and biologists. The student will work within the Imaging Concepts Group consisting of two academics, ten PhD and EngD students and six post-doctoral researchers conducting fundamental research into the development of a range of advanced imaging techniques and their application in biological, medical, consumer imaging, remote sensing and surveillance fields. The group conducts collaborative research with industry and academic researchers across, Glasgow, the UK and Internationally within newly refurbished researcher laboratories benefitting from over £1M of recent investment in equipment.

Scott Deans

University of Glasgow

Integrated Biosensors for Field-Based Diagnostics

There is a significant interest in moving medical diagnostics from hospital central laboratories and clinics, into the hands of local healthcare workers and patients. This change in healthcare provision has the potential to lead not only to significant cost savings for the healthcare systems, but also to earlier detection of diseases, which generally translates in better outcomes for patients, as well as the ability to monitor the efficacy of treatment more easily and frequently, giving the ability to patients and doctors to tailor the therapies when required, minimising side-effects while maximizing efficiency.

However the widespread adoption of point-of-care sensing systems has been limited by difficulties in establishing appropriately sensitive performance in real patient samples (blood, saliva, urine or faeces for example), in a major part due to fouling of the sensors. Strategies to avoid such non-specific effects require extensive sample preparation that have been increasing cost and complexity beyond the levels acceptable by the users. Recently it has been shown that Surface Acoustic Wave (SAW) devices, employed in communications, carry a mechanical energy that can be widely used as highly sensitive biosensing platform. Uniquely, we have demonstrated a new proprietary technology using phononic metamaterials that has enabled us to create a “tool-box” of different diagnostic functions, including dispensing, mixing, heating, and moving. This has enabled us to develop a suite of diagnostic tests to detect infectious diseases (e.g. malaria, sexually transmitted diseases, tuberculosis). However, the eventual sensing events at the end of the assays in this platform are still using an optical modality, making the diagnostic devices bulky and complex, since they are using different techniques to perform different functions, limiting their potential impact in point-of-care applications, especially in low-resource settings.

This project is now focused on the development of sensors using the phononic structures to enable complete integration of a ‘sample-to-result’ biosensor. In an analogy with optical technologies associated with photonic crystals, the student will be designing, fabricating and testing novel resonant acoustic structures for ultrasensitive sensing. The devices will be tested on mock samples in the first instance (after their initial acoustic validation using laser vibrometry), but the student will have the opportunity of validating them on real samples through our local partnership with the West of Scotland Virus Centre (Dr. Rory Gunson), as well as explore their use in low-resource settings in collaboration with our partners in Africa (e.g. Professor Wambebe in Uganda). We will also work together with our long term partner Epigem (a UK SME) to ensure that the designs and material choices are amenable to mass manufacturing (using reel-to-reel processes). The student will be able to visit Epigem to transfer the new technology when available.

This work aligns in particular to the EPSRC strategic theme in healthcare technologies and its strand on optimizing treatment. It also aligns with the research area on microsystems.

Stuart Wilson

University of Glasgow

Hybrid Computational-Optical Techniques for Microscopy and Retinal Imaging

As part of the Imaging Concepts group, Stuart works in the exciting and fast-moving field of computational optical imaging, combining optics and imaging science with computational techniques for recovering images.

His research aims to devise new optical techniques for recording image information in the presence of high levels of aberrations or clutter introduced by the optics – or by the sample to be imaged – and develop algorithms for recovery of three-dimensional images from this information. These new techniques will then be adapted for application in retinal imaging, microscopy (for example, fluorescence and two-photon microscopy) for life-science applications for in vitro, ex vivo and in vivo imaging.

The Imaging Concepts Group consists of two academics, ten PhD and EngD students and six post-doctoral researchers conducting fundamental research into the development of a range of advanced imaging techniques and their application in biological, medical, consumer imaging, remote sensing and surveillance fields. The group conducts collaborative research with industry and academic researchers across, Glasgow, the UK and Internationally within newly refurbished researcher laboratories benefitting from over £1M of recent investment in equipment.

Giovanna Marocco

University of Glasgow

MEMS Based Attitude Sensors for CubeSats
In this EngD project I am working within the Institute for Gravitational Research, University of Glasgow and Clyde Space Ltd (https://www.clyde.space/). The aim of this research project is to develop a novel high sensitive sensor for attitude control of spacecraft for the CubeSat systems developed by Clyde Space. The first step of the project will consist in the design of a MEMS gradiometer using Finite Element Method modelling. The device will be fabricated using the facilities of James Watt Nanofabrication Centre. The characterisation of the structure will take place in 1 g environment and in launch conditions. The project will involve the integration of electrostatic feedback electrodes for closed loop operation, shock stops to limit the movement of the mass of more than 10 um and passive during launch. Low power electronics will be developed to integrate the MEMS device accordingly to CubeSat power unit specifications. I hope that towards the end of the project, we can secure a flight of the device to gain some data from a space environment.