Contextual segmentation of large, high-dimensional medical images
Applications are now CLOSED
State-of-the-art serial block face scanning electron microscopy (SBF-SEM) is used in cellular research to capture layers of large images from a block of embedded tissue. Collectively, these 2D images create a 3D digital copy of the tissue sample. The fine-grained resolution of these images means that a large number of small structures can be observed. This is helpful for scientists from different disciplines to explore cellular structures, and for the purpose of this project – neuronal structures, whilst investigating various diseases. With such wealth of information it is time-consuming to annotate and isolate the structures of interest even when using state-of-the-art automated and semi-automated approaches. Novel machine learning based approaches are needed to accurately and efficiently extract complex structures from complex high-dimensional images. Successfully achieving the goals of this project will enable scientists to explore diseases, such as diabetic retinopathy, at a faster and more data-driven manner than ever before.
State-of-the-art serial block face scanning electron microscopy (SBF-SEM) is used in cellular research to capture layers of large images from a block of embedded tissue. This technique has recently been used to successfully construct the first three-dimensional ultrastructural analysis of the neurovascular unit in the retina . Once key cell morphologies of the retina are identified, they can be analysed to examine the heterocelluar interactions and spatial relationships. This enables medical researchers to develop a greater understanding of structure and function of key retinal cells in both diseased and healthy states.
However, the structural complexity of the retina in three-dimensions means that key structures are often occluded by other structures or are difficult to track across different layers of the image. Furthermore, the size and complexity of the resultant three-dimensional image means that analysis of SBF-SEM images is often costly and time-consuming. Segmentation of the image is currently completed in a manual, or at best semi-automated, manner resulting in lengthy annotation processes that are at risk to human error.
Similar high-dimensional instance segmentation has already been explored in video segmentation where different frames of a video (analogous layers of microscopy images) are segmented into distinct classes . Specifically, models looking at multi-object tracking and segmentation (MOTS) problems aim to leverage information between neighbouring frames to provide more accurate and computationally efficient segmentation . However, further research is needed to extend such methods to handle large, densely populated images such as three-dimensional SBF-SEM images that include occlusions. By exploiting the context in which pixels occur, relative to the information contained in surrounding pixels within a layer and across adjacent layers, it is hoped that accurate and computationally efficient instance segmentation methods can be developed. Enabling the automated isolation of key retinal structures can accelerate biomedical analysis into diseases such as diabetic retinopathy, and other cell-focused investigations.
The project will aim to develop novel machine learning methods with the follow specific objectives:
- Develop novel methods to automatically align and adjust sequences of SBF-SEM images.
- Develop state-of-the-art segmentation methods that utilise contextual information from adjacent SBF-SEM images.
- Exploit HPC resources to optimise high-throughput analysis of SBF-SEM images.
Whilst the methods developed in this project will be directly applied to SBF-SEM imaging, they will also be transferrable to more general modalities such as video analysis, other medical imaging technologies such as CT and MRI data, and longitudinal imaging studies.
 Albargothy, M.; Azizah, N.; Stewart,S.; Troendle, E.; Steel, D.; Curtis, T.; Taggart, M.; “Investigation of heterocellular features of the mouse retinal neurovascular unit by 3D electron microscopy”, Journal of Anatomy (2022).
 Wang, W.;Zhou, T.; Porikli, F.; Crandall, D.; Van Gool, L.; “A Survey on Deep Learning Technique for Video Segmentation”, I EEE Transactions on Pattern Analysis and Machine Intelligence (2022).
*Please note that the deadline for applications from international candidates closed on 28 February*
Please note that funding may be available for this project (still to be confirmed). To be eligible for consideration for a DfE Studentship (covering tuition fees and maintenance stipend of approx. £17,668 per annum), a candidate must satisfy all the eligibility criteria based on nationality, residency and academic qualifications. The Studentship is open to UK and ROI nationals, and to EU nationals with settled status in the UK, subject to meeting the specific DfE nationality and residency criteria. Full eligibility information can be viewed via: https://www.economy-ni.gov.uk/publications/student-finance-postgraduate-studentships-terms-and-conditions
The minimum academic requirement for admission is normally an Upper Second Class Honours degree from a UK or ROI Higher Education provider in a relevant discipline, or an equivalent qualification acceptable to the University.
Computer Science overview
The School of Electronics, Electrical Engineering and Computer Science (EEECS) aims to enhance the way we use technology in communication, data science, computing systems, cyber security, power electronics, intelligent control, and many related areas.
You’ll be part of a dynamic doctoral research environment and will study alongside students from over 40 countries world wide; we supervise students undertaking research in key areas of computer science, including: computing systems, artificial intelligence and cybersecurity. As part of a lively community of over 100 full-time and part-time research students you’ll have the opportunity to develop your research potential in a vibrant research community that prioritises the cross-fertilisation of ideas and innovation in the advancement of knowledge.
Within the School we have a number of specialist research centres including a Global Research Institute, the Institute of Electronics, Communications and Information Technology (ECIT) specialising in Cyber Security, Wireless Innovation and Data Science and Scalable Computing.
Many PhD studentships attract scholarships and top-up supplements. PhD programmes provide our students with the opportunity to acquire an extensive training in research techniques.
Computer Science Highlights
- ECIT brings together, in one building, internationally recognised research groups specialising in key areas of advanced digital and communications technology.
- Queen’s researchers have strong links with the local industry, which boasts a rich mix of local startups and multi-nationals. Belfast is the second fastest growing region in the UK in terms of Knowledge Economy activity (Northern Ireland Economy Report, 2018).
- CSIT brings together research specialists in complementary fields such as data security, network security systems, wireless-enabled security systems, intelligent surveillance systems; and serves as the national point of reference for knowledge transfer in these areas.
World Class Facilities
- The state-of-the-art £14m Computer Science Building and the Institute of Electronics, Communications and Information Technology offer bespoke research environments.
The Institute of Electronics, Communications and Information Technology (ECIT), with state-of-the-art technology, offers a bespoke research environment.
Internationally Renowned Experts
- You will be working under the supervision of leading international academic experts.
Research students are encouraged to play a full and active role in relation to the wide range of research activities undertaken within the School and there are many resources available including:
- A wide range of personal development and specialist training courses offered through the Personal Development Programme
- Access to the Queen's University Postgraduate Researcher Development Programme
- Office accommodation with access to computing facilities and support to attend conferences for full-time PhD students
To do a PhD was one of the most challenging but rewarding decisions I have taken. While having a PhD was helpful in the job market, the real benefit was in stretching my mind and deepening my thinking. This is proving particularly useful as I head up a new local R&D team which has to stay ahead of the game by exploiting the latest research.
R&D Team Leader, Mintel
Research within the School is organised into research themes combining strengths by working together on major projects, in many cases in collaboration with key technology companies.
ECIT brings together internationally recognised research groups specialising in key areas of advanced digital and communications technology.
PhD Opportunities are available in a wide range of computer science subjects, aligned to the specific expertise of our PhD supervisors.
Queen’s is a leader in commercial impact and one of the five highest performing universities in the UK for intellectual property commercialisation. We have created over 80 spin-out companies. Three of these -
Kainos, Andor Technology and Fusion Antibodies - have been publicly listed on the London Stock Exchange.
Queen’s has strong collaborative links with industry in Northern Ireland, and internationally. It has a strong funding track record with EPSRC and the EC H2020 programme.
The research profile produced by the 2014 UK Research Excellence Framework (REF) graded 80 per cent of our research activity as 'world-leading' or 'internationally excellent', confirming the School's reputation as an internationally-leading department.
For further information on career opportunities at PhD level please contact the Faculty of Engineering and Physical Sciences Student Recruitment Team on askEPS@qub.ac.uk. Our advisors - in consultation with the School - will be happy to provide further information on your research area, possible career prospects and your research application.
People teaching you
Course structureThere is no specific course content as such. You are expected to take research training modules that are supported by the School which focus on quantitative and qualitative research methods. You are also expected to carry out your research under the guidance of your supervisor.
Over the course of study you can attend postgraduate skills training organised by the Graduate School.
You will normally register, in the first instance, as an ‘undifferentiated PhD student’ which means that you have satisfied staff that you are capable of undertaking a research degree. The decision as to whether you should undertake a PhD is delayed until you have completed ‘differentiation’.
Differentiation takes place about 8-9 months after registration for full time students and about 16-18 months for part time students: You are normally asked to submit work to a panel of up two academics and this is followed up with a formal meeting with the ‘Differentiation Panel’. The Panel then make a judgement about your capacity to continue with your study. Sometimes students are advised to revise their research objectives or to consider submitting their work for an MPhil qualification rather than a doctoral qualification.
To complete with a doctoral qualification you will be required to submit a thesis of approx 80,000 words and you will be required to attend a viva voce [oral examination] with an external and internal examiner to defend your thesis.
A PhD programme runs for 3-4 years full-time or 6-8 years part-time. Students can apply for a writing up year should it be required.
The PhD is open to both full and part time candidates and is often a useful preparation for a career within academia or consultancy.
Full time students are often attracted to research degree programmes because they offer an opportunity to pursue in some depth an area of academic interest.
The part time research degree is an exciting option for professionals already working in the education field who are seeking to extend their knowledge on an issue of professional interest. Often part time candidates choose to research an area that is related to their professional responsibilities.
If you meet the Entry Requirements, the next step is to check whether we can supervise research in your chosen area. We only take students to whom we can offer expert research supervision from one of our academic staff. Therefore, your research question needs to engage with the research interests of one of our staff.
- Assessment processes for the Research Degree differ from taught degrees. Students will be expected to present write up their work at regular intervals to their supervisor who will provide written and oral feedback; a formal assessment process takes place annually.
This Annual Progress Review requires students to present their work in writing and orally to a panel of academics from within the School. Successful completion of this process will allow students to register for the next academic year.
The final assessment of the doctoral degree is both oral and written. Students will submit their thesis to an internal and external examining team who will review the written thesis before inviting the student to orally defend their work at a Viva Voce.
- Supervisors will offer feedback on the research work at regular intervals throughout the period of registration on the degree.
Full time PhD students will have access to a shared office space and access to a desk with personal computer and internet access.
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School.
For information on international qualification equivalents, please check the specific information for your country.
English Language Requirements
Evidence of an IELTS* score of 6.0, with not less than 5.5 in any component or equivalent qualification acceptable to the University is required (*taken within the last 2 years).
International students wishing to apply to Queen's University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes.
For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs.
If you need to improve your English language skills before you enter this degree programme, INTO Queen's University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree.
|Northern Ireland (NI) 1||TBC|
|Republic of Ireland (ROI) 2||TBC|
|England, Scotland or Wales (GB) 1||TBC|
|EU Other 3||£25,600|
1 EU citizens in the EU Settlement Scheme, with settled or pre-settled status, are expected to be charged the NI or GB tuition fee based on where they are ordinarily resident, however this is provisional and subject to the publication of the Northern Ireland Assembly Student Fees Regulations. Students who are ROI nationals resident in GB are expected to be charged the GB fee, however this is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
2 It is expected that EU students who are ROI nationals resident in ROI will be eligible for NI tuition fees. The tuition fee set out above is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
3 EU Other students (excludes Republic of Ireland nationals living in GB, NI or ROI) are charged tuition fees in line with international fees.
All tuition fees quoted are for the academic year 2021-22, and relate to a single year of study unless stated otherwise. Tuition fees will be subject to an annual inflationary increase, unless explicitly stated otherwise.
Computer Science costs
There are no specific additional course costs associated with this programme.
Additional course costs
Depending on the programme of study, there may also be other extra costs which are not covered by tuition fees, which students will need to consider when planning their studies . Students can borrow books and access online learning resources from any Queen's library. If students wish to purchase recommended texts, rather than borrow them from the University Library, prices per text can range from £30 to £100. Students should also budget between £30 to £100 per year for photocopying, memory sticks and printing charges. Students may wish to consider purchasing an electronic device; costs will vary depending on the specification of the model chosen. There are also additional charges for graduation ceremonies, and library fines. In undertaking a research project students may incur costs associated with transport and/or materials, and there will also be additional costs for printing and binding the thesis. There may also be individually tailored research project expenses and students should consult directly with the School for further information.
Some research programmes incur an additional annual charge on top of the tuition fees, often referred to as a bench fee. Bench fees are charged when a programme (or a specific project) incurs extra costs such as those involved with specialist laboratory or field work. If you are required to pay bench fees they will be detailed on your offer letter. If you have any questions about Bench Fees these should be raised with your School at the application stage. Please note that, if you are being funded you will need to ensure your sponsor is aware of and has agreed to fund these additional costs before accepting your place.
How do I fund my study?1.PhD Opportunities
Find PhD opportunities and funded studentships by subject area.2.Funded Doctoral Training Programmes
We offer numerous opportunities for funded doctoral study in a world-class research environment. Our centres and partnerships, aim to seek out and nurture outstanding postgraduate research students, and provide targeted training and skills development.3.PhD loans
The Government offers doctoral loans of up to £26,445 for PhDs and equivalent postgraduate research programmes for English- or Welsh-resident UK and EU students.4.International Scholarships
Information on Postgraduate Research scholarships for international students.
Funding and Scholarships
The Funding & Scholarship Finder helps prospective and current students find funding to help cover costs towards a whole range of study related expenses.
How to Apply
Find a supervisor
If you're interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions.
To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here.
You might be asked to provide a short outline of your proposal to help us identify potential supervisors.