PhD Studentship: Biological Image Analysis
Automated Analysis of Intra-Nuclear Heterochromatin Organisation using 3D Fluorescence Imaging
University of Dundee
Computer Vision & Image Processing Group (School of Computing)
Storey Lab., Cell & Developmental Biology (College of Life Sciences)
N.B.: Full award (stipend and fees) will only be available to students satisfying UK residence requirements. Non-EU students need not apply.
We seek highly motivated applicants for an interdisciplinary 3-year PhD studentship. The successful candidate will research computational methods for automatic analysis of 3D fluorescence microscopy images of nuclei during neural differentiation. This is an exciting opportunity to receive research training in the context of a collaborative effort between highly regarded research teams in two different disciplines: neural developmental biology and computer vision. The student will be based at the University of Dundee's main campus and will work jointly under the supervision of Prof. Stephen McKenna (Chair of Computer Vision, School of Computing) and Prof. Kate Storey (Professor of Neural Development and Head of the Division of Cell and Developmental Biology, College of Life Sciences).
The project will focus on the development of algorithms and software for analysis of fluorescence images of neural cells. Storey's group uses advanced fluorescence microscopy imaging to study cell differentiation during neurogenesis, and the effects of perturbations on these processes. We aim to develop methods for segmentation and analysis of nuclei so that the organisation of chromatin within nuclei during cell differentiation can be studied quantitatively. The student will also be required to learn about and perform some immunocytochemistry and imaging work.
The successful applicant will have:
- a first class degree in a numerate subject (such as computer science, computer engineering, computational biology, applied mathematics, physics), and preferably a Masters level degree.
- strong programming skills
- an interest in, or exposure to, computer vision and image processing
- an interest in cell and developmental biology
Eligibility
This studentship is partly funded by EPSRC and all applicants should check their eligibility before applying. Specifically, a full award (stipend and fees) will only be available to students satisfying the UK residence requirements as described here: www.epsrc.ac.uk/funding/students/pages/eligibility.aspx. The annual stipend is currently £13,590. Students from EU countries other than the UK are generally eligible for a fees-only award. Non-EU students need not apply.
How to Apply
Applicants should send a CV with a covering letter, preferably by 7 November 2011, to Professor Stephen McKenna, School of Computing, University of Dundee, Dundee DD1 4HN, or by email to stephen@computing.dundee.ac.uk and k.g.storey@dundee.ac.uk
Further details can be found at: http://www.computing.dundee.ac.uk/projects/vision/DTAAd.pdf
Storey Lab, Cell and Developmental Biology, College of Life Sciences
With more than 1000 staff and research students and external funding in excess of £30 million per year, the College of Life Sciences is one of the largest and most productive research institutes in Europe. Our reputation is genuinely global and is reflected in the fact that researchers in our laboratories represent no fewer than 58 different nationalities. Yet Dundee is no ivory tower. Our research is having a major impact on the economy of Tayside by stimulating the regional biotechnology industry which currently accounts for 16% of local jobs. We collaborate with the world's major pharmaceutical and biotechnology companies in the fight against diseases such as cancer, diabetes and rheumatoid arthritis. Our Drug Discovery Unit is actively developing drugs for the treatment of neglected tropical diseases including malaria and African sleeping sickness and translating innovative drug targets in oncology, eczema, type-2 diabetes, anti-bacterials and anti-virals. Our Microbiology and Plant Sciences research groups are involved in major environmental issues like the assessment of the occurrence and impacts of toxic blue-green algal blooms in lochs, reservoirs and rivers throughout the world, the development of new bio-fuels and bio-energy generation.
Besides performing research at the highest international standards the College considers training and nurturing of the next generation of researchers a top priority. The PhD Programme therefore represents a major activity in the College and is aimed at making this period an exciting and rewarding experience. The core part of all PhD programmes consists of a piece of original research, directed towards solving important, novel and open questions. All courses include compulsory and optional taught elements in subject specific and generic skills which are delivered throughout the duration of the course.
Computer Vision and Image Processing (CVIP), School of Computing
CVIP is an internationally visible research group currently comprising two full professors, a senior lecturer and around 10 postdocs and PhD students working on image analysis for medical and life sciences applications, human activity analysis, and image indexing and recognition. Funded from a variety of sources including UK research councils, charities and Europe. Recent and current projects include a discipline hopping award on microscopy image analyses; grants from CSO and BCRT on analysis of breast cancer histopathology images; TSB projects on content-based image browsing and video analysis; EPSRC projects on human body and action modelling for communication and animation; development of cutting-edge instruments for ophthalmology and optometry with a market-leading UK company (OPTOS plc); work with the £30M Centre for Secure Information Technology in Belfast; and the recent €3M European Research Council project, CODIR.
The School of Computing offers an excellent and supportive environment for research. School research is organised in two areas, Human Centred Research and Intelligent Systems. Each has about 35 staff and current research funding of about £3.5M. In the 2008 research assessment exercise, two thirds of our research was rated world leading or internationally excellent (4* or 3*). Healthcare informatics and medical image processing are internationally visible strengths of the School. For further information see www.computing.dundee.ac.uk/projects/vision
The University of Dundee
The University of Dundee is an established university with a progressive and dynamic outlook. Never complacent, we constantly strive to build on our achievements: investing in excellent facilities, pushing the boundaries of research and developing new ways of e-learning. "Dundee is one of the prize catches in higher education...so apply soon for one of the best university experiences." (Sunday Times University Guide, 2010). We are also one of the world's top 200 universities (Times Higher Education World University Rankings, 2010) with much of our research described as 'world leading' or 'internationally excellent', according to the most recent Research Assessment Exercise (2008). A £200-million campus redevelopment programme, including award-winning teaching accommodation, the prize-winning Queen Mother Building hosting the School of Computing, high-quality student housing, and major extensions to the library and Institute of Sport & Exercise, has recently been completed. City attractions, including a vibrant music scene, galleries, cinemas and theatre, are only a few minutes away. Dundee is big enough to have a great buzz about it (both on and off campus), yet small enough to be friendly and accessible. Dundee University Students Association (DUSA) is regarded as one of the best Students' Unions in the UK and was the 2010 runner-up in the Club Mirror Students' Union of the Year Award.Surf the university web pages for more information at www.dundee.ac.uk.
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