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Machine learning for predicting cellular states in 3D lattice light sheet microscopy

   Warwick Medical School

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  Dr T Bretschneider  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

PhD in Interdisciplinary Biomedical Research - Fully-funded studentship available for entry in September 2020

This industrial Collaborative Award in Science and Engineering (iCASE) studentship is offered by Warwick’s MRC Funded Doctoral Training Partnership (DTP). The training program involves an exciting one-year MSc in Interdisciplinary Biomedical Research and then a three-year PhD project, co-supervised by experts from both academia and industry. The student will benefit from a comprehensive training programme that offers advanced workshops, career planning, transferable skills training and cohort learning events and conferences with ~ 50 other PhD students.

Prof. Till Bretschneider - University of Warwick:
Prof. Andrew McAinsh - University of Warwick:
Prof. Nigel Burroughs - University of Warwick:
Dr Benjamin Atkinson and Dr. Hella Baumann - 3i - Intelligent Imaging Innovations Ltd.:

Project summary:
Novel lattice-light sheet microscopy (LLSM) is an ideal tool to resolve fast cellular dynamics by optically sectioning single cells at rates of 1 second per volume. To achieve these speeds only one cell can be imaged at a time, however, reducing chances of capturing rare events like cell divisions significantly. In this project the student will develop an integrated pipeline for online image analysis, employing deconvolutional and recurrent neural networks to predict the stages of mitotic cell division. Anticipation of rare events will be used to automate recordings and increase the throughput of LLSM, building on the expertise of 3i in microscopy control and design.

MSc Course (Year One)
A one-year masters in Interdisciplinary Biomedical Research. This will include six months of taught modules in areas such as frontier techniques and research skills in biomedicine, programming, advanced microscopy and imaging, mathematical modelling and physical biology of the cell and two 12-week research projects.

PhD Project (Years Two - Four)
A three-year PhD project. Students will be supervised jointly by a Warwick Principal Investigator and an industry partner, and will undertake a placement with the industry partner for a minimum of three months.

Entry requirements:
Applicants should be highly motivated and have a good undergraduate degree (2i or above) or international equivalent in computer science with an interest in machine learning, image analysis and software development for the biomedical, health and clinical sciences. Please see the website for further information about academic entry and residency requirements.

If you are interested in joining our dynamic DTP community, please apply by 23 December 2019. Short-listed candidates will be informed by 31 January 2020. Interviews will take place on 13 February 2020.

Funding Notes

Studentships covering full fees, consumables and annual stipend of £17,780 * are available. See for full information.

* figure to be confirmed
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