Skip to main content

3D microscopy of swimming worms

PGR-P-717

Coronavirus information for applicants and offer holders

We hope that by the time you’re ready to start your studies with us the situation with COVID-19 will have eased. However, please be aware, we will continue to review our courses and other elements of the student experience in response to COVID-19 and we may need to adapt our provision to ensure students remain safe. For the most up-to-date information on COVID-19, regularly visit our website, which we will continue to update as the situation changes www.leeds.ac.uk/covid19faqs

Key facts

Type of research degree
PhD
Application deadline
Ongoing deadline
Project start date
Thursday 1 September 2022
Country eligibility
International (open to all nationalities, including the UK)
Funding
Competition funded
Source of funding
University of Leeds
Supervisors
Professor Netta Cohen
Schools
School of Computing
<h2 class="heading hide-accessible">Summary</h2>

The microscopic roundworm Caenorhabditis elegans is long and thin, and moves by undulating its body. While its locomotion behaviours have been characterized in detail on the surface of a dish, little is known about its locomotion in more natural habitats. In the Cohen lab, we have been recording the motion of the animal in 3D volumes. We have collected about 20TB of video data (primarily from healthy wild type animals, across a range of fluid environments) and have in place a data analysis pipeline for the 3D reconstruction of body postures and coordinates over time. In this project, you will compare behaviours, postures and muscle activation patterns in different media, and across different genetic strains. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

<h2 class="heading hide-accessible">Full description</h2>

<p>In this project, we are interested in comparing behaviours, postures and muscle activation patterns in different media, and across different genetic strains. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.</p> <p>Experimentally focused projects are likely to combine:</p> <ul> <li>Worm maintenance and scope for molecular biology and genetic manipulation of the worm</li> <li>Behavioural assays, bright field and/or fluorescent imaging and optogenetic experiments</li> <li>Extensive data handling and use of computer vision algorithms for image/video analysis (in particular 3D spatiotemporal reconstructions)</li> </ul> <h5>Background</h5> <p>This studentship forms part of a larger collaborative and interdisciplinary project, that currently includes two academics (Thomas Ranner and Netta Cohen), two postdoctoral fellows and three PhD students. We study the neuromechanical basis of behaviour in the nematode worm <em>C. elegans</em>. Research combines biological experiments, mathematical and computational modelling of the neural control as well as investigations of the physics of the worm and its interaction with the environment. We are seeking to appoint up to four further PhD candidates focusing on the undulatory motion of this worm: one project on the mathematical understanding of numerical methods for biomechanical models (with Thomas Ranner), one on modelling the neural control of locomotion (with Netta Cohen), one experimental project, combining behavioural experiments and machine vision (with Netta Cohen) and one exploring the dynamics of the worm&rsquo;s behaviour (with Netta Cohen). All projects are envisioned within this multidisciplinary setting. You will join a multi-disciplinary, dynamic, and creative group within the School of Computing at the University of Leeds, with close ties to the Fluid Dynamics Centre for Doctoral Training, the Hope Laboratory and the van Oosten-Hawle Laboratory in the Faculty of Biological Sciences, where additional biological experimental facilities are housed. Informal enquires are welcome from all potential candidates.&nbsp;</p>

<h2 class="heading">How to apply</h2>

<p>Formal applications for research degree study should be made online through the&nbsp;<a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University&#39;s website</a>. Please state clearly in the Planned Course of Study section that you are applying for <em><strong>PHD Computing FT</strong></em> and in the research information section&nbsp;that the research degree you wish to be considered for is <em><strong>3D microscopy of swimming worms</strong></em>&nbsp;as well as <a href="https://eps.leeds.ac.uk/computing/staff/301/professor-netta-cohen">Prof Netta Cohen</a>&nbsp;as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p> <p>&nbsp;</p>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.5 overall with at least 6.5 in writing and at 6.0 in reading, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

<p><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong>&nbsp;&ndash;&nbsp;The&nbsp;<a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a>, <a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>, <a href="https://phd.leeds.ac.uk/funding/198-akroyd-and-brown-scholarship-2022">Akroyd &amp; Brown</a>, <a href="https://phd.leeds.ac.uk/funding/199-frank-parkinson-scholarship-2022">Frank Parkinson</a> and <a href="https://phd.leeds.ac.uk/funding/204-boothman-reynolds-and-smithells-scholarship-2022">Boothman, Reynolds &amp; Smithells</a> Scholarships are available to UK applicants. &nbsp;<a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.&nbsp;</p> <p><strong>Non-UK</strong>&nbsp;&ndash; The&nbsp;<a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>&nbsp;is available to support the additional academic fees of Non-UK applicants. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a>&nbsp;is available to nationals of China. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a>&nbsp;is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p>

<h2 class="heading">Contact details</h2>

<p>For further information regarding the application procedure,&nbsp;please contact Doctoral College Admissions<br /> e:&nbsp;<a href="mailto:phd@engineering.leeds.ac.uk">phd@engineering.leeds.ac.uk</a>, t: +44 (0)113 343 5057</p> <p>For further information regarding the project, please contact Prof Netta Cohen<br /> e:&nbsp;<a href="mailto:N.Cohen@leeds.ac.uk">N.Cohen@leeds.ac.uk</a></p>


<h3 class="heading heading--sm">Linked research areas</h3>