Biological Imaging and machine vision for 3D shape reconstruction

The aim of this project will be to construct and use a 3D imaging system to record the motion of worms crawling and swimming in fluid environment. Using machine vision, 3D shape reconstruction will be performed, and the shapes obtained will be modeled using statistical methods. A first prototype system already exists, including the hardware and image detection and tracking software.<br /> <br /> The worms under investigation are known as C. elegans (Caernohabditis elegans). In their natural habitat, these microscopic (1mm in the adult) worms must navigate complex and heterogeneous environments in 3D. And yet to date, their behaviour has only been characterised in 2D (See e.g. Berri et al, HFSP J. 3, 186-19 2009, Stephens et al, PLoS Comput Biol 4, e1000028 2008, and Padmanabhan et al. arXiv:1202.2832 2012). The ability to record, track and characterise their behaviour in 3D will be a first step towards the modeling of the neural control of the observed behaviors.<br /> <br /> The earliest start date for this project will be 1 October 2020.

<hr /> <p>The aim of this project will be to construct and use a 3D imaging system to record the motion of worms crawling and swimming in fluid environment. Using machine vision, 3D shape reconstruction will be performed, and the shapes obtained will be modeled using statistical methods. A first prototype system already exists, including the hardware and image detection and tracking software.</p> <p>The worms under investigation are known as C. elegans (Caernohabditis elegans). In their natural habitat, these microscopic (1mm in the adult) worms must navigate complex and heterogeneous environments in 3D. And yet to date, their behaviour has only been characterised in 2D (See e.g. Berri et al,&nbsp;<a href="http://dx.doi.org/10.2976/1.3082260" title="External link to dx.doi.org. Opens in a new browser window">HFSP J. 3, 186-19&nbsp;</a>2009, Stephens et al,&nbsp;<a href="http://www.ploscompbiol.org/article/info%3Adoi/10.1371/journal.pcbi.1000028" title="External link to www.ploscompbiol.org. Opens in a new browser window">PLoS Comput Biol 4, e1000028</a>&nbsp;2008, and Padmanabhan et al.&nbsp;<a href="http://arxiv.org/abs/1202.2832" title="External link to arxiv.org. Opens in a new browser window">arXiv:1202.2832</a>&nbsp;2012). The ability to record, track and characterise their behaviour in 3D will be a first step towards the modeling of the neural control of the observed behaviors.</p>

<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>Biological Imaging and machine vision for 3D shape reconstruction</strong></em>&nbsp;as well as&nbsp;<a href="https://engineering.leeds.ac.uk/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 style="margin-bottom:11px"><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability.</em></p> <p class="MsoNoSpacing">Applications will be considered on an ongoing basis. &nbsp;Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application. &nbsp;We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed.</p> <p>Please note that you must provide the following documents at the point you submit your application:</p> <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> <li>Funding information including any alternative sources of funding that you are applying for or if you are able to pay your own fees and maintenance</li> </ul> <p>&nbsp;</p>

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.

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.

<p style="margin-bottom:12px"><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> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> are available to UK applicants. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p><strong>Non-UK</strong> &ndash;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> <p><strong>Important:</strong>&nbsp; Any costs associated with your arrival at the University of Leeds to start your PhD including flights, immigration health surcharge/medical insurance and Visa costs are <strong>not</strong> covered under these studentships.</p> <p>Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.</p>

<p>For further information about your application,&nbsp;please contact Doctoral College Admissions: e:&nbsp;<a href="mailto:EMAIL@leeds.ac.uk">p</a><a href="mailto:phd@engineering.leeds.ac.uk">hd@engineering.leeds.ac.uk</a></p> <p>For further information about this project, please contact Professor Netta Cohen by email:&nbsp;&nbsp;<a href="mailto:N.Cohen@leeds.ac.uk">N.Cohen@leeds.ac.uk</a></p>