Biological Imaging and machine vision for 3D shape reconstruction

PGR-P-283

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Key facts

Type of research degree: PhD
Application deadline: Ongoing deadline
Country eligibility: International (open to all nationalities, including the UK)
Funding: Non-funded
Additional supervisors: Professor Netta Cohen
Schools: School of Computing

<h2 class="heading hide-accessible">Summary</h2>

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.

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

<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, <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 </a>2009, Stephens et al, <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> 2008, and Padmanabhan et al. <a href="http://arxiv.org/abs/1202.2832" title="External link to arxiv.org. Opens in a new browser window">arXiv:1202.2832</a> 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>

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

<p>Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University's website</a>. Please state clearly in the research information section that the research degree you wish to be considered for is ‘Biological Imaging and machine vision for 3D shape reconstruction’ as well as <a href="https://engineering.leeds.ac.uk/staff/301/Professor_Netta_Cohen">Prof Netta Cohen</a> as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below).</p> <p> </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> – The <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 </a>, <a href="https://phd.leeds.ac.uk/funding/198-akroyd-and-brown-scholarship-2022">Akroyd & 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 & Smithells</a> Scholarships 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> – The <a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship </a> is available to support the additional academic fees of Non-UK applicants. The <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> is available to nationals of China. The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> 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 your application, please contact Doctoral College Admissions by email: <a href="mailto:EMAIL@leeds.ac.uk">p</a><a href="mailto:phd@engineering.leeds.ac.uk">hd@engineering.leeds.ac.uk,</a> or by telephone: +44 (0)113 343 5057</p> <p>For further information regarding the project, please contact Professor Netta Cohen by email:  <a href="mailto:N.Cohen@leeds.ac.uk">N.Cohen@leeds.ac.uk</a></p>

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