3D Microscopy of Swimming Worms

Key facts

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.

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.

Experimentally focused projects are likely to combine:

Worm maintenance and scope for molecular biology and genetic manipulation of the worm

Behavioural assays, bright field and/or fluorescent imaging and optogenetic experiments

Extensive data handling and use of computer vision algorithms for image/video analysis (in particular 3D spatiotemporal reconstructions)

Background

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 C. elegans. 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’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.

To apply for this project you will need to make a formal application for research degree study through the University website. You will need to create a login ID with a username and PIN.

• For Application type please select Research Degrees – Research Postgraduate.

• The admission year for this project is 2027/28 Academic Year.

• You will need to select your Planned Course of Study from a drop-down menu. For this project, scroll down and select PHP Computer Science Full Time.

• The project start date for this project is 1 October 2027, please use this as your Proposed Start Date of Research.

• Please state clearly in the Research Information Section that the research degree you wish to be considered for is 3D microscopy of swimming worms as well as Prof Netta Cohen as your proposed supervisor.

Please state clearly in the Finance section, the funding that you are applying for, if you are self-funding or externally sponsored.

More information on how to apply is available on our website here. You will be required to provide a personal statement which outlines your interest in the project you are applying for, why you have chosen it and how your skills map onto the requirements of the project.

We will assess applications continuously as we receive them. We welcome and strongly encourage any potential applicants to contact the supervisor(s) for an informal discussion, prior to applying, and recommend submitting your application early.

If you are applying with external sponsorship or you are funding your own study, please ensure you provide your supporting documents at the point you submit your application:

Full Transcripts of all degree study or if in final year of study, full transcripts to date including the grading scheme

Personal Statement outlining your interest in the project

If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below).

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.

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.

This is a non funded PhD project. Applicants are expected to be self funded or to secure external funding.

You can find out more about our Funding Opportunities on our Postgraduate Research Opportunities website.

Important: Please note that all costs associated with your arrival at Leeds (visa, Immigration Health Surcharge, flights etc) would have to be met by yourself, or you will need to find an alternative funding source.

For further information about your application, please contact PGR Admissions by email to phd@engineering.leeds.ac.uk

For further information about this project, please contact Professor Netta Cohen by email to N.Cohen@leeds.ac.uk

• Type of research degree: PhD
• Application deadline: Monday 31 May 2027
• Project start date: Friday 1 October 2027
• Country eligibility: International (open to all nationalities, including the UK)
• Funding: Non-funded
• Supervisors: Professor Netta Cohen
• Schools: School of Computer Science

Research areas