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Visualising extremophiles & their environment


Department of Physics

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Dr L Wilson , Dr James Walker , Dr V Hodge No more applications being accepted

About the Project

An EPSRC studentship (with the standard financial and student eligibility conditions) is available at the University of York for a joint project between the Department of Physics (Dr. Laurence Wilson, LW) and the Department of Computer Science’s Digital Creativity Lab (Dr. James Walker, JW & Dr. Victoria Hodge, VH).
The student will investigate new ways to process 3D data to visualise swimming extremophile microorganisms and their environments, incorporating visual measurements (e.g. photographs, depth measurements, holographic data) and non-visual sources (e.g. spatially localised chemical monitoring). The current proposal addresses areas in which the visualisation of these high-dimensional data sets has proved an increasing problem.
The project will equip a student with skills at the cutting edge of 3D imaging, image processing, remote sensing, data analytics and data visualisation.

1) The student will develop a data reduction and visualisation strategy for spatial data acquired in Boulby Mine (see Fig. 1). This UKRI (formerly STFC) facility has been host to scientists for around 20 years. Research in the lab has expanded from particle physics to extremophile biology. LW’s lab has been working at Boulby for some time to collect and study the behaviour of microorganisms that live there. The student will begin work with our existing image data sets and acquire more from the mine to build a spatially accurate mine tunnel in a VR environment (Unity or comparable). Existing data has been obtained from 3D cameras and other sensors attached to our drones. Information about the locations for our sample collection is essential context for understanding their swimming behaviour; this information will be integrated with our microscopy data, which is central to part (2).

2) The student will develop visualisations of 3D data from our custom-designed holographic microscopy system. The data is in the form of 3D swimming tracks of single cells. We already have a good quantity of this data, but to unlock more information, we need a way to explore our data sets and present them for a deeper analysis. This need is becoming increasingly acute as we move to look at the effect of chemical stimulus (an added dimension) on swimming behaviour. VR and other 3D visualisation methods would be a powerful tool for such investigations. The ability to reduce high-dimensional data to accessible formats has been used in both the scientific realm (see Fig. 2, LW’s publications 1-3, below) and in the creative realm. The student will produce an environment for exploring our existing holographic data sets, allowing an immersive exploration of our sample volumes that contain swimming cells. This allow us to develop our intuition and give the ability to explore data through visualisation tools such as VR. This aspect will be coupled with the environmental monitoring/location visualisation in part (1) above to give a holistic picture of the extremophile microorganisms’ lifestyle.

General information about the supervisors’ labs can be found on their websites:
https://www.york.ac.uk/physics/research/physics-of-life/next-generation-optical-microscopy (LW)
https://digitalcreativity.ac.uk/people/dr-james-walker (JW)
https://digitalcreativity.ac.uk/people/dr-victoria-hodge (VH)

Funding Notes

3 years tuition fees plus stipend for UK students.
Students from EU countries other than the UK are generally eligible for a fees-only award unless they have completed an undergraduate degree in the UK.


Academic entry requirements: Applicants should have, or expect to achieve, at least a 2:1 Honours degree (or equivalent) in physics, electronics, computer science, or a cognate discipline.

References

Project is jointly organised between Physics and Computer Science


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