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Computational Biomedical Imaging: building a better light-sheet microscope


Project Description

A PhD studentship is available in the Imaging Concepts Group at Glasgow University, researching computational imaging for light sheet fluorescence microscopy (LSFM). The aim of the project is to research ways to image biological samples using less light, resulting in less harm to the specimen and therefore allowing longer timelapse imaging studies.

Modern variations on LSFM use complex illumination strategies such as Bessel beam light sheets and “lattice light sheet microscopy” (see references below). These techniques offer important advantages, but have the drawback that they require the final images to be deconvolved in order to get a clear image - which has negative implications for the signal-to-noise-ratio. This project will develop a detailed theoretical and experimental understanding of how the complex imaging and illumination optics of these state of the art micrscope systems interact to influence the quality of the imaging. The student will research ways to use pupil phase masking and point spread function engineering to help with these challenges. We will acquire images that initially seem to be lower quality, but that have been carefully crafted so that subsequent computational processing will yield a better image than would have been obtained using conventional methods.

The student will be based in the School of Physics and Astronomy at Glasgow University, supervised by Dr Jonathan Taylor and Prof Andrew Harvey. The student will join at an exciting time for the group, following substantial external investment in experimental microscopy and imaging capabilities that your research will integrate with. The Imaging Concepts Group consists of about 20 researchers (PhD/EngD students, postdocs, visiting scholars and academics) conducting leading-edge research in advanced imaging techniques and their commercial and biomedical applications, and we collaborate with a range of academic and industrial partners in the UK and abroad. More information about our research and our group can be found at http://www.gla.ac.uk/schools/physics/research/groups/imagingconcepts . Although the main focus of this project is on experimental and computational optics, the project is motivated heavily by real-world problems with the ultimate aim of improving human health, and the student will be expected to engage with biological researchers to understand the challenges faced in cutting-edge experimental research.

Existing research in our group includes: adaptive/compressive imaging in microscopy & computer vision, realtime image analysis for heartbeat-synchronized imaging, and hyperspectral imaging for medical and industrial applications. The successful applicant will have the opportunity to take a leading role in the computational aspects of some of these projects – as well as entirely new research areas – working in collaboration with our current PhD students and postdoctoral researchers.

The project calls for a student with a strong theoretical background, coupled with an enthusiasm for working on problems in experimental imaging with very practical motivations and applications at the life-science interface. The ideal student will have:
- Experience and aptitude in computer programming (languages such as Python or Matlab) to solve numerical and mathematical problems in experimental physics;
- Some familiarity with the mathematics of Fourier optics and image formation, and keen to develop their understanding further;
- Proven problem-solving abilities;
- An enthusiasm for innovation and creative thinking;
- A first-class degree (awarded, or predicted) in Physics or a related physical science.

Interested applicants are invited to send a CV and covering letter to , describing briefly what interests them about this specific project, and detailing how they meet the above criteria. Informal inquiries are also welcomed at the same address. The position is available for an October start and is one of several research opportunities available in our research group.

Funding Notes

Dedicated funding is not currently available for this project. Strong (1st class degree) students with an interest in this project would need to identify a scholarship fund to apply for (e.g. scholarship from their home country).

References

Further reading related to this project can be found in the following publications:

“Multi-aperture foveated imaging”. G. Carles, S. Chen, J. Downing, N. Bustin, A. Wood, and A. R. Harvey. Optics Letters 41 1869 (2016).

“Extended depth-of-field imaging and ranging in a snapshot”. P. Zammit, A. R. Harvey, G. Carles. Optica 1 209 (2014).

“Adaptive foveated single-pixel imaging with dynamic super-sampling”. D. B. Phillips, M.-J. Sun, J. M. Taylor, M. P. Edgar, S. M. Barnett, G. G. Gibson, M. J. Padgett. Science Advances 3 e1601782 (2017).

“High-resolution 3D optical microscopy inside the beating zebrafish heart using prospective optical gating”, J. M. Taylor, J. M. Girkin, G. D. Love. Biomedical Optics Express 3 3043-3053 (2012).

“A line scanned light-sheet microscope with phase shaped self-reconstructing beams”. F. O. Fahrbach and A. Rohrbach. Optics Express 18 24229 (2010).

“Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution”. B.-C. Chen et al., Science 346 p 1257998 (2014).
and https://www.janelia.org/open-science/advanced-imaging-center/instruments/lattice-light-sheet-microscope

How good is research at University of Glasgow in Physics?

FTE Category A staff submitted: 44.90

Research output data provided by the Research Excellence Framework (REF)

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