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Advanced microscopy for blood flow field mapping in the heart

School of Physics and Astronomy

About the Project

A PhD studentship is available in the Imaging Concepts Group at Glasgow University, developing and applying advanced optical microscopy and computational imaging techniques to measure and study the blood flow and heart function in the developing zebrafish heart. Since the zebrafish is transparent, advanced optical techniques make it possible to directly image in 3D the fluid flow in the complex environment of the heart itself.

Precise measurement of 3D fluid flow inside a living organism is a challenge for which our group has recently developed a solution, based on light sheet fluorescence microscopy and advanced image processing techniques. The student will build on these initial results to develop improved methods for flow imaging using light sheet microscopy, as well as sophisticated mathematical analysis to reliably measure the flow from high-speed imagery, extracting the maximum amount of quantitative information from the limited number of observations made. The focus of this project is therefore on developing advanced optical imaging and computational analysis specifically tailored to a challenging application in biology, and it requires a student with a strong grounding in physics and/or mathematical analysis/modelling/inverse problems, and experience in computer programming.

To date we have successfully profiled the blood flow at different depths within the 3D structure of the live zebrafish heart, and explored how it varies across the whole heartbeat. Research challenges for this project could include:
- Fusing image data from multiple orientations to build up a true 3D model of the flow field;
- Incorporating knowledge about the physics of incompressible fluid flows for noise removal and quantification of accuracy;
- Developing a model that will allow us to determine heart phase from flow images alone, without any additional inputs (important for applications on commercial microscope systems);
- Integrating experimental measurements with mathematical models of fluid flow.
- Feasibility studies of rapid measurements of 3D flow fields using fast volume imaging techniques such as light field microscopy

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. 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. More information about our research and our group can be found at .

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) to solve numerical and mathematical problems in experimental physics;
- Some familiarity with the mathematics and practicalities of optics and image analysis, 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).


“3D + time blood flow mapping using SPIM-microPIV in the developing zebrafish heart”. V. Zickus, J.M. Taylor. Biomedical Optics Express 9 2418-2435 (2018).
“Hybrid optical gating for long-term 3D time-lapse imaging of the beating embryonic zebrafish heart”, J.M. Taylor, C.J. Nelson, F.A. Bruton, A.K. Baghbadrani, C. Buckley, C.S. Tucker, J.J. Mullins, M.A.Denvir. [Under review].

"Intracardiac fluid forces are an essential epigenetic factor for embryonic cardiogenesis”
“Live imaging and modeling for shear stress quantification in the embryonic zebrafish heart”
"Estimation of divergence-free 3D cardiac blood flow in a zebrafish larva using multi-view microscopy”

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