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EASTBIO: Optical coherence refraction microscopy: Profiling biophysical properties of retinal cell spheroids


   Centre for Regenerative Medicine


Edinburgh United Kingdom Biomedical Engineering Biophysics

About the Project

While the study of regenerative process has focused on the control and profiling of biochemical signals, intrinsic and extrinsic physical cues are increasingly recognised to play a role in cell regulation. In particular mechanical forces have been shown to direct stem cell behaviour in development and regeneration in vivo.

Our ability to fluorescently tag biological target, and more recently to profile their gene expression has been key to the recent progress in our understanding of regeneration. There is now a need to develop transformative tools that can seamlessly retrieve the physical properties of cells and tissues to understand better their role in regeneration.

The aim of the Ph.D. is to develop and validate a novel imaging method, optical coherence refraction microscopy, developed across the Bagnaninchi and Yang Groups, to retrieve the physical properties of retinal organoids.

Optical interferometry is the method of choice in physics to make precise measurement in astrophysics, metrology applications and more recently biology with the development of quantitative phase imaging (QPI) and optical coherence tomography methods to optically section 3D samples. The Bagnaninchi lab has developed transformative methods to retrieve additional information from QPI methods, in particular mechanical, rheological and metabolic properties of cells and tissues.

With Dr. Yang we have recently implemented a novel tomographic method, described first in 2019 in nature photonics by Zhou et al, that has the potential to improve considerably the imaging quality and accuracy of the measurements through multiple angle acquisition and machine learning.

The Ph.D. will work on the optical coherence refraction microscopy set up, implement machine learning algorithms, and map in 3D the physical properties of retina cell spheroids in collaboration with Prof. Baljean; with the final goal to co-register physical measurements and biological information from confocal microscopy to understand better the emergence of distinct cell population in retina spheroids.

The EastBio Ph.D. student will be embedded in the Postgraduate (PG) student programme from the Centre for Regenerative Medicine (CRM) and will benefit from interdisciplinary research training in cellular microscopy, artificial intelligence, data driven innovation and biophysics.

Application procedures:

EASTBIO How to Apply webpage

  • EASTBIO Application
  • Equality, Diversity and Inclusion (EDI) survey
  • Reference Forms 

(forms listed above can be downloaded here: http://www.eastscotbiodtp.ac.uk/how-apply-0)

Please send your completed EASTBIO Application Form and EDI survey along with a copy of your academic transcripts to  before the deadline. 

You should also ensure that two references have been sent to  by the deadline using the EASTBIO Reference Form.

The EASTBIO team will run a series of 1-hour online sessions in November/December, open to applicants who have queries about the application process. Please view EASTBIO How to Apply webpage for details. 

Unfortunately due to workload constraints, we cannot consider incomplete applications.


Funding Notes

UKRI-funded studentships are open to students worldwide and will cover tuition fees at the UK rate, plus a stipend to support living costs and an annual research grant of £5,000 for the first three years of the PhD research. The proportion of international students appointed through the EASTBIO DTP is capped at 30%. All students must meet the eligibility criteria as outlined in the UKRI guidance on UK, EU and international candidates. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions, esp. TGC 5.2 & Annex B.

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