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PhD POSITION - Real-time 3D optical imaging of endocrine signalling mechanisms in fish development

Centre of Marine Sciences (CCMAR)

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Dr Teresa Correia , Dr D Power , Dr R Guerra , Dr A Bassi No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project


3D optical imaging techniques can provide detailed information throughout mesoscopic scale (mm-cm) samples (e.g zebrafish). Several techniques have been developed (e.g. light-sheet microscopy and optical projection tomography) for examining the signalling pathways that govern the development and health of organisms. However, current techniques are restricted to small optically transparent samples, such as embryos and larvae, which have low scattering properties.

The aim of the project is to develop and evaluate the next generation of optical imaging tools for high-resolution 3D whole-body imaging of in vivo mesoscopic samples. This research will address challenges associated with imaging adult fish owing to scattering and hence, enable longitudinal studies using the same (model and non-model) fish. The system will be used to obtain new insights into the tissue and organ specific cellular and molecular changes promoted by the endocrine and retinoic acid systems.
This project will involve the design and implementation of novel optical imaging instrumentation and control software, illumination and detection strategies and deep learning approaches for scan acceleration and image analysis. The new methods will be validated in phantoms and developing (model and non-model) fish. The project will also involve publishing in high impact journals and presenting findings at international conferences.

The student will join the Comparative Endocrinology and Integrative Biology (CEIB) and Center of Electronics, Optoelectronics and Telecommunications (CEOT) groups at UAlg. The successful candidate will benefit from working in a multidisciplinary team with strong expertise in optical imaging, image processing and molecular endocrinology. The supervisory team consists of Dr. Teresa Correia (CEIB, King’s College London), Prof. Deborah Power (CEIB) and Dr. Rui Guerra (CEOT). The project includes a secondment opportunity at Politecnico di Milano with Prof. Andrea Bassi (photonics group).

The ideal candidate should have:
• An Honours Degree in Physics, although degrees in other related physical sciences or engineering disciplines may be considered.
• Experience with optical imaging instrumentation is essential.
• Enthusiasm for working on problems in experimental optical imaging and life-science applications. Interest in both theoretical and practical work.
• Experience and aptitude in computer programming to solve mathematics and physics problems (e.g. Python, Matlab, or C++) and for hardware configuration (LabVIEW).
• Enthusiasm for innovation and creative thinking, and enjoy team work.
• Candidates whose first language is not English should have an IELTS score of 6.5 or equivalent.

If you’d like to express your interest or discuss your suitability for this post, please contact via e-mail Dr. Teresa Correia: [Email Address Removed]
If you apply and you do not receive a response within 2 weeks it is because you do not meet the eligibility criteria.

You can find this offer via the Offer Finder:
Select “CCMAR - Centro de Ciências do Mar do Algarve” from the dropdown list under “RESEARCH CENTER". You can also search this position by title.

If you want to apply for this INPhINIT fellowship, click on the following link to create your personal account and fill in the on-line application form:

Funding Notes

PhD POSITION - INPhINIT doctoral fellowship program “la Caixa”
The doctoral fellowship programme INPhINIT “la Caixa” is devoted to attracting talented Early-Stage Researchers—of any nationality—who wish to pursue doctoral studies in Spanish or Portuguese territory. Sponsored by “la Caixa” Foundation, it is aimed at supporting the best scientific talent and fostering innovative and high-quality research in Spain and Portugal by recruiting outstanding international students and offering them an attractive and competitive environment for conducting research of excellence.


Relevant References:
1. V. Ntziachristos, Going deeper than microscopy: the optical imaging frontier in biology, Nat. Methods, 7:603–614 (2010).
2. A. Bassi, B. Schmid, J. Huisken, Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development, Development, 142: 1016-20 (2015).
3. T Correia, N. Lockwood, S. Kumar, et al, Accelerated optical projection tomography applied to in vivo imaging of zebrafish, PLOS ONE, 10(8): e0136213 (2015).
4. D. Power, I. Einarsdóttir, K. Pittman et al, The molecular and endocrine basis of flatfish metamorphosis, Rev. Fish. Sci., 16:83-109 (2008).

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