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PhD fellowship: Multimodal light-sheet microscope for imaging live whole-body organisms

Centre of Marine Sciences (CCMAR)

, , , Sunday, October 18, 2020 Competition Funded PhD Project (Students Worldwide)

About the Project

Research 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 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).

Relevant Websites:
Center of Electronics, Optoelectronics and Telecommunications website:
Comparative Endocrinology And Integrative Biology website:
Department of Physics, Politecnico di Milano:

Job Position Description:
The successful candidate will design and construct the optical imaging system, implement the image acquisition software and analysis. The student will develop novel illumination and detection strategies to overcome the challenges associated with imaging juvenile/adult organisms owing to scattering. This will involve speeding up acquisitions to enable high-quality images in real-time and the development of deep-learning based image reconstruction and processing methods. The student will design and perform experiments to test and validate the system.

The ideal student 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.

Funding Notes

Fifteen CCMAR-FCT Doctoral Research Fellowships will be awarded to graduates that comply with the requirements and wish to carry out research towards a doctoral degree. Research work should be developed following one of the topics proposed by CCMAR scientists and may be entirely or partially carried out at CCMAR.

The Call for applications is open between 12 September 2020 and midnight (Lisbon time) of 18 October 2020.
Applications should be submitted online through a dedicated online form. For further information on how to apply and detailed guidance notes go to:

View Website


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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