Competition funded PhD project

Several techniques are available for imaging in 3D the fluorescence emitted by translucent biological samples, such as juvenile flatfish, embryos and larvae. In particular, light-sheet microscopy has become in few years the state-of-the-art technique for examining the signaling pathways that govern the development and health of organisms. However, standard light-sheet microscopes relies on optical filters, which restricts their applicability to samples that embed few fluorescent markers.

This PhD Project aims at developing hyperspectral light-sheet strategies that can image and separate the contributions from differently colored fluorophores, which are used to label different biological tissues simultaneously, and remove the auto-fluorescence from the signal of interest.

In particular, this research will address challenges associated with the reconstruction of a hyperspectral cube from few linear measurement. This project will involve the design and implementation of novel image reconstruction algorithms, focusing on recent advances in the field of deep learning. The new methods will be validated in developing (model and non-model) fish. The project will also involve publishing in high impact journals and presenting findings at international conferences.

The project will be developed at the Centre for Marine Sciences (CCMAR) and Center of Electronics, Optoelectronics and Telecommunications (CEOT), Faro, Portugal; and Biomedical Imaging Laboratory CREATIS, Lyon, France.

If you’d like to express your interest or discuss your suitability for this post, please contact via e-mail:

Dr. Teresa Correia: Teresa[dot]Correia[at]

Dr. Nicolas Ducros: nicolas[dot]ducros[at]