Developing a microfluidic system for population level 3D, high-resolution imaging of nano- and microplankton

Assoc Prof Peter Glynne-Jones Dr Daniel Mayor, Dr Kathryn Cook

This PhD brings together advanced imaging technologies [1,2] with expertise in plankton monitoring and ecology to develop a next generation system capable of imaging populations of nano- and microplankton in 3D at resolutions that will reveal detailed morphology and distribution of organelles to enable deeper insights into factors affecting plankton health and population dynamics.


Monitoring plankton is crucial for understanding, protecting and managing the health of marine and freshwater environments. Plankton play a key role in the global carbon cycle, and deeper understanding of how they will be impacted by global warming is key to preventing and mitigating large scale impacts. Current imaging cytometers such as FlowCam provide reduced image quality due to their 2D nature and the blurring caused by the optics required to increase depth of field to cover a relatively deep flow cell. They are thus limited in their ability to provide data beyond identification and cell volume. We recently demonstrated that ultrasonic focusing can produce higher resolution imaging of phytoplankton [1].  Building on this you will develop a new approach [2] to acquire multiple images and combine them tomographically, producing 3D, micron resolution images at rates of tens of cells per second.   


The PhD will focus on the following areas:

  1. Designing a microfluidic device to both: a) acoustically focus phytoplankton within an imaging plane and b) integrate an optical system that uses chromatic aberration (via a phase plate and multi-colour or hyper-spectral camera) to obtain images from multiple focus planes for each passing cell.  
  2. Develop and optimise reconstruction algorithms (including AI) to produce 3D tomograms of each cell using the transport of intensity (TIE) approach.
  3. Characterise the system and investigate the trade-offs between low-cost, robust configurations and higher resolutions. This can be compared the the FlowCam based in our labs as a benchmark.
  4. Implement reconstruction algorithms on graphical processor boards (e.g. NVIDIA Jetson) to facilitate real-time reconstruction in a compact system.
  5. Working in collaboration with our world leading group in plankton research, the device will be used to pioneer a range of new studies including the real-time impacts of stressors and nutrient availability on lipid storage to give new insights into factors affecting population dynamics.


University of Southampton

The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the university’s microfluidics labs in the School of Engineering.

While existing interest in plankton culture, monitoring, microfluidic systems, and imaging would be useful, we have existing expertise in these areas and are able to provide masters level training through specific courses in all of these diverse areas. 

Eligibility & Funding Details: 

Please see for details.

Background Reading: 

[1] Hammarstrom, B., Vassalli, M., & Glynne-Jones, P. (2019). Acoustic focussing for sedimentation-free high-throughput imaging of microalgae. Journal of Applied Phycology, 1-9.

[2] Morales, J., Hammarstrom, B., Lippi, G. L., Vassalli, M., & Glynne-Jones, P. (2021). Acoustofluidic phase microscopy in a tilted segmentation-free configuration. Biomicrofluidics, 15(1), [014102].