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Department of Chemical Engineering and Biotechnology



I develop mathematical techniques for making accurate, quantitative measurements from optical image data.

I primarily work with fluorescence microscopy. Some of my work involves "optical nanoscopy" methods for super-resolution imaging -- the 2014 Nobel prize in Chemistry was awarded to three groups who pioneered these ways of using of visible light microscopes to measure structures far smaller than the wavelength of light. There is currently huge scope for improving on the mathematical methods that underlie this field, and for applying super-resolution to new materials and disciplines. 

In my current research, I am particularly interested in methods for determining the geometry of fluorescent shell structures. These methods are valuable for studying multilayered objects such as viruses, spores, and bubbles. I am also interested in related methods for measuring complex fluid properties (rheometry) using optical microscopy and similar methods. 


Super-resolution by Ellipsoid Localisation Microscopy (ELM)

We have developed a new optical nanoscopy method for inferring the exact size and order of concentric protein layers in concentric shell micro-organisms such as bacterial spores and viruses. [With Graham Christie.] By feeding the inferred parameters back into an equation for the shell's image, a super-resolved reconstructed image can be generated. 

A simple computer program can identify images of bacteria spores, and fit an equation to the pixel values, enabling high precision inference of their structure


           Raw image data


                     Time-resolved ellipsoidal shell visualisation

Inferred super-resolution image

This method of Ellipsoid Localisation Microscopy can be used to make fast, time-resolved axis and layer measurements on fluorescent shells, and may be used for dynamic measurements of bacteria (e.g. growing), viruses (e.g. transiting cell membranes) or bubbles (e.g. in complex fluids). With Zihui Zhang


Plane 1


Plane 2

Although three-dimensional structures generally require more descriptive parameters, the principle of ellipsoid localisation microscopy can be applied to them, given more complex measurement data such as obtained from a bifocal microscope (also with Zihui Zhang). 


Super-resolution by Fluorescent Shell Model Fitting

In collaboration with Bob Turner (University of Sheffield) we have developed fluorescent shell inference methods related to the ELM technique above, for inferring the layer order and growth of more complex shell structures such as cylindrical cell walls.


Super-resolution Single Molecule Localisation Microscopy (SMLM)

Super-resolution microscopy or "Optical Nanoscopy" -- which was the Nature Method of the Year 2008 and received the Nobel prize in Chemistry in 2014 -- is the name for a class of modern techniques for optical imaging at sub-diffraction resolution. The ability to use light to non-invasively study structures at scales previously accessible only to electron microscopy is a major step forwards for imaging biological and similar materials under physiological (i.e. wet) conditions. The Laser Analytics group develops super-resolution imaging platforms, as well as other advanced optical microscopes (such as fluorescence lifetime, anistropy, and spectral imaging) and applies them to various research projects though collaborations.

One of the most powerful super-resolution imaging techniques is SMLM (single molecule localisation microscopy). This microscopy technique is so new that the resolving power of the technology has advanced ahead of the theory about how the method works. This creates the needs for some interesting studies, for example I am one of the researchers who have mathematically studied what the resolution of a Localisation Microscope system actually is (see: for example), and how it may be optimised. 


Hydration Imaging and Permeability Inference

Video data is rich in information, and good image analysis software can precisely infer hydration front kinetics in a tablet undergoing dissolution in bile acid. [With Krishnaa Mahbubani.] 

The transmitted light image of a tablet undergoing hydration by water stained with a large dye molecule (a) can be analysed with spectral thresholding to identify regions that are (b) permeated with the dye, (c) hydrated but not stained, and (d) dry. This software analysis can then be applied to image stacks to infer the parameters of hydration kinetics for various materials. 

Darcy flow hydration imaging. This project involves imaging the ingress of a hydration front into solid drug tablet, in order to quantify the permeability of tablets to water as a function of composition and fabrication route. Fully hydrated tablets become more transparent than dry material, due to decreased refractive index contrast between pores and solid, and hence the propagation of a hydration front can be tracked via transmitted light imaging. The permeation of water can be described by Darcy flow, with a permeablity constant that can be fitted to the hydration front velocity after using computational image analysis to track the hydration front through suitable stacks of time-lapse image data. 



Single Molecule Tracking Rheometry 


                       Liquid state                                                    Gel state


We have adapted our localisation microscopy software to evaluate fluid viscosity by tracking individual fluorescent proteins. We are currently working on correlating this data with single molecule fluorescence polarisation, which provides a readout of molecule orientation. 

Super-resolution localisation microscopy is based on determining fluorescent molecule position at high precision (<10 nm). By time-resolving the tracks of fluorescent molecules it is possible to determine molecular viscosity, or to fit diffusion transport parameters to the observation - the latter can be used to measure effective viscosity at an extremely fine spatial resolution, however representing such observations as a 3D viscosity "map" remains a data processing challenge. 


Fluid correlation velocimetry 

We have adapted the established technique of fluorescence correlation spectroscopy (Elson 1974) to work with reflected terahertz pulses, which allows us to measure flow fields inside complex and optically opaque fluids [with Axel Zeitler]. Link to the paper in Optics Letters (2016).



Figure. Sketch of Terahertz Correlation Spectroscopy principle for velocimetry based on time-resolved echoes of moving reflectors.

Figure. Measured echoes of terahertz pulses. The red region shows a time-varying echo from a silica bead, and the blue background shows constant background. 

Figure. Profile of lateral flow speed along a radial cross section of a Taylor-Couette viscometer, obtained by terahertz correlation spectroscopy. 


Fluorescence anisotropy imaging relies on the fact that polarised illumination of a fluorescent sample will preferentially excite molecules aligned parallel to the light source polarisation. The resulting fluorescence light is itself partially polarised, but its polarisation decays over time due to rotational diffusion, and the timescale of polarisation decay allows the viscosity of a fluid to be determined within the very fine volume corresponding to the environment of a fluorescent molecule. This offers potential for measuring the rheological properties of fluid boundary layers involved in droplet transport within porous materials. 


Fluorescence correlation spectroscopy (FCS)

FCS is an established confocal microscopy technique for measuring the viscosity and velocity of fluids containing dilute fluorescent dyes. I am interested in combining FCS with super-resolution microscopy, to measure viscoelasticity in fine structures, and to use wavelet transform signal processing to extract more finely time resolved data. 



My PhD research involved developing non-platinum electrocatalysts for hydrogen fuel cells, and I remain interested in the topic of sustainable energy. A long-term goal is to develop optical imaging techniques able to address proton transport and rheology within the polymer electrolyte membranes used in low temperature fuel cells. 



Laser Analytics group. 

Quantitative Imaging group. 


BA, Natural Sciences, University of Cambridge, 2005

MA, University of Cambridge, 2009

PhD, Materials Science, University of Cambridge, 2009

Research Associate, CEB, University of Cambridge, 2009 to 2013

Lecturer, CEB, University of Cambridge, 2013

Fellow of Churchill College


Key publications: 

Generation of strength in a drying colloidal dispersion: How the fracture toughness depends on film properties, N. Birk-Braun, K. Yunus, E. Rees, W. Schabel, A. Routh, Phys Rev E (2017) doi:10.1103/PhysRevE.95.022610 

Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets, Analytical Chemistry (2017), doi:10.1021/acs.analchem.6b02528

TriSPIM: light sheet microscopy with isotropic super-resolution, Optics Letters, 15 September (2016) doi:10.1364/OL.41.004170  

RainSTORM: Structure validation via artifact analysis in localization based super-resolution microscopy (in preparation)

Terahertz correlation spectroscopy infers particle velocity and rheological properties, Optics Letters, 14 July (2016) doi:10.1364/OL.41.003289  

Ellipsoid localisation microscopy infers the size and order of protein layers in Bacillus spore coats, Biophysical Journal, 17 Nov Issue (2015). Journal front cover. doi:10.1016/j.bpj.2015.09.023 

CYK4 promotes antiparallel microtubule bundling by optimizing MKLP1 neck conformation. (Davies T, Kodera N, Kaminski-Schierle G S, Rees E J, Erdelyi M, Kaminski C F, Ando T, Mishima M) Plos Biology (2015) doi:10.1371/journal.pbio.1002121

Fluorescence anisotropy measurements of individual nanolitre droplets enable quantitative steady-state affinity determination, (submitted to Anal. Chem.)

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function, Neuron (2015) doi:10.1016/j.neuron.2015.10.030 (Contribution: single protein tracking) 

Origin and compensation of imaging artefacts in localization-based super-resolution microscopy. Methods (2015) doi:10.1016/j.ymeth.2015.05.025

Structural analysis of herpes simplex virus by optical super-resolution imaging, Nature Communications (2015) doi:10.1038/ncomms6980 

A quantitative protocol for intensity-based live cell FRET imaging, Methods Mol Biology (2014), doi:10.1007/978-1-62703-649-8_19 

Direct Observations of the Formation of Amyloid β Self-Assembly in Live Cells Provide Insights into Differences in the Kinetics of Aβ(1–40) and Aβ(1–42) Aggregation, (Esbjörner E K, Chan F, Rees EJ, Erdelyi M, Luheshi LM, Bertoncini CW, Kaminski CF, Dobson CM, Kaminski-Schierle GS) Chemistry and Biology (2014), 21 (6): 732–742 

Elements of Image Processing in Localisation Microscopy, Journal of Optics (2013) doi:10.1088/2040-8978/15/9/094012

Blind Assessment of Localisation Microscope Image Resolution, Optical Nanoscopy (2012),

In Situ Measurements of the Formation and Morphology of Intracellular ß-Amyloid Fibrils by Super-Resolution Fluorescence Imaging, JACS (2011)

An Adaptive Filter for Studying the Life Cycle of Optical Rogue Waves, Optics Express (2010) doi: 10.1364/OE.18.026113

Electrocatalysis by Nanocrystalline Tungsten Carbides and the Effects of Codeposited Silver, Journal of Power Sources (2009) doi: 10.1016/j.jpowsour.2008.01.002

University Lecturer
Doctor Eric  Rees

Contact Details


Person keywords: 
Applied Optics