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Quantitative Imaging

Quantitative Imaging group


We design original methods for accurate measurement using image data, with applications in biomedical research and complex materials. 


We have wide experience in super-resolution microscopy, especially in computational inference methods for quantifying structures too small to resolve by conventional imaging. We developed many of these techniques with the Laser Analytics group, and use them mainly for biological research. We also work on classic chemical engineering problems, such as developing software tools to image and model flow inside granular materials and non-Newtonian fluids. 

 

Key publications are listed for Eric Rees on his department page, and a comprehensive listing is on ORCID. We make all of the imaging software developed during our research publicly available via the group github: github.com/quantitativeimaging

 

The following selection of recent projects shows the huge range of research which is tractable to modern computational image analysis.

 

Research projects

Ellipsoid localisation microscopy


Bacterial spores are amazingly robust microorganisms, in large part due to their protective protein coats. The coats are multi-layered structures, but previous studies have found it hard to measure which proteins localise in which layers. With Graham Christie's Molecular Microbiology group, we developed ellipsoid localisation microscopy (ELM) which allows us to measure this information using the simple kind of traditional fluorescence microscope that has been widely available for decades. This work made it to the front cover of the Biophysical journal!

ELM Figure 5 submission

Figure. The ellipsoid localisation microscopy (ELM) capability developed by Rees and Christie. Microscopy of Bacillus spores containing a fluorescent protein (a, left) lacks the resolution to distinguish the multi-layered coat structure which imbues these spores with elements of their resilience and infectivity. We use computational inference to obtain super-resolved images (a, right). The sequential protein layers can thus be distinguished (b, c). We will apply this to quantify B. anthracis structure to elucidate mechanisms of super-dormancy and decontamination, and to enable ‘spray and visualise’ tests for contamination.

 

Single molecule localisation microscopy

Sparse single molecule localisation methods (SMLM) allow us to reconstruct optical super-resolution images with resolution as fine as 10-20 nm, making these the highest resolution of the sub-diffraction imaging methods which won the 2014 Nobel prize in chemistry. 

We published one of the earlier studies on the mathematical limits of resolution in SMLM, as well as introductory review on the methods from the time when we developed software to do imaging on amyloid fibril formation. 

Localisation ejr F1

 

Terahertz 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).

 THz_sketchLaminarFlow

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

 

THz_timeResolvedEchoes

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. 

 

THz_Fig3Col

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

Imaging and modelling uplift in granular materials

- Project with Prof Davidson, Jethro Akroyd, and several IIB students including RAF and KK... Details to follow. 

 

Hydration Imaging

 Fig HydrationMasks v1

Video data is rich in information. In this project, we developed image analysis software to quantify 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. 

example anim hydration ejr

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. 

hydration graph

 

Fluorescence anisotropy 

This method 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.

 

People 

Eric Rees (University Lecturer)
James Manton (PhD student)

 

Collaborations

Graham Christie, Molecular Microbiology group
- Measurements of spore coat structure

Clemens Kaminski, Laser Analytics group
- Super-resolution technique development

Gabi Kaminski, Molecular Neuroscience group
- Imaging protein conformation changes

Jon Davidson, Jethro Ackroyd
- Particle tracking and modelling flow in granular materials

Axel Zeitler, Terahertz applications group
- Terahertz correlation velocimetry: measuring flow in optically opaque fluids.

Alex Routh
- Crack propagation dynamics