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Accurate estimation of displacement and deformation of tissue and cells from time-lapsed images

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  • Full or part time
    Dr E Dall'Ara
    Prof Rod Hose
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

This project will be part of an EPSRC funded PhD network (three projects in total) where the candidates will form, together with the supervisors and co-supervisors, a research group focused on the development and improvement of current elastic registration methods in musculoskeletal applications. The network will be part of the INSIGNEO institute for in silico medicine (
We have in Sheffield a digital volume correlation algorithm for computing bone tissue strains in Micro Computed Tomography (microCT) time-lapsed compression tests. This currently recognised as the most accurate method, amongst those reported in the literature, worldwide [Dall’Ara, 2014; Palanca, 2015]. This algorithm, whilst a vast improvement over previous methods, still has some significant limitations. Whilst displacement is measured at the spatial resolution of the microCT images (typically 10 microns), deformation is measured reliably only at a spatial resolution of approximately 500 microns. For some applications this is insufficient.

Using the features of Sheffield Image Registration Toolkit (ShIRT v2), we plan to explore new regularisation terms that optimise the registration for deformation rather than for displacement and to apply these to time-lapse images of cell motility and bone tissue compression, in order to capture, both displacement and the deformation (of the tissue or of the cells) over time with a comparable level of accuracy. ShIRT has been used to track, from time-lapsed images, the motility of cells, and was shown to out-perform any automated commercial system [Hand, 2009].

At the tissue level the candidate will use high resolution microCT images of trabecular bone compressed at different apparent strain levels, by using a special jig developed in Sheffield. At the cell level similar mechanical testing will be performed on the single cell that will be imaged with confocal microscope and/or atomic force microscope.
The accuracy of the newly developed method will be investigated and then applied to validate computational models for the two above mentioned applications.

Funding Notes

Salary (£14,057 per annum), fees (EU and UK) and consumables will be covered by the EPSRC.

All candidates must be eligible according to the EPSRC rules

Entry Requirements:
Candidates must have a first or upper second class honors degree or significant research experience. Strong mathematical background is required; experience with image registration and microCT and/or confocal microscopy images will be advantageous.


Interested candidates should in the first instance contact Prof Rodney hose ([email protected])

Please complete a University Postgraduate Research Application form available here:

Please clearly state the prospective main supervisor in the respective box and select “Human Metabolism” as the department.

Dall’Ara E, Barber DC, Viceconti M. About the inevitable compromise between spatial resolution and accuracy of strain measurement for bone tissue: a 3D zero-strain study, J Biomech, 47(12):2956-63, 2014

Hand AJ, Sun T, Barber DC, Hose DR, MacNeil S. Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration, J Microsc, 234(1):62-79, 2009

Palanca M, Tozzi G, Cristofolini L, Viceconti M, Dall’Ara E. 3D Local Measurements of Bone Strain and Displacement: Comparison of Three Digital Volume Correlation Approaches, J Biomech Eng, 1;137, 2015

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