Image-based analysis and computational modelling of the pacemaker cells in the gut

Background:

The stomach and intestines have coordinated rhythmic contractions necessary for the efficient digestion of food. The rhythmic contractions are coordinated by underlying electrical events, generated by a network of pacemaker cells known as the interstitial cells of Cajal (ICC). The degradation of the ICC network is associated with a number of significant gastrointestinal disorders. For example, in gastroparesis (a condition commonly associated with diabetes) the loss of ICC correlates with disease severity. Analyses of the structure and function of the ICC network are an active area of research.

The candidate will have the opportunity to work closely with leading bioengineers and clinicians at Auckland Bioengineering Institute and the neurophysiologists based at the Université Libre de Bruxelles in Belgium. You will devise, develop and implement novel techniques to solve large scale image processing and computation problems. These results will be used to provide novel insights into current clinical challenges.

The candidate will need to have:
• Grade point average of 8 out of 9 (an “A” student)
• A 4 year undergraduate degree with evidence of research experience.
• Strong background in matlab, computational programing, algorithm development.

Ideally the candidate should also have interests in:
• engineering, physics, applied mathematics, physiology;
• numerical analysis and quantification techniques;
• 2d and 3d image processing techniques;
• computational/mathematical modelling and finite element/difference methods.

Objective
The main aim of this project is to develop a framework to analyse confocal microscopy images of the gastrointestinal tract. The system will (i) segment the ICC network structure, (ii) quantify the structural properties of the network, (iii) construct a computational mesh of the ICC network and simulate propagation of slow wave activity over this network, (iv) quantify the functional properties of the network. Finally, the framework will be expanded to quantify the effects of varying degrees of network degradations, and to derive a full stomach simulation based upon image based ICC networks.

If you meet entry requirements for PhD studies please provide a single pdf containing cover letter, CV, academic transcripts.