Auckland Bioengineering Institute

3D Cardiac Cell Modelling

Our aim

We aim to develop a quantitative understanding of the anatomical design of the cardiac cell and its role in regulating cardiac cell excitation and contraction, known as excitation-contraction coupling (ECC).

This quantitative model will incorporate key organelles in ECC as well as key ion channels and pumps that regulate calcium movement in and out of the cytoplasm, such as the sodium-calcium exchanger (NCX), and ryanodine receptors (RyRs). Cells within the heart vary in shape, size, and the spatial arrangement of the ECC organelles. Our approach is to extract salient features of the cellular assembly using spatial statistics analysis techniques across a large sample of cells to create a standardized 3D multi-component cell model. Such a model will enable researchers to perform modelling studies on a wide variety of experimental data collected from a wide variety of cells.

We are collaborating with Associate Professor Christian Soeller at the Department of Physiology at the University of Auckland, and Associate Adjunct Professor Masahiko Hoshijima and Professor Mark Ellisman at the National Center for Microscopy and Imaging Research (NCMIR) at UC San Diego to acquire fluorescence light microscopy, and 3D electron tomography data of cardiac cells, respectively. Each approach provides a different set of advantages and information that is required to create a comprehensive model. Here are a list of current projects underway.

Calcium signalling in the cardiac cell

This project investigates the mechanisms by which calcium plays a role as a long-term signal for hypertrophic growth at same time as playing a role in excitation-contraction coupling in the complex 3D environment of the cardiac cell.


The diabetic heart under the mathematical microscope

Diabetes is known to cause significant changes to cardiac cell ultrastructure as well as energy production within the cell. This project involves the quantification of changes in cardiac cell ultrastructure in health and disease and the subsequent development of 3D computational models using these measurements to provide an integrated picture of the effect of structural changes and mitochondrial metabolism changes on overall cell function.

Postgraduate opportuntites

All positions for postgraduate projects have been filled.

However, we are always looking for bright and enthusiastic students interested in areas such as computational cellular physiology, electron tomography, confocal microscopy, image processing, spatial statistics theory and modelling. If this sounds like you, please email the Associate Director Postgraduate ( to discuss your research options.