Auckland Bioengineering Institute

Extended-volume confocal microscope

Optics layout for confocal microscope.

When constructing computer models of the function of various organs of the body, as is performed by a number of research groups in the ABI, it is often helpful, or even necessary, to know the underlying tissue structure at high resolution. Two common approaches are often used: firstly MRI, which provides the full geometry but at a relatively low resolution (0.1 mm); secondly, confocal microscopy, which is more highly resolved (around 1 micrometer) but only for small regions.

At the ABI, we have developed a novel approach which uses confocal microscopy in conjunction with a high-precision 3-axis stage and an ultramiller. This enables a tissue sample to be imaged confocally (using a laser to excite a fluorescent marker attached to the tissue of interest) to a depth of several tens of microns, before the imaged volume is removed and an extended volume image created. The first-generation system was constructed around 10 years ago, and has acquired images of a large number of different samples of different tissue types and sizes, acquiring large-scale 2D and 3D images of those samples. However, this system was developed using proprietary hardware, based on decades-old technology.

We are currently building a new extended-volume confocal microscope using modern hardware and software tools. The design is based around a National Instruments Real-time PXI computer with a FPGA, which can be programmed to control all of the instrumentation (stage, laser, scanner) and simultaneously acquire image data from the PMT (photo-multiplier tube).

Researchers and graduate students


Dr Robert Kirton


  1. G. B. Sands, D. A. Gerneke, D. A. Hooks, C. R. Green, B. H. Smaill, and I. J. LeGrice, "Automated Imaging of Extended Tissue Volumes using Confocal Microscopy," Microscopy Research and Technique, vol. 67, pp. 227-239, 2005
  2. G. B. Sands, D. A. Gerneke, B. H. Smaill, and I. J. Le Grice, "Automated Extended Volume Imaging of Tissue using Confocal and Optical Microscopy," in Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE, 2006, pp. 133-136

Related research groups

  • Tissue Structure
  • Cardiac Electromechanics
  • Cardiac Mechanics
  • Cardiac Electrophysiology