Rights: University of Waikato. All Rights Reserved. Published 29 February 2012 Download

Dr Rebecca Campbell (University of Otago) explains how she builds three-dimensional computer models of whole neurons (brain cells). Rebecca describes why images from confocal laser scanning fluorescence microscopy (confocal microscopy) are a good starting point for building the models. She talks about how models help her to understand the shape of neurons and how they connect with each other.

Jargon alert: Confocal microscopy is a specialised form of optical microscopy that makes it possible to take pictures of many thin slices in a sample without actually slicing the sample up. The individual slices can then be built up into a three-dimensional model.


One of the strengths of confocal microscopy is that we can put together a whole GnRH neuron in three-dimensional space and look at the features of the neuron itself and also begin to appreciate how it’s connected with other GnRH neurons within the brain.

Using the confocal microscope, we take these images throughout the specific focal planes of a depth of tissue and so we end up with a 3D dataset. So we take individual 2D images in a 3D volume, and we put it back together to make a 2D image that appears three-dimensional.

So once we have a 3D rendering of our GnRH neurons, we can rotate them in space, so using specific software, we can turn them around, we can turn them upside down, and this really helps us to appreciate where specific features are on this cell. So the relationship between two dendrites – are they far away in space, which they might look in this orientation, or if we turn them on their side, are they actually close together? So by rotating these 3D rendered images, we can learn an awful lot more than simply looking at them in two dimensions from one particular perspective.