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Computer 3-D reconstructions of simple nervous systems

We have created a number of computer aided 3-D reconstruction of simple systems of neurons from serial histological or EM sections, using a Silicon Graphics computer running ICAR 5.0.1 (ISG Technologies Inc., Canada). To create the reconstructions, we grab images from negatives that are aligned, seriatim, using AMICUS (ISG) software, or align digital images using freeware (sEM Align: John Fiala). Using such aligned stacks, it is possible to compare each image with others in the stack, to check its vertical and rotational registration. Surface rendering and cut-plane functions allow realistic views of the final solid object to be generated. The reconstruction can be: a) illuminated from different directions to highlight particular surface features, or b) cut into, to form a window that reveals particular internal features from the grey-scale information of the original sections, or c) rotated in real time to reveal features of the reconstruction to best advantage. These methods are initially laborious but because they yield visually compelling images they can often yield novel scientific insights. Various examples can be seen:


a) A reconstructed stack of serial light micrographs of 1 micron sections through the compound eye and underlying optic lobe of Drosophila (by L. Maillet Frotten)

b)Two photoreceptor terminals (red) entwined by three neurites from an amacrine cell reconstructed from 180 serial electron micrographs of the lamina in the housefly Musca domestica, by former graduate student, Xiangqun Hu.


c) The nervous system of the ascidian larva, Ciona intestinalis. (by S. Stanley). The nucleus of each cell has been reconstructed from a series of semithin sections, and colour-coded depending on the cell type. We proceed in the expectation that it will be possible eventually to identify each cell uniquely, or as a member of a small group, by its unique pattern of gene expression.

A Selection of movies made from reconstructions