For the three-dimensional visualisation of organic structures, the methods used here first of all require two-dimensional image stacks. These can be transmission electron microscopic (TEM) serial sections in the form of photographs through the structure to be reconstructed or image stacks generated in the confocal laser scanning microscope (CLSM).

When reconstructing with the aid of TEM serial sections, the structure to be reconstructed is embedded in synthetic resin and cut into ultra-thin sections with a thickness of 60 - 85 nm on the microtome. These sections are then photographed chronologically and imported into the Amira® computer programme. In Amira®, each section is placed on its own plane, whereby the distance between the individual planes can be selected according to the real distance. The structure to be reconstructed can now be traced on each individual section and connected across all planes. In a final step, a surface is assigned to the resulting solid.

In three-dimensional reconstruction using the CLSM, the microscope generates image stacks of the corresponding specimen in an automated process, whereby the distance between the individual images can be defined individually. With this method, the structures to be examined must first be labelled with an appropriate fluorescent marker in order to be visible under the fluorescence microscope. The finished image stack can be read directly into Amira®; the reconstructed structure is visible as a three-dimensional solid that can be freely rotated in space.

Fine adjustments to the surface structure of the reconstructed bodies can then be made using the Maya® computer programme.