A simple microcomputer-based three-dimensional serial section reconstruction system (MICROS)

We have developed a computer system which enters and aligns serial sections and displays the completed reconstructions at different rotations in space. The system uses commercially available hardware, including a Hewlett-Packard 9845T microcomputer and an H-P 9874A digitizer. The software for the system is written in the BASIC language. The system consists of two programs, one for section digitization, the other for rotation and display of the reconstructions. Sections are digitized directly from micrographs or back-projected slides. The outlines of cells or other structures are traced from these media using a hand-held cursor on the digitizer. The positions of elements (inputs) which contact the structure and fiducials are also digitized. The sections are aligned by simultaneously displaying two consecutive sections on the graphics CRT screen. The sections are coarsely superimposed by centering around screen center using a centering algorithm. They are precisely aligned by rotating and translating the images with a reference cursor. Special functions for inserting and deleting sections and rapid section scanning are available for editing. The aligned sections are stored using a linked-list file structure on either floppy disks or tape cartridges. The rotation program replots the completed reconstructions on the graphics CRT or digital plotter. The program will reproduce the reconstructions at any scale and at any rotation in the x-, y- or z-planes. A hidden line algorithm removes hidden lines to give a 3-dimensional (3-D) perspective to the reconstructions. The positions of inputs and fiducials are represented by symbols. We use the system to reconstruct cells and neural processes. The 3-D reconstructions allow us to: (a) examine the spatial distribution and density of synaptic contacts on neurons; (b) study complex neuronal shapes; (c) examine the vectors of neural processes. The computer reconstruction system, which is moderately priced, should also prove useful for reconstructing many other types of biological profile.