BioGraf 3D: an algorithm for optimization and graphical representation of nuclear structure spatial distributions.

BioGraf 3D is a computer algorithm for rapid three dimensional visualization and analysis of digitized three dimensional biological data to aid in the subsequent generation of models of nuclei or cells. This graphically oriented program permits unlimited three dimensional perspective viewpoints of data in onscreen single frame, zoom or stereo forms. Analysis of data is enhanced by an optimization problem solution which determines viewpoint coordinates whereby maximum clustering of preselected structures is achieved. Mathematical representation of the transformations and optimization is presented in detail. Biograf 3D is written in the C programming language for IBM and compatible personal computers. In this study BioGraf 3D is utilized to examine the infrastructure of the nucleus and the spatial distribution of meiotic chromosomes in the hermaphroditic nematode Caenorhabditis elegans.