The software package 3-D TOP is a measurement software which has been developed to meet the needs of those who analyze mechanical serial sections in histology and optical sections in laser scanning microscopy. The semiautomatic definition of topological centerlines is the backbone of this software. The three basic advantages in using the concept of topology are (a) resolving ambiguities for surface rendering, (b) flexible definition of objects for automatic identification, labeling, and measurement, and (c) topological quantification of complex forms. A specific application of this software to lung research is demonstrated. (C) 1996 Academic Press, Inc.