Three-dimensional volumes representing biological structures can be obtained by methods such as serial section reconstruction, optical sectioning and tomographic reconstruction. Investigation and communication of these structures to others is greatly facilitated by computer-based visualization procedures. Synu a suite of programs we have developed, allows interactive investigation of three-dimensional volumes and is capable of producing high-quality three-dimensional images of the data. We have found the interactive manipulation and rendering capabilities of these programs to be invaluable for the discovery and communication of three-dimensional structural relations. With SynuView, it is possible to easily and rapidly explore the morphology and spatial distribution of an object or class of objects and their relation to other structures in the volume from many angles of view. This exploration is facilitated by the capability of the software to manipulate the contents of the reconstruction and to assign individual characteristics such as transparency to structures. Synu has been distributed to, and is in use in over 100 laboratories. We have recently completed a software package, Ducky, which is a major extension and revision of Synu. Ducky provides a more flexible and versatile software system for processing, rendering, and animating 3D datasets (Hessler, et al, 1995). The system is based on a powerful run-time interpreted langnage similar to C. The language includes many built-in functions for animation, rendering, shading, surface definition, and the creation of interactive menu and window-based visualization environments. Both volume and surface rendering methods are provided and may be combined in a single visualization. Scripts can be written in this language to create animations of a sequence of different views of a structure either within a 3D volume or across a series of volumes. To aid the unsophisticated user, scripts are provided to perform frequently used visualization tasks such as those provided by SynuView. The system is readily extendible. Existing scripts can be modified or new scripts written to create additional interactive environments and processes. The addition of motion to visualization can greatly facilitate comprehension and communication of complex three dimensional structures and their interrelationships. While our previous program, SynuMovie, can make simple movies of structures spinning around an axis, the scripting language provides a method for creating an animation in which the investigator can navigate through a volume showing selected views of components of the structure. In preliminary tests, we have found this versatile new software valuable not only for the examination and analysis of three-dimensional data, but also for creating three-dimensional model data to evaluate the application of various reconstruction algorithms to specific biological structures such as dendritic spines. We are currently performing final debugging and completing documentation in preparation for general distribution of these programs.
Showing the most recent 10 out of 384 publications
