The nuclearShape project is collection of programs designed to characterize the shapes and 
configurations of cell nuclei from stacks of digitized confocal microscope images. The programs
assume these images are encoded using the Zeiss LSM format. The project is still under development,
and the software has only been partially tested. Use these programs with caution.

The nuclearSlice application computes the relative concavity of the two-dimensional projection of
a stack of images. For each projection, a two-dimensional convex hull (the smallest enclosing
convex polygon) is constructed. The deficit is defined as the area of the region that falls within
the convex hull, but outside of the nuclear projection. The relative concavity is then defined as
the ratio of the deficit to the projection area.  This application can be run as a background process,
in order to analyze a large number of data sets that require minimal user interaction, or as an
interactive process using a graphical interface.

The nuclearSurface application copmutes the relative concavity of a three-dimensional nuclear
volume. It currently only runs as a batch process.

These programs were originally created and programmed in C++ by Robert R. Snapp at the University of Vermont.