nda                      General Commands Manual                     nda



NAME
       sda - to do surface density analysis of point positions on a surface

SYNOPSIS
       sda [-comfile filename] [graph options]

DESCRIPTION
       This program analyzes the distances between positions along a surface
       and computes the average density of points in objects specified as
       neighbor "types" around points in objects specified as reference
       "types".  Density is computed in bins, where each bin corresponds to a
       range of distances, and density is the number of neighbors located at
       that range of distances, divided by the total area of the surface at
       that range of distances.  The neighbor count and area are summed over
       all the reference points and stored internally, so that more data can
       be summed if desired.

       The input model must have one or more meshed, closed contour objects,
       where the mesh triangles define the surface.  Points are taken from
       scattered point objects.  Individual points sizes are not taken into
       account, so distances are from center to center.  Each point is
       "dropped" onto the surface by projecting it into the plane of each tri-
       angle within a certain minimum distance in Z.  If the projection is
       located within that triangle, this is a candidate position on the sur-
       face.  The program picks the candidate position that is closest to the
       point as its position on the surface.

       The program is based on nda and nearly all the options are the same.
       See the nda man page for a description of the options and the gen-
       eral treatment of densities.  Most of the initial entries match those
       to nda or are otherwise self-explanatory.  One critical entry is for
       the "Minimum distance between sphere and surface in um", where the
       default in 30 times the Z slice thickness and the entry must be in
       microns.  Units are in microns and the model file must have a pixel
       size defined, but it can be in either nm or um.

       Two options are different from nda: 36 to do many sets with random
       positions or shuffled types, and 21 to compute a kernel density over
       the surface and save in a model file.  The latter is the origin of the
       surface display in "yeastpore.mod", distributed in the tiny "imod_data"
       sample of IMOD files.  A kernel density is computed by setting up a
       two-dimensional "kernel" function with a certain half-width (ressem-
       bling a Gaussian but without tails), centering that function at each
       point position, and adding in the function value at each underlying
       point on the surface.  The result is a smoothed density, where the
       amount of smoothing is set by an entry for the mean number of spheres
       to include in the kernel area.

       The program was developed for:
       Winey, M., Yarar, D., Giddings, T. H. Jr., and Mastronarde, D. N.
       1997.  Nuclear pore complex number and distribution throughout the Sac-
       charomyces cerevisiae cell cycle by three-dimensional reconstruction
       from electron micrographs of nuclear envelopes.  Molecular Biology of
       the Cell  8: 2119-2132.

AUTHOR
       David Mastronarde

SEE ALSO
       nda, mtk

BUGS
       Email bug reports to mast at colorado dot edu.





IMOD                                 5.2.0                              nda