Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

FENESTRA(1)							    FENESTRA(1)

NAME
	fenestra - find areas of holes in model objects

SYNOPSIS
	fenestra

DESCRIPTION
  This program will measure the sizes of holes through model objects
  described by a series of contours, such as fenestrations in Golgi
  cisternae.  It assumes that the objects have been modeled in Z planes
  while the holes appear when looking at the X or Y face of the model.
  For each model object, you must first create a separate object with
  points specifying the locations of the holes.  In general, each hole
  should be marked by two points, on the first and last Z planes
  where the opening occurs.  These points should be placed fairly
  carefully midway between the two contours and underneath the contour
  that closes off the hole on the adjacent Z place.
  
  You may place the locator points in separate contours or in the same
  contour, although in the latter case one must be particularly
  careful to enter a pair of points for each hole.  A hole occurring on
  only one Z plane may be specified by either one point or two, but if
  you use one point you MUST place that point in a separate contour.
  
  
  The program works by finding points on either side of the hole that
  are closest to the line connecting the two locator points.  Given
  all of these edge points, it then finds the plane that fits these
  points best.  The normal to this plane is taken as the best
  direction for viewing the hole.  An initial area is computed from
  the polygon determined by projecting the points into that plane.
  Then, the program reexamines the contours at the edge of the hole
  and finds the points that encroach the most upon the hole, when
  viewed from the best direction determined from the initial points.  
  These points are used to compute a "minimized" area.  An equivalent
  diameter is reported, based on this minimized area.

  The program can read a series of model files and place the output in
  a single text file.
  
  Entries to the program:
  
  Name of output file for areas and diameters
  
  0 for short output of minimized area and equivalent diameter, or 1
  for long output identifying the locator point contour number and
  location, the projection angles, and tyhe initial area
  
  For output of the points from which area was computed, as contours
  showing the outline of each hole, enter the number of a new object
  for the initial points, and another number for an object for the
  refined points.  Enter 0,0 for no output, or 0 and an object # for
  just the refined points.  Make sure the same object numbers will
  work for all of the models that will be processed.
  
  Model file name, or a blank line if there are no more models to
  process.
  
  A list of the numbers of the objects to be analyzed (Ranges
  may be used, e.g., 1-3,6,8)
  
  A list of the numbers of the corresponding objects with locator
  points (again, ranges may be used)
  
  An identifier or type number for each object being analyzed.
  
  IF you selected output of contours, enter the name of the new model
  file.
  
  The program will now loop back and ask for another input model to
  analyze.  Enter a blank line when done.
  

HISTORY
	  Written by David Mastronarde  9/14/97