Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

MTMODEL(1)							   MTMODEL(1)

NAME
	mtmodel - to build a MT model out of individual points

SYNOPSIS
	mtmodel

DESCRIPTION
  MTMODEL builds a model using a list of unconnected points.
  It links points from one section to the next by considering each
  point and seeing if the x-y coordinates are within a certain radius 
  of a point in the next section.  It can first do a scan through the
  points with a narrow radius, then further scans with progressively
  bigger radii (ignoring points that are already matched in a previous
  scan).  By default, all objects will be given color 250 (red), but
  one can have objects colored in a cycle of colors or coded for their
  length and termination.
  
  One can add the points in the list to an existing model if desired.
  Simply enter the name of this model file as the first entry in the
  program.  The points at the ends of existing objects will be examined
  first for their possible connections to new points.  Any new points
  within a specified number of pixels of the existing points will be
  discarded.  The color and other attributes of the objects in the
  existing model will remain unchanged.
  
  ENTRIES:

  Name of file with old model to extend, or Return if none
  
  IF you are extending a model, next enter the minimum distance to 
     allow between a new point and a point in the existing model.

  Name of point list file
  Name of new model file to create

  Radius to search for matching points in first scan, radius to search
     in last scan, number of scans
  
  1 to use colors to code for the size of objects and whether they
     start at the beginning or end of the data stack
  
  IF you specify 1, next enter the minimum object length which should
     be coded with the colors for "long" objects
  
  1 to change the default colors.
  
  IF you enter 1 here, next specify a list of colors from 247 to 255.
     Ranges (e.g. 250-253) may be entered.
     If you are not coding for object length/endpoints, then the
     default is to color every object red.  In this case, if you change
     the default, colors will be assigned to objects by cycling
     repeatedly through the list that you enter.
     If you are coding for colors, the default color list, and the
     order in which colors should be respecified in the list, is:

  single point=magenta
  points in every section = white
  long from beginning section = orange
  short from beginning section = red
  long from end section = blue
  short from end section = light blue (cyan)
  long in middle only = green
  short in middle only = yellow
  
  
  Minimum number of connected points required to make an object in the
     output model.  Points that would conenct into objects smaller than
     this minimum number will be discarded.

  Finally, if there are gaps in the progression of Z values in the list
     of points, the program will tell you how many gaps.  Enter 1 to
     connect points across the gaps; otherwise all objects will end at
     the gaps.

HISTORY
  Written by David Mastronarde, 9/8/88