Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

CHECKMTMOD(1)							 CHECKMTMOD(1)

NAME
	checkmtmod - check various features of a MT model

SYNOPSIS
	checkmtmod

DESCRIPTION
  CHECKMTMOD will check a microtubule tracking model built on serial
  sections for three kinds of errors: branch points, skipped sections,
  and failure of the Z coordinate to increase monotonically. In
  addition, it can search for situations where the start of one contour
  is near the end of another contour, so that one can then check
  whether these contours are in fact the same microtubule.
  
  All branch points are reported.  The Z coordinate is expected to
  increase monotonically within each contour, so there will be a report
  whenever Z stays the same or decreases.  If an entire contour is in
  one Z plane, there will be just one report for that contour.
  Z values are expected to occur in a regular progression, and gaps in
  that progression will be reported unless they occur at missing
  sections, at which no contours have points.
  
  You can specify a list of additional sections on which some points
  may be intentionally missing.  The program will then not report the
  contours that skip over that section.  You can enter a list with
  ranges, such as 1-3,37,78.

  To search for starts near ends, enter a distance within the X-Y plane
  to search, and the maximum difference in Z coordinates to search.
  (Enter / to accept the default values for these parameters, or enter
  0,0 to skip the search).
  
  Enter the scaling in Z relative to the X and Y scaling (this would
  be the same as the scale value used to display
  the model at the true scale).  This value is needed to compute angles
  between trajectories of MTs with nearby ends.  If you are not
  searching for starts near ends, it doesn't matter what you enter.

  When searching for starts near ends, the program will report
  the starting and ending points whenever those two points are within
  the selected distance in the X-Y plane and the Z value of the
  starting point minus the Z value of the ending point is positive and
  less than the selected difference in Z values.  The program also
  fits a line to the last three points in the contour that ends, and
  another line to the first 3 points in the contour that starts.  It
  uses these lines to extrapolate the trajectory of each contour to the
  position in Z midway between the ending and starting points.  It then
  reports the distance between these extrapolated positions, and the
  angle between the trajectories in degrees.
  
  For each match, the program outputs on two lines the following
  information:

  # of contour that ends, X, Y, Z coordinates of the ending point,
  # of contour that starts, X, Y, Z coordinates of the starting point,
  separation between objects extrapolated to a single plane in Z,
  and angle between the trajectories of the objects.
  
  This information on extrapolated separation and angle can be used
  to zero in on the matches that need to be examined in the model;
  most "matches" can be eliminated without examination because either
  the angle or the separation is unreasonably large.

HISTORY
  Written by David Mastronarde, 1/21/90, jazzed up 4/32/93, modified for
    IMOD 4/25/97