checkmtmod(1)                                                    checkmtmod(1)

       checkmtmod - check various features of a MT model


       Checkmtmod will check a microtubule tracking model built on serial sec-
       tions 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 con-
       tours 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 progres-
       sion 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 con-
       tours 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 start-
       ing 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 end-
       ing and starting points.  It then reports the distance between these
       extrapolated positions, and the angle between the trajectories in

       For each match, the program outputs on two lines the following informa-

       # 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.

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

       Email bug reports to mast at colorado dot edu.

BL3DEMC                              4.7.3                       checkmtmod(1)