mtlengths(1)                                                      mtlengths(1)

       mtlengths - compute lengths of MTs in a model


       Mtlengths computes the lengths, in microns, of contours in IMOD models,
       and produces a list giving the object number and contour length for
       each contour.  This list may be used to generate a histogram of lengths
       with a program such as Genhstplt.  One may optionally add a certain
       amount of length to each contour at its high Z end, so that the length
       calculation will include the thickness of every section in which a con-
       tour appears.

       If the reconstruction is from serial sections that were significantly
       tilted during microscopy, the program can adjust for these tilts given
       the proper information.  Prepare a file in which the first line shows
       the Z value and the tilt of the first tilted section (or of the first
       section, if that one was tilted), and each successive line shows the Z
       value and tilt for each section on which tilt was changed.  Z values
       should occur in ascending order.

       If the contours are mainly perpendicular in the model (e.g., micro-
       tubules in good cross-section in tilted images), then this simple
       adjustment for tilting is adequate.  However, if trajectories are
       oblique, the program can do a more complex adjustment for the tilting
       if it is given information about the location of the tilt axis in the
       images.  This information consists of the angle of the axis in raw
       images (i.e., the angle of rotation from the vertical to the tilt
       axis), and optionally the list of transformations applied to align the
       raw images.  When the program adjusts for obliqueness, there is a
       potential ambiguity about the sign of the tilt angles.  It thus com-
       putes lengths both with the tilt angles as given and with their signs
       inverted.  It reports the fraction of line segments that come out
       longer with the angles as given than with the angles inverted.  This
       fraction is referred to as the fraction that are "better", because it
       is assumed that the tilting was done in the direction that reduced the
       obliqueness of the fibers by as much as possible.  This fraction is
       reported for each range of Z values at a single tilt angle, and over-
       all.  If the fraction better is less than 0.5, one should rerun the
       program, selecting the option to invert tilt angles.  On this run, the
       angles will be considered to be specified as the negative of the angles
       in the tilt file, and the fraction of segments that are longer with the
       angles as specified will be greater than 0.5.

       These adjustments for tilting are irrelevant for a tomographic recon-

       The program can also be provided with an object containing a contour
       that serves as a length marker.  It will report the length of this con-
       tour both without and with the correction for obliqueness, and with the
       length given for both polarities of the tilt angle.

       If one corrects for obliqueness, there is also an option to produce a
       set of transformations that can be applied to produce the model that
       would have been obtained if the sections had not been tilted.  Imod-
       trans(1) or Xfmodel can be used to transform the model.

       The output of the program depends on whether one is correcting for
       obliqeness.  If one is not, the output consists of the object number
       and the length for each MT.  With obliqueness correction, the output
       consists of the object and contour number, the length uncorrected for
       obliqueness, the length with angles as specified, and the length with
       angles inverted.  On the final run, with the polarity of angles
       selected as inverted if necessary, the desired lengths will be in the
       fourth column.

       Mtlengths uses the PIP package for input (see the manual page for
       pip) and can take input interactively if correction for obliqueness
       is not required.  The following options can be specified either as com-
       mand line arguments (with the -) or one per line in a command file or
       parameter file (without the -).  Options can be abbreviated to unique
       letters; the currently valid abbreviations for short names are shown in

       -model (-mo) OR -ModelFile     File name
              Input model file.

       -output (-o) OR -OutputFile    File name
              Output file for lengths.  The output file may be omitted for
              output to terminal or log file.

       -tilt (-t) OR -TiltFile   File name
              File with tilt information in the format described above.

       -extra (-ext) OR -ExtraLength       Floating point
              Fraction of a section to add at the high Z end of each contour
              to account for section thickness.  The default is 0.

       -magnification (-mag) OR -Magnification       Floating point
              Magnification of film images, or 1 if CCD images.  This option
              is required if there is no scale in the model header.

       -scale (-sc) OR -ScaleDigitized     Floating point
              Microns per pixel at which film was digitized, or pixel size in
              microns for CCD images.  This option is required if there is no
              scale in the model header.

       -section (-se) OR -SectionThickness      Floating point
              Section thickness in nanometers.  This option is required if
              there is no scale in the model header.

       -exclude (-exc) OR -ExcludeObjects       List of integer ranges
              Objects to exclude from length measurement.

       -marker (-mar) OR -MarkerObject     Integer
              Object number of length marker for measuring overall spindle

       -correct (-c) OR -CorrectObliques
              Correct lengths of oblique MTs when sections are tilted.

       -axis (-ax) OR -AxisAngle      Floating point
              Rotation angle from the vertical to the tilt axis in the raw
              images.  This entry is required when correcting for obliqueness.

       -align (-al) OR -AlignmentTransforms     File name
              File with transforms used to align the images.  This entry is
              optional and is relevant only when correcting for obliqueness.

       -invert (-i) OR -InvertAngles
              Change the sign of the tilt angles when adjusting lengths of
              oblique fibers.

       -untilt (-un) OR -UntiltTransforms       File name
              Output file for transforms that will correct model for tilted

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter

       -help (-h) OR -usage
              Print help output.

              Read parameter entries from standard input.

       For compatibility with older command files, the program will also
       accept input interactively if started with no command line arguments,
       but it will not be able to correct for obliqueness.  The interactive
       entries to the program are:

       Name of model file

       Name of file with tilt information, or Return if none

       IF the model has no scaling information in its header, make the follow-
       ing three entries:

          Magnification of negatives (without any commas), or 1000

          Scale, in microns per pixel, at which negatives were digitized, or
          pixel size on specimen in nanometers

          Section thickness in nanometers

       Amount to add to the high Z end of each object in order to account
          for section thickness.  For example, enter 1 to allow a section's
          worth of length for each section that an object appears in.

       Name of output file in which to place list of lengths, or Return for
          output to the terminal

       List of IMOD objects to exclude from the output, or Return to output
          all objects.

       Written by David Mastronarde, 1/27/90; modified for IMOD 4/24/97;
       incorporated obliqueness correction and switched to PIP input, 9/4/03

       Email bug reports to mast at colorado dot edu.

BL3DEMC                              4.7.3                        mtlengths(1)