mtlengths(1) General Commands Manual mtlengths(1)
NAME
mtlengths - compute lengths of MTs in a model
SYNOPSIS
mtlengths
DESCRIPTION
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-
struction.
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.
OPTIONS
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
parentheses.
-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
length.
-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
sections.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output.
-StandardInput
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.
HISTORY
Written by David Mastronarde, 1/27/90; modified for IMOD 4/24/97;
incorporated obliqueness correction and switched to PIP input, 9/4/03
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.12.61 mtlengths(1)