mtrotlong(1)                                                      mtrotlong(1)



NAME
       mtrotlong - extract MTs rotated into longitudinal orientation

SYNOPSIS
       mtrotlong

DESCRIPTION
       Mtrotlong can be used to extract a series of subvolumes with fibrous
       elements such as microtubules (MTs) rotated into a longitudinal orien-
       tation, and with one end of the item in the center of the extracted
       subvolume.  To use it, model each fiber in 3dmod with a single open
       contour along its axis.  Then run Mtrotlong with entries indicating
       which contours to analyze and how to orient them, and it will produce
       an IMOD command file for extracting the subvolumes with Rotatevol.
       This command file would then be run with "subm command_file".  This
       allows the rotation angles to be edited if necessary to produce a bet-
       ter result, using angles found in the Slicer window.

       The program will determine the orientation near the end of a fiber by
       fitting to a specified number of points.  It is thus desirable to have
       different fibers modeled with points at roughly equivalent spacings.
       For example, if some fibers are modeled very densely while others are
       modeled with only a few points over a long distance, then the fit will
       be over a very short distance in the former case and over a very long
       distance in the latter if it is determined from the same number points
       in each case.  The orientation may be less than optimal in both cases.
       Another way to avoid this problem is to enter different values for the
       number of points to fit.

       The program can produce subvolumes with double the sampling in the Z
       dimension, i.e. half the pixel size.  Do do this, it issues commands to
       extract the volume twice, one with an odd Z size and once with an even
       Z size, which results in a half-pixel offset.  These files are then
       combined by running Newstack with a file named "interleave", which
       is also produced by Mtrotlong.

       The program will extract a volume at either the starting or the ending
       point of a contour.  To have it do both, just make two entries for the
       contour.  Each subvolume will be named with a starting letter that
       encodes the object number, the contour number, an ending letter that
       encodes with it is from the start or end of a contour, and the exten-
       sion .st.

       Inputs to the program:

       Name of input model file

       Name of output command file

       Name of input image file

       1 if the volume has been flipped or rotated so that the X/Y planes are
       the plane of the sample, or 0 if not (i.e. if it still needs to be
       loaded into 3dmod with flipping)

       1 for an isotropic volume, 2 for a volume with double sampling (half
       the pixel size) in the Z dimension

       X, Y and Z size of a single isotropic extracted volume.  If the sam-
       pling is doubled in Z, the final volume will have Z size 2 * NZ + 1

       Single letter codes for each object; for example if object 1 has
       kinetochore and object 2 has nonkinetochire MTs, the entry could be
       "kn"

       Two single letter codes for volumes extracted from contour starts and
       ends, respectively.

       A series of lines with the following format:

       Object number, contour number, 0 or 1 to extract from contour start or
       end, 0 or 1 to rotate so that the fiber extends upward or downward from
       the middle, and the number of points to fit over

       A line with 0,0,0,0,0 to end the series and exit the program

HISTORY
       Written by David Mastronarde about 1996
       Incorporated in IMOD 9/11/06

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                        mtrotlong(1)