Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

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
  orientation, 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 better 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 extension .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 sampling
  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