Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

RESAMPLEMOD(1)							 RESAMPLEMOD(1)

NAME
	resamplemod - Turn a model perpendicular to Z axis and resection

SYNOPSIS
	resamplemod [options] input_file output_file

DESCRIPTION
  Resamplemod can be used to resample or resection a model of fiber
  trajectories after rotating it so that the fibers run parallel to the Z
  axis.  The program can find the mean trajectories of the fibers themselves
  and then rotate the model to bring the mean trajectory parallel to the Z
  axis, or one can supply a special contour to indicate the axis that should
  be rotated to the vertical.  Contours will be resampled at single pixel
  intervals so that the model will have the correct dimensions when it has the
  same Z scale factor as the original model.

  Resamplemod uses the PIP package for input (see the manual page for pip)
  The following options can be specified either as command line arguments
  (with the -) or one per line in a command file or parameter file (without 
  the -):

 -input OR -InputFile   File name
    Input model file.

 -output OR -OutputFile   File name
    Output model file.

 -exclude OR -ExcludeObjects   List of integer ranges
    Objects to exclude from resampling; for example, closed contour objects.

 -direction OR -DirectionObjects   List of integer ranges
    Objects to use to determine mean direction of fibers.  The default is to
    use all of the objects; enter a list to use a subset of objects, or just a
    single object number if you have created a special object with a contour
    to indicate the direction.

 -main OR -MainAxis   Integer
    Dominant axis along which fibers run (1 = X, 2 = Y, or 3 = Z.) The default
    is the Z axis (3), which is appropriate for serial section models.  A
    different axis is generally needed for a model from a tomogram.  If the
    model was built on a tomogram loaded into 3dmod with flipping (-Y), enter
    a number that refers to the axis that was seen in 3dmod.

 -skip OR -SkipInversion
    Do not invert contours that go from high to low along the main axis.  The
    default is the reorder contours if necessary so that they go from low Z to
    high Z in the output model.

 -param OR -ParameterFile   Parameter file
    Read parameter entries as keyword-value pairs from a parameter file.

 -help OR -usage
    Print help output.

  -StandardInput
     Read parameter entries from standard input.


HISTORY
  Written by David Mastronarde, 2000; incorporated in IMOD 9/5/03