Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

BOXAVG(1)							 BOXAVG(1)

NAME
  boxavg - averages images from specified locations in an image file

SYNOPSIS
  boxavg [options] image_input_file model_input_file average_output_file

DESCRIPTION

  Boxavg will average images at points specified in an IMOD model file.
  By default, it take all points from open contour and scattered point
  objects, but specific objects can be selected instead.  After computing 
  an average, it can then align each extracted image with the average by
  searching for the shift that minimizes the standard deviation of the
  difference between the two.

  Boxavg uses the PIP package for input exclusively (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 -):

 -image OR -InputImageFile   File name
    Input file with images containing features to average.  If this option is
    not entered, the first non-option argument will be used for this input
    file.

 -points OR -PointModelFile   File name
    Name of model file with points to be averaged.  If this option is not
    entered, the second non-option argument will be used for this input file.

 -output OR -OutputFile   File name
    Output file for average image.  If this option is not entered, the third
    non-option argument will be used for this output file.

 -piece OR -PieceListFile   File name
    Name of piece list file if image is montaged or out of sequence

 -objects OR -ObjectsToAverage   List of integer ranges
    List of objects with points to average (comma-separated ranges allowed). 
    The default is to take all points from all open contour or scattered point
    objects.  This option can be used to select a subset of objects in the
    model or force the use of a closed contour object.

 -box OR -BoxSizeXandY   Two integers
    Size of box to average in X and Y

 -mode OR -ModeOfOutput   Integer
    Mode for output: 0 for byte, 1 for integer, 2 for real, 6 for unsigned
    integer.  The default is the same as that of the input.

 -passes OR -PassesThroughData   Integer
    Number of passes through the data, either 1 or 2.  On the second pass, the
    boxes will be aligned to the average from the first pass.  The default is
    2; enter 1 to skip the alignment pass.

 -linear OR -LinearInterpolation
    Use linear instead of cubic interpolation when extracting box

OBSOLETE OPTIONS 
  These options are not needed when Xcorrstack is used to correlate 
  an average with images.

 -size OR -SizeOfOutputXandY   Two integers
    Size of output file in X and Y (default is same size as box)

 -fill OR -FillValue   Floating point
    Value to fill with when output array is bigger than box.  The default is
    the mean along the edge of the average image.  This entry is ignored if
    the output is the same size as the box.

 -split OR -SplitIntoCorners
    Split average into the four corners of the output array

 -zero OR -ZeroMean
    Shift the output to have a zero mean value.  This option is ignored if the
    data mode of the output is bytes or unsigned integers.

 -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, 4/26/89
  Converted to PIP, using a model file and non-integer coordinates, 10/21/07