Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

EXTRACTTILTS(1)							EXTRACTTILTS(1)

NAME
	extracttilts - Extract tilt angles or other info from image file header

SYNOPSIS
	extracttilts  [option] input_image_file [output_file]

DESCRIPTION
  EXTRACTTILTS will extract one kind of information from the header of an
  image file, if it is present, and produce a file with a list of the values.
  The default behavior is to extract tilt angles; these can be extracted from
  headers in the Agard/FEI format or from headers produced by SerialEM. 
  Enter an option to extract one of the other kinds of information written by
  SerialEM.

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

 -input OR -InputFile   File name
    Image file with header information to extract

 -output OR -OutputFile   File name
    Output file for header values.  If no output file is given, the values are
    printed to standard output.

 -tilts OR -TiltAngles
    Extract tilt angles from header (the default behavior).  The angles are in
    degrees.

 -stage OR -StagePositions
    Extract stage positions from header.  The positions are in microns.

 -mag OR -Magnifications
    Extract magnifications from header

 -intensities OR -Intensities
    Extract intensities from header.  On the Tecnai, these are the intensity
    values reported by Tecnai scripting, which range from 0 to 1 and differ by
    a scaling factor from the percent C2 readout in the Tecnai user interface.
     On the JEOL, they correspond to the percent C3 readout shown in SerialEM.

 -exp OR -ExposureDose
    Extract incident dose on specimen during camera exposure, referred to as
    exposure dose in SerialEM.  The units are electrons per square Angstrom.

 -warn OR -WarnIfTiltsSuspicious
    When extracting tilt angles, warn if more than half of them are near zero
    or any are bigger than 95 degrees.

 -help OR -usage
    Print help output

  -StandardInput
     Read parameter entries from standard input.

  If the program is started with no command line arguments, it reverts to
  interactive input with the following entries:
  
  Image file with tilt information
  Output file for tilt angles, or Return to print to standard output


HISTORY
  Written by David Mastronarde, 1999
  Converted for PIP input and to get other information, 3/17/04