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. In addition to extracting data stored in the image file header, the program can extract from a metadata file written by SerialEM in the autodoc format. A wider range of information can be stored in such a file than in the header. The metadata file must have the same number of sections as the image file. 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. If this option is not entered, the first non-option argument will be taken as the input file. -output OR -OutputFile File name Output file for header values. If this option is not entered, the second non-option argument will be taken as the output file. If no output file is given, the values are printed to standard output. -mdoc OR -MdocMetadataFile Obtain values from a metadata file named with the name of the input file plus '.mdoc', instead of from the extended header of the image file. A file with this name is generated by SerialEM when an option is selected to save extra information in a metadata file. -other OR -OtherMetadataFile File name Obtain values from the metadata file with the given name, instead of from the extended header of the image file. -tilts OR -TiltAngles Extract tilt angles from header or metadata file (the default behavior). The angles are in degrees. -stage OR -StagePositions Extract stage positions from header or metadata file. The positions are in microns. -mag OR -Magnifications Extract magnifications from header or metadata file. -intensities OR -Intensities Extract intensities from header or metadata file. 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. -camera OR -CameraExposure Extract camera exposure time, in seconds, from metadata file. -pixel OR -PixelSpacing Extract pixel size in Angstroms from metadata file -defocus OR -Defocus Extract defocus in microns from metadata file. The value is the focus readout of the microscope, not the defocus measured by autofocusing. -warn OR -WarnIfTiltsSuspicious When extracting tilt angles, warn if more than half of them are near zero or any are bigger than 95 degrees. -all OR -AllPieces Extract the selected item for all pieces of a montage. The default is to output the value for the last piece of the montage at each Z value. -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