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