Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells DENSMATCH(1) DENSMATCH(1) NAME densmatch - Scale densities in one volume to match those in another SYNOPSIS densmatch [-report] Reference_file File_to_scale [Output_file] DESCRIPTION Densmatch scales the density values in one volume so that its mean and standard deviation match that of another volume. To determine the mean and S.D. for each volume, it samples up to 100000 pixels in the central eighth of each volume (central half in X, Y, and Z). It can write the scaled values either to a new file or back into the file of the volume being scaled. THE LATTER WILL DESTROY THE ORIGINAL VALUES IN THAT FILE. Densmatch uses the PIP package for input (see the manual page for pip) and can still take sequential input interactively, but with no options. 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 -): -reference OR -ReferenceFile File name Input file with reference volume (the one being matched to). This file can be entered on the command line as the first non-option argument. -scaled OR -ScaledFile File name Input file with volume to be scaled to match. This file can be entered on the command line as the second non-option argument. -output OR -OutputFile File name Output file for the scaled volume. This file can be entered on the command line as the third non-option argument. If this file is omitted, the program will write the scaled values back to the input file. -report OR -ReportOnly Report scaling factors without writing scaled data to file. The program will report two numbers, a factor to multiply by then a constant to add; these numbers can be supplied to the -multadd option of Newstack. -xminmax OR -XMinAndMax Two integers Starting and ending X coordinates of region to analyze for mean and SD in reference volume. The default is NX/4, 3*NX/4, where NX is the size of the reference volume in X. X, Y, and Z coordinates are numbered from 0. -yminmax OR -YMinAndMax Two integers Starting and ending Y coordinates of region to analyze in reference volume. The default is NY/4, 3*NY/4, where NY is the size of the reference volume in Y. -zminmax OR -ZMinAndMax Two integers Starting and ending Z values of region to analyze in reference volume. The default is NZ/4, 3*NZ/4, where NZ is the number of slices in the reference volume. -offset OR -OffsetRefToScaledXYZ Three floats Displacement of the volume being scaled relative to the reference volume in X, Y, and Z; namely, the amount to add to a pixel coordinate in the reference volume to obtain the coordinate of the corresponding pixel in the file being scaled. -help OR -usage Print help output -StandardInput Read parameter entries from standard input. If there are no command-line arguments, Densmatch takes sequential input the old way, with the following entries: Name of the first volume, the one whose densities are being matched Name of the second volume, the one being scaled Name of an output file, or a blank line to have the scaled values written back into the second file. HISTORY Written by David Mastronarde, November 1995 Converted to PIP input, added reporting option, 8/23/04