Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells RESAMPLEMOD(1) RESAMPLEMOD(1) NAME resamplemod - Turn a model perpendicular to Z axis and resection SYNOPSIS resamplemod [options] input_file output_file DESCRIPTION Resamplemod can be used to resample or resection a model of fiber trajectories after rotating it so that the fibers run parallel to the Z axis. The program can find the mean trajectories of the fibers themselves and then rotate the model to bring the mean trajectory parallel to the Z axis, or one can supply a special contour to indicate the axis that should be rotated to the vertical. Contours will be resampled at single pixel intervals so that the model will have the correct dimensions when it has the same Z scale factor as the original model. Resamplemod uses the PIP package for input (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 -): -input OR -InputFile File name Input model file. -output OR -OutputFile File name Output model file. -exclude OR -ExcludeObjects List of integer ranges Objects to exclude from resampling; for example, closed contour objects. -direction OR -DirectionObjects List of integer ranges Objects to use to determine mean direction of fibers. The default is to use all of the objects; enter a list to use a subset of objects, or just a single object number if you have created a special object with a contour to indicate the direction. -main OR -MainAxis Integer Dominant axis along which fibers run (1 = X, 2 = Y, or 3 = Z.) The default is the Z axis (3), which is appropriate for serial section models. A different axis is generally needed for a model from a tomogram. If the model was built on a tomogram loaded into 3dmod with flipping (-Y), enter a number that refers to the axis that was seen in 3dmod. -skip OR -SkipInversion Do not invert contours that go from high to low along the main axis. The default is the reorder contours if necessary so that they go from low Z to high Z in the output model. -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, 2000; incorporated in IMOD 9/5/03