matchrotpairs(1) matchrotpairs(1) NAME matchrotpairs - find transform between best matching pair of rotated views SYNOPSIS matchrotpairs [options] file_a file_b output_transform DESCRIPTION Matchrotpairs is used to find the transformation between two images rotated by about 90 degrees from each other. This transformation is then supplied to Finddistort, which will use it to compute the abso- lute stretch component of an image distortion field. However, the stretch cannot be computed accurately if one of the images is of a tilted specimen, because a tilt will shrink the image slightly perpen- dicular to the tilt axis. Also, the specimen cannot be assumed to be horizontal at zero tilt. The solution to these problems is to use a specimen with some features distributed at different heights, take a small tilt series of the specimen (e.g., at -4, -2, 0, 2, and 4 degrees), rotate it by 90 degrees, and take another such tilt series. Matchrotpairs can then be used to search for the pair of views from the two series that match the best, using essentially the same procedure as in Transferfid. The difference between these images can then be assumed to be the result of the rotation alone, even if the specimen is tilted in each of these two views. The recommended procedure would be to run Finddistort first to find a zero-stretch distortion field, and to supply this field to Matchrot- pairs. The two best matching images will be undistorted and these undistorted images should then differ only by a stretch, allowing the stretch to be determined with the greatest accuracy. Options -za <z1,z2> The starting and ending sections from the first input file to include in the search, numbered from 1. The default is to use all sections from the first file. -zb <z1,z2> The starting and ending sections from the second input file to include in the search, numbered from 1. The default is to use all sections from the second file. Note that the two tilt series can be placed in the same file, that file name can be given for both input files, and the -za and -zb options can be used to indicate where the two tilt series are in the file. -a <value> Use this option to specify the direction of rotation from the first to the second axis. Only the sign of this number matters, so you can enter -1 or -90 for clockwise rotations, or 1 or 90 for counterclockwise rotations. In the absence of this option, the program will consider both directions of rotation. -m Run Midas on the central pair of views, and use the alignment that you set in Midas as the initial alignment for all pairs of views that are considered. A correction for stretch will be applied in the initial alignment of the other pairs and may be needed in some cases. -d <file> Name of file with zero-stretch image distortion field from Find- distort(1). -b <value> The binning of the images, which usually needs to be specified when undistorting. -t Leave temporary files in /usr/tmp or its equivalent for diagnos- ing problems. -P Output process ID. FILES The best matching pair will be undistorted if the -b option is given and stacked into a file with the root name of the output file and the extension ".stack". If the output file already exists, a backup image of the original is created with the ~ extension. AUTHOR David Mastronarde <mast at colorado dot edu> SEE ALSO finddistort, transferfid, midas BL3DEMC 4.3.7 matchrotpairs(1)