xfalign(1) xfalign(1) NAME xfalign - Automatic image alignment using xfsimplex SYNOPSIS xfalign [options] <input image file> <output transform file> DESCRIPTION xfalign will search for the linear transformations that align each sec- tion to the previous one in an image stack, or that align each section to a single reference image. It runs Xfsimplex repeatedly to find these transformations. Because Xfsimplex performs an incremental search for a local optimum in alignment, it cannot find the right alignment if there is a large displacement between the images. Xfalign has options for initially finding such displacements by cross-correla- tion using tiltxcorr, and for working from a set of initial dis- placements computed previously. These methods will work only on images where there are enough similar features between one section and the next to guide the alignment. It may take some experimentation to find settings that will give good results with a particular kind of data. The major factors to vary would be the choice of filter to be applied before the search, and the amount of binning to apply to the images in the search. If images are not already roughly in alignment, the other variable is whether cross- correlation will work adequately or whether another method of prealign- ment is needed. The images can be reduced in size by binning. More reduction will make the search run faster and remove or average out more high-frequency noise. The default reduction is by a factor of 2; no reduction should be needed for very small images and more reduction might be helpful for large images (say, 1K x 1K or bigger). Prefiltering uses the four parameters sigma1, sigma2, radius1, radius2 that are used to specify filtering for several other programs (see Fil- terplot(1). Low-pass filtering to reduce noise (e.g., sigma2 = 0.05, radius2 = 0.25) is somewhat redundant to binning the images, and may not be needed with the default image reduction. If the images contain large areas of light and dark that correspond between sections and so are good cues for alignment, then prefiltering, if any, should not include a high-pass filter (i.e., leave sigma1 at 0 or do not filter). However, if there are large areas of light and dark that do not corre- spond and would be misleading, a high-pass filter should be applied (e.g., sigma1 = 0.05 to flatten the contrast of areas larger than 20-40 pixels). If the cues for alignment are mostly relatively fine fea- tures, it may help to enhance them with a band-pass filter. This can be done by setting a sigma2 such as 0.05 and both radius1 and radius2, such as 0.15 and 0.2, to provide a Gaussian fall-off with sigma of 0.05 around the band from 0.15 to 0.2 reciprocal pixels. Alternatively, a band-pass filter can be specified with a single parameter, a negative entry for sigma1, such as -0.1 to get a band-pass filter centered at 0.14 reciprocal pixels. Another filtering option is to use a Sobel filter, which will highlight edges in the image. If initial cross-correlations are chosen, a filter is included whose default values will remove some high frequency noise (sigma2 = 0.05, radius2 = 0.25) and prevent the correlation from being thrown off by very low frequency trends in the images (sigma1 = 0.01). If there are large light and dark patches that do not correspond well between images, the low frequency filter set by Sigma1 should be increased. If images are particularly noisy, radius2 could be decreased. When initial cross-correlation is used, the program will produce two transform files, the one specified as your output file, and another file with the initial transformations. The name of the latter file will be the root name of your output file, with the extension .xcxf (e.g., setname.xcxf if your output file is setname.xf). If some of the initial displacements are bad, there are two possible approaches to repairing the deficiencies. You can use midas to correct the final transformations, in which case you will have to introduce any rota- tions, size changes or stretches manually as well. Alternatively, you can edit the initial transformations, then rerun xfalign with the -ini- tial option specifying that existing .xcxf file, instead of the -prex- corr option. This would give xfalign a chance to find the more complex linear transformations properly for the sections that had bad initial alignments the first time. Options Options may be abbreviated to one to three letters, the minimum needed to unambiguously specify the particular option. The -prexcorr option cannot be used with either the -ref or the -initial options. Xfalign uses the PIP package for input (see the manual page for pip). Options can be specified either as command line arguments (with the -) or one per line in a command file (without the -): -InputImageFile File name Input file with images to align -OutputTransformFile File name Output file for transforms -size OR -SizeToAnalyze Two integers Size of image area to analyze in X and Y. The default is to analyze the whole image, ignoring the amount around the edges specified by the -matt option. -offset OR -OffsetToSubarea Two integers When analyzing a subarea, this entry specifies the offfset to the center of subarea being analyzed in X and Y. Positive off- sets are used for an area up from and to the right of the cen- ter. -matt OR -EdgeToIgnore Floating point In Xfsimplex, omit areas of images near their edges. Enter a value < 1 to indicate the fraction of the image extent to omit, or > 1 to indicate the number of pixels to omit. If a subarea is being analyzed, this amount is ignored inside the subarea and the fraction is relative to the subarea size. The default is 0.05. -reduce OR -ReduceByBinning Integer Binning factor to reduce by (default 2) -filter OR -FilterParameters Multiple floats Filter images before searching with the given sigma1, sigma2, radius1, and radius2 values, which have the same meaning as in many other programs. See Xfsimplex for description. -sobel OR -SobelFilter Apply edge-detecting Sobel filter to each image. This filter will be applied after binning and filtering if any. -params OR -ParametersToSearch Integer In Xfsimplex, search for the given number of semi-natural param- eters. Enter 2 to search only for translations, 3 to search for rotations in addition, 4 to search for magnifications as well, or 6 to search for the full transformation as represented by semi-natural parameters (rotation, magnification, difference between X and Y axis stretch, difference between X and Y axis rotation.) The default is 0, in which case Xfsimplex searches for the transformation by varying the formal parameters of the 2 by 2 transformation matrix. The one advantage of using 6 instead of 0 is that the search can be limited, and the amount of stretch is limited by default. -limits OR -LimitsOnSearch Multiple floats Limits for each of the variables being searched. Each number entered specifies the maximum amount that the respective vari- able can change from its initial value. Enter a 0 to avoid lim- iting a parameter. If the search is being done on formal param- eters, then only the first two (shift in X and Y) can be lim- ited, so only 1 or 2 values will be meaningful. If the search is on semi-natural parameters, then you can enter more or fewer values than the number of variables being searched. Extra val- ues are ignored, missing values retain their default values. The default is 0,0,0,0,0.1,4; i.e., difference between X and Y axis stretch is limited to 10% and difference between X and Y axis rotation is limited to 4 degrees. -bilinear OR -BilinearInterpolation With this option, Xfsimplex will use bilinear rather than near- est neighbor interpolation when transforming an image. This slower option should be used when trying to find accurate align- ments between small images. -ccc OR -CorrelationCoefficient Compute the standard cross-correlation coefficient instead of difference between images. The difference measure that is mini- mized will be 1 minus the CCC, but the CCC itself is printed in the trace and final output. It takes < 5% more time to compute the CCC. -local OR -LocalPatchSize Integer Size of square subareas (patches) within which to compute a mea- sure of image difference, in pixels before binning, if any. This option should prevent the need for low frequency filtering, which would increase execution time by roughly 10%. Patch sizes on the order of 1/20 to 1/10 of the image size should be effec- tive. see Xfsimplex for more details. -reference OR -ReferenceFile File name Align each image in the input image stack to the single image in the given image file. Images can be skipped. -prexcorr OR -PreCrossCorrelation Find preliminary translational alignments with tiltxcorr. This option is not available with a reference file. -xcfilter OR -XcorrFilter Multiple floats Change the filter that is used in cross-correlation by tiltx- corr(1) to have the given sigma1, sigma2, radius1, radius2. The default is 0.01,0.05,0,0.25. -initial OR -InitialTransforms File name Search for transformations starting from the transforms in the given existing file. -skip OR -SkipSections List of integer ranges List of sections to skip, while maintaining alignment across skipped sections. The program will not find the transform for aligning a listed section to the previous one. Section numbers are separated by the ',' character for single sections or the '-' character for ranges. Section numbers start with zero and go up to nz-1. When a section is skipped, the following section will be aligned to the last unskipped section and a unit trans- form will be output for the skipped section. The default is to use all of the sections. -break OR -BreakAtSections List of integer ranges List of sections to break alignment at. This option is like "-skip" in that no transform is found for aligning a listed sec- tion to the previous one and a unit transform is written for the listed section. However, the following section will be aligned to the listed section, and nothing will be aligned to the previ- ous section. This breaks the chain of alignment through the series of sections. -bpair OR -PairedImages Break the alignment after every pair of sections, i.e., at all even section numbers. -tomo OR -TomogramAverages Align averaged slices from the top and bottom of tomograms of serial sections. The image file is assumed to contain pairs of top and bottom averages, i.e., from the top of the first tomo- gram, the bottom of the second, the top of the second, etc., ending in the bottom of the last tomogram. The program will align only a bottom average to the previous top average, and the number of transforms output will equal the number of tomograms, not the number of averages in the image file. The same number of transforms are assumed to be present in a file of initial alignments entered with the "-initial" option. -diff OR -DifferenceOutput Output the final difference measure or cross-correlation coeffi- cient found by Xfsimplex for each pair of images. The differ- ence measure is the mean difference per pixel expressed as a multiple of the image standard deviation. -StandardInput Read parameter entries from standard input FILES When using prealignment by cross-correlation, the initial transforms will be placed into a file with the same root name as the transform output file but with the extension .xcxf. If an output file already exists a backup image of the original is created with the ~ extension. AUTHOR David Mastronarde SEE ALSO xfsimplex, tiltxcorr BUGS Report bugs to mast at colorado dot edu BL3DEMC 4.3.7 xfalign(1)