xcorrstack(1) General Commands Manual xcorrstack(1)
NAME
xcorrstack - to cross-correlate a single image with a whole image stack
SYNOPSIS
xcorrstack [options] image_stack single_image output_stack
DESCRIPTION
Xcorrstack cross-correlates each of the sections in one image stack
with a single image in a second image file. A subset of sections may
be done. The correlation may be filtered with the same set of parame-
ters as in other IMOD programs (see man page for Enhance). The sin-
gle image may be smaller than the images in the stack. In this case,
by default the single image will be placed in an array of the larger
size, with the MIDDLE of the smaller image moved to the LOWER-LEFT cor-
ner of the larger array. As a consequence of this shift, the coordi-
nates of the peaks in the correlation will correspond to the coordi-
nates of the centers of features in the image stack that best match the
single image. If the single image and stack have the same dimensions,
then you have a choice as to whether to keep the single image as it is
or to move its middle into the lower left corner. Displacements
between images would then be reflected by the positions of peaks in the
correlogram relative to the (0,0) pixel (if the image is not shifted)
or relative to the middle (NX/2,NY/2) pixel (if the image is shifted.)
Images will be padded if necessary for taking the FFT, so their size
may be odd or contain large prime factors.
Filtering is specified with the standard four parameters used in other
IMOD programs. The filter functions produced by these options can be
visualized with the program Filterplot; see that man page a full
description of their effects.
OPTIONS
Xcorrstack 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 -). Options can be abbreviated to
unique letters; the currently valid abbreviations for short names are
shown in parentheses.
-stack (-st) OR -StackInputFile File name
Input file with stack of images to correlate with a single
image. If this option is not entered, the first non-option argu-
ment will be used for this input file.
-single (-sin) OR -SingleInputFile File name
Input file with single image to correlate with the stack of
images. If this option is not entered, the second non-option
argument will be used for this input file.
-output (-o) OR -OutputFile File name
Output file for correlation images. If this option is not
entered, the third non-option argument will be used for this
output file.
-sections (-se) OR -StartingEndingSections Two integers
Starting and ending sections in the input stack to correlate
with the single image. Sections are numbered from 0. The Z
origin of the output file will be adjusted so that a model gen-
erated on the input stack will display correctly on the correla-
tion stack.
-rad1 OR -FilterRadius1 Floating point
Low spatial frequencies in the cross-correlation will be attenu-
ated by a Gaussian curve that is 1 at this cutoff radius and
falls off below this radius with a standard deviation specified
by FilterSigma2. Spatial frequency units range from 0 to 0.5.
Use FilterSigma1 instead of this entry for more predictable
attenuation of low frequencies.
-rad2 OR -FilterRadius2 Floating point
High spatial frequencies in the cross-correlation will be atten-
uated by a Gaussian curve that is 1 at this cutoff radius and
falls off above this radius with a standard deviation specified
by FilterSigma2.
-sig1 OR -FilterSigma1 Floating point
Sigma value to filter low frequencies in the correlations with a
curve that is an inverted Gaussian. This filter is 0 at 0 fre-
quency and decays up to 1 with the given sigma value. However,
if a negative value of radius1 is entered, this filter will be
zero from 0 to |radius1| then decay up to 1.
-sig2 OR -FilterSigma2 Floating point
Sigma value for the Gaussian rolloff below and above the cutoff
frequencies specified by FilterRadius1 and FilterRadius2
-mode (-m) OR -ModeOfOutput Integer
Mode for correlation images: 0 for byte, 1 for short integer, 2
for floating point, 6 for unsigned short integer, or 12 for
16-bit floating point. Except for floating point output, each
correlation image will be scaled to fill the positive dynamic
range of the mode. The default is the same mode as the input,
although the default mode of floating point output for MRC files
is governed by the value of environment variable
IMOD_WRITE_FLOATS_16BIT. Mode 12 is allowed only if the output
format is MRC.
-split (-sp) OR -SplitIntoCorners
If the single image is the same size as the input stack, this
option can be used to the middle shifted to the lower left cor-
ner, just as occurs for smaller single images.
-fill (-f) OR -FillValue Floating point
Value to fill when embedding image into a larger array. The
default is to fill with the mean at the edge of the image.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde 4/26/89
Converted to PIP, got rid of redundant filters, adjusted origin 10/29/07
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 xcorrstack(1)