Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
CORRSEARCH3D(1) CORRSEARCH3D(1)
NAME
corrsearch3d - search for array of 3D displacements between two volumes
SYNOPSIS
corrsearch3d
DESCRIPTION
Corrsearch3d will determine the 3D displacement between two image
volumes at a regular array of positions. At each position, it extracts
a patch of a specified size from each volume, then searches for a local
maximum in the cross-correlation between the two patches, computing
correlations in real space at each displacement between the patches.
The starting point of the search is based upon the displacements of
adjacent patches that have already been determined. If there are no
such adjacent patches, or if no maximum is found for displacements
within a specified range, the program uses FFT-based cross-correlation
instead of real-space correlation. The program works from the center
of the volume outward, analyzing patches in the X direction, then in
the shorter of Y and Z dimensions, then in the longer of those
dimensions. An optional model file can be entered with contours
enclosing the area where patches should be analyzed; patches outside
this area are excluded. Information about the source volume for the
file being transformed can be entered so that the program can analyze
patches only from regions that are good in the second image file. In
addition, a model can be provided enclosing good areas in the source
for the second file.
The data being correlated can be filtered by convolving with a 3x3x3 or
5x5x5 Gaussian kernel in real space. This smoothing is applied to one
of the two patches before correlating them. The degree of filtering is
controlled by the sigma (standard deviation) of the Gaussian, which
should be a small number on the order of 1. Computation time will
increase by ~30% when smoothing with a 3x3x3 kernel and it will double
with a 5x5x5 kernel. By default, the program will select a 3x3x3
kernel for sigma less than 1.5 and a 5x5x5 kernel for larger sigmas,
unless the size is explicitly selected. The useful range of sigma is
probably 0.5 to 3.
Low and high frequency filtering can also be applied in Fourier space,
but this is useful only for testing because it is used only with the
rare FFT-based correlations.
The program works with files whose thin dimension is in either Y or Z.
If the volumes are offset from each other (such as adjacent tomograms),
this offset can be specified with the -InitialShiftXYZ option. The
displacements computed by the program are in addition to this global
shift.
The program outputs an initial line with the total number of
patches, then one line for each patch, containing the X, Y, and Z
coordinates of the patch, the displacement between the two files
in X, Y, and Z, and the correlation coefficient.
Corrsearch3d uses the PIP package for input (see the manual page for pip)
and can take input interactively for options that existed when it was
converted, to maintain compatibility with patchcrawl3d. 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 -):
-ref OR -ReferenceFile File name
Reference image file that is being aligned to
-align OR -FileToAlign File name
Image file that will be transformed into alignment
-output OR -OutputFile File name
Output file for patch displacements
-region OR -RegionModel File name
Model file with contours enclosing regions to take patches from
-size OR -PatchSizeXYZ Three integers
Size of patches in X, Y, and Z
-number OR -NumberOfPatchesXYZ Three integers
Number of patches in the X, Y and Z directions
-xminmax OR -XMinAndMax Two integers
Starting and ending X coordinates of region to take patches from. X, Y,
and Z coordinates are numbered from 1.
-yminmax OR -YMinAndMax Two integers
Starting and ending Y coordinates of region to take patches from
-zminmax OR -ZMinAndMax Two integers
Starting and ending Z coordinates of region to take patches from
-taper OR -TapersInXYZ Three integers
Number of pixels over which to taper the patches in X, Y and Z. The
default is 10% of the patch dimensions.
-pad OR -PadsInXYZ Three integers
Number of pixels to pad each side of the patch in X, Y, and Z for Fourier
correlations . The default is 20% of the patch dimensions.
-maxshift OR -MaximumShift Integer
Maximum displacement to determine by searching. This is in addition to
the local offset determined from adjacent patches. The default is 10.
-volume OR -VolumeShiftXYZ Three floats
Overall displacement of the volume being aligned 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 aligned. This shift is excluded from the shifts
reported in the output file. If no volume shift is entered, it is set
equal to half the difference in size between the two volumes, if any.
-initial OR -InitialShiftXYZ Three floats
Initial displacement between the center of the volume being aligned and
the center of the reference volume in X, Y, and Z. This is the amount to
add to the coordinate of a feature near the center of the reference volume
to obtain the coordinate of the same feature in the file being aligned,
after accounting for any overall volume displacement entered with -volume.
This shift will be used to start the search and will be included in the
shifts reported in the output file.
-bsource OR -BSourceOrSizeXYZ Text string
File name or X, Y and Z size of source of file being aligned. This size
must be entered if a 3-D transformation is supplied; otherwise the size of
the file being aligned is used.
-bxform OR -BSourceTransform File name
File with 3-D transformation that was used to generate the file being
aligned from its source file.
-bxborder OR -BSourceBorderXLoHi Two integers
Size of borders to be excluded on the lower and upper sides in X in the
original source volume for the file being aligned
-byzborder OR -BSourceBorderYZLoHi Two integers
Size of borders to be excluded on the lower and upper sides in Y or Z
(whichever is the longer dimension) in the original source volume for the
file being aligned.
-bregion OR -BRegionModel File name
Model file with contours enclosing areas in the original source volume for
the file being aligned that are suitable for correlation.
-kernel OR -KernelSigma Floating point
Sigma for real-space smoothing with 3D Gaussian kernel (in pixels). The
smoothing is with a 3x3x3 or 5x5x5 kernel whose coefficients are
proportional to a Gaussian with the given sigma centered on the central
pixel. Each patch from the first volume is smoothed before being used for
either the correlation search or a Fourier correlation.
-ksize OR -KernelSize Floating point
Size in pixels of the 3D Gaussian kernel used for real-space smoothing.
The size can be either 3 or 5. The default is 3 for a kernel sigma below
1.5 and 5 for larger sigmas since the filtering reaches a point of
diminishing returns at about this sigma with a size of 3.
-lowpass OR -LowPassRadiusSigma Two floats
Cutoff radius and sigma for a low pass filter that imposes a
high-frequency Gaussian roll-off in the Fourier cross-correlations. The
default is no high-frequency filtering.
-sigma1 OR -HighPassSigma Floating point
Sigma value to filter low frequencies in the Fourier correlations with a
curve that is an inverted Gaussian. This filter is 0 at 0 frequency and
decays up to 1 with the given sigma value.
-messages OR -FlipYZMessages
Exchange Y and Z in error messages if Y is short dimension
-debug OR -DebugMode Integer
Set to 1 for debugging output, 2 to obtain a dummy patch output file to
assess the positions of the patches, and 3 to do Fourier correlations at
all positions, plus direct correlation searches wherever possible. In the
latter case each line of the patch output file will have the results from
the Fourier correlation, followed by the results from direct correlation,
ending with a 3D distance between the two results.
-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.
If the program is started with no command line arguments, it reverts to
interactive input with the following entries:
Name of reference image file being aligned to
Name of image file that will be transformed to match
Name of output file for patch positions and displacements
Name of a temporary file for output from onepatchcorr
Name of a model file with contours that enclose the areas where
patches should be analyzed, or Return to analyze patches at all
locations
Size of patches in X, Y and Z
Number of patches in the X, Y and Z directions
Size of borders to be excluded on the lower and upper sides in X,
the lower and upper sides in Y, and the lower and upper sides in Z
Number of pixels over which to taper the patches in X, Y and Z
Maximum displacement to determine by searching
Either the X, Y, and Z size or the name of the original source
volume for the second image file. Return to omit analysis of
positions in this file.
Name of the 3-D transformation file used to generate the second
image file from its source volume, or Return to omit analysis of
positions in the second file.
Size of borders to be excluded on the lower and upper sides in X
and the lower and upper sides in Z in the original source volume
for the second image file.
HISTORY
Written by David Mastronarde 7/16/01
7/20/02: Added analysis of areas to exclude based on positions in the
source for the second volume
8/16/06: Converted to PIP, incorporated FFT correlations internally,
added filtering, made it extract the B patches based on the local
shift instead of using the same coordinates in both volumes,
added model file for B and initial displacement, handled volumes
in both orientations.