Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
CCDERASER(1) CCDERASER(1)
NAME
ccderaser - erase X-rays, defects and fiducial markers from images
SYNOPSIS
ccderaser [options] [input_file] [output_file]
DESCRIPTION
This program replaces deviant pixels with interpolated values from
surrounding pixels. It is designed to correct defects in electron
microscope images from CCD cameras. It can use two algorithms to
automatically remove peaks in intensity caused by X-rays. It can also
take an IMOD model file with specifications of regions to be replaced; in
this mode it can be used to erase gold fiducial markers. With a model,
the program can replace a group of adjacent pixels with interpolated
values, or all of the pixels along a line. It can do this on only a
specific image, or on all of the sections in the file. The program can
operate in trial mode, without making an output file, and it can output a
model file with points at the pixels to be replaced.
AUTOMATIC X-RAY REMOVAL: The automatic removal of X-rays works by dividing
the area of each image into patches for scanning. The mean and standard
deviation (SD) of the pixels in a patch are computed. The patch is then
scanned for pixels that deviate from the mean by more than a criterion
number of SDs (the scan criterion, a relatively low number to keep from
missing peaks). When such a pixel is found, the program searches
neighboring pixels to find a peak in intensity. It then computes the mean
and SD of pixels in an annulus around the peak and makes sure that the
peak deviates from this local mean by more than a criterion number of SDs
(the peak criterion). Neighboring pixels inside the inner radius of the
annulus are added to the list of pixels to be replaced if they deviate by
a lower criterion (the grow criterion). The patch of pixels is then
replaced by fitting a polynomial to adjacent pixels and interpolating from
the polynomial.
After the peaks are found in a patch, the program next finds the
difference between each pixel and the mean of the eight adjacent pixels.
The mean and SD of this difference is computed, then pixels are sought
that deviate from the mean by yet another criterion, the difference
criterion. When such a pixel is found, neighboring pixels are examined
and added to the patch of pixels to replace if their difference exceeds
the grow criterion. If the number of pixels in the patch does not exceed
a specified maximum, replacement proceeds as above; otherwise the patch is
ignored.
Two methods are used because the first method is probably more reliable
for dealing with strong peaks that extend over several pixels, while the
second method is definitely better for finding small X-rays.
Tuning the removal of X-rays would primarily involve adjusting three of
the criteria. The peak and difference criteria would be adjusted down or
up to increase or decrease the number of deviant pixels that are found.
The grow criterion would be adjusted down or up depending on whether too
few or too many pixels are included in a patch that is replaced.
MANUAL REMOVAL OF DEFECTS AND MARKERS: For manual removal of defects,
prepare an IMOD model file to specify the points to be replaced. There
can be four kinds of objects:
1) Pixel objects, in which there is a point inside of every pixel to be
replaced, and each contour corresponds to a separate patch of points.
2) Boundary objects, in which each contour encloses a separate patch of
pixels to be replaced.
3) Line objects, in which each contour defines a horizontal or vertical
line of points to be replaced.
4) Circle objects, used to replace pixels in a circle around each point.
Pixel, boundary, and line objects can be applied either on the section
where they are drawn, or on all sections. For example, one might have two
different pixel objects, one for patches to be replaced on a single
section and one for patches to be replaced on all sections.
TO set up a pixel object, make the object type be scattered points, and
turn on drawing of circles, but leave the sphere radius at zero. To
specify a patch of points, start a new contour and place a point inside of
EVERY pixel in the patch. Each separate patch should be in a
separate contour. If the correction is to be made on only a single
section, all of the points must lie on that section; but the points for a
patch to be corrected on all sections can be on more than one section,
because sometimes they are more discernable on particular sections.
A boundary object should be the default, closed contour type. Draw a
contour around each patch of pixels to be erased. A pixel is will be
included in the erasure if its center is inside or on the boundary line.
A line object should be closed or open contour type. To specify a line of
points, make a contour with two points, at the start and end of the line
to be replaced. Lines must be horizontal or vertical. Each pixel will be
replaced by the average of the two pixels on either side of the line. Put
each line in a different contour. Ajdacent lines will be detected and
erased together.
To set up a circle object, make the object type be scattered points, set
the sphere radius to an appropriate value, and check the option to display
spheres only on their center section. If necessary, you can give some of
the points sizes that are different from the default by opening a dialog
with Edit-Point-Size. A pixel will be replaced if its center lies inside
or on the circle. For small radii, the fact that the default sphere
radius is constrained to an integer may be a problem; if so, use the
-better option to enter a floating point default radius for Ccderaser to
use. For using circle objects to remove gold markers, -merge should also
be used so that adjacent markers are removed together, and -exclude will
help keep dark pixels just outside the circle from making the filled in
region too dark.
Ccderaser uses the PIP package for input (see the manual page for pip)
and can take input interactively only for specifying manual replacement
with a model file, to maintain compatibility with old command files. 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 image file. This may also be entered after all arguments on the
command line.
-output OR -OutputFile File name
Output image file. This may also be entered after an input file name on
the command line. If no output file is specified and the program is not
run in trial mode, pixels will be replaced in the input file. USE
REPLACEMENT OPTION WITH CAUTION.
-find OR -FindPeaks
Find and erase peaks a criterion # of SDs above or below background. This
option must be included for automatic removal of X-rays.
-peak OR -PeakCriterion Floating point
Criterion # of SDs above local mean for erasing peak based on intensity
(the default is 10 SDs).
-diff OR -DiffCriterion Floating point
Criterion # of SDs above mean pixel-to-pixel difference for erasing a peak
based on differences (the default is 10 SDs)
-grow OR -GrowCriterion Floating point
Criterion # of SDs above mean for adding points to peak (the default is 4
SDs).
-scan OR -ScanCriterion Floating point
Criterion # of SDs of mean of scan area for picking peaks in initial scan
(the default is 3 SDs).
-radius OR -MaximumRadius Floating point
Maximum radius of peak area to erase (the default is 2.1 pixels).
-maxdiff OR -MaxPixelsInDiffPatch Integer
Maximum number of pixels in a patch that exceeds the difference criterion.
If the number of pixels that satisfy the criteria exceed this limit, none
of the pixels in the patch will be replaced. The default is 2.
-outer OR -OuterRadius Floating point
Outer radius of annulus around a peak in which to calculate local mean and
SD (the default is 4.1 pixels). This option and -width are mutually
exclusive.
-width OR -AnnulusWidth Floating point
Difference between outer and inner radius of the annulus around a peak in
which to calculate local mean and SD (the default is 2.0 pixels). This
option and -radius are mutually exclusive.
-xyscan OR -XYScanSize Integer
Size of regions to compute mean and SD in for initial scans (the default
is 100 pixels).
-edge OR -EdgeExclusionWidth Integer
Width of area to exclude on all edges of image in pixels (default 0).
-points OR -PointModel File name
Output model file with points replaced in peak search. Each patch of
points will be in a separate contour. Patches are sorted into separate
objects based on how much the peak exceeds a criterion.
-model OR -ModelFile File name
Input model file specifying points or lines to be erased.
-lines OR -LineObjects List of integer ranges
List of objects that define lines to be replaced. Ranges can be entered,
and / to specify all objects.
-boundary OR -BoundaryObjects List of integer ranges
List of objects that contain boundary contours around pixels to be
replaced. Ranges can be entered, and / to specify all objects.
-allsec OR -AllSectionObjects List of integer ranges
List of objects with points to be replaced on all sections. Ranges can be
entered, and / to specify all objects.
-circle OR -CircleObjects List of integer ranges
List of objects that contain scattered points for replacing pixels within
a circle around each point. The sphere radius, which can be an individual
value for each point, is used to indicate the size of circle to replace.
Ranges can be entered, and / to specify all objects.
-better OR -BetterRadius Multiple floats
For circle objects, this entry specifies a radius to use for points
without an individual point size instead of the object's default sphere
radius. This entry is floating point and can be used to overcome the
limitations of having an integer default sphere radius. If there are
multiple circle objects, enter one value to apply to all objects or a
value for each object.
-merge OR -MergePatches
Merge patches in the model if they touch each other, as long as the
resulting patch is still within the maximum radius. Patches from objects
with points to be replaced on all sections are ignored. This option
should be used if an output model from automatic peak finding is modified
and used as an input model.
-border OR -BorderSize Integer
Size of border around points in patch, which contains the points which
will be fit to (the default is 2 pixels)
-order OR -PolynomialOrder Integer
Order of polynomial to fit to border points (the default is 2, which
includes terms in x, y, x**2, y**2 and x*y).
-exclude OR -ExcludeAdjacent
Exclude points adjacent to patch points from the fit; in other words,
compute the polynomial fit to points that do not touch the ones being
replaced.
-trial OR -TrialMode
Analyze for replacement points without writing output image file.
-verbose OR -verbose
Print details on patches being replaced
-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:
Input image file
Output image file, or <Return> to place modified sections back into
the input file. USE REPLACEMENT OPTION WITH CAUTION
Model file
A list of objects which specify points or lines to be replaced on
all sections, or / if all objects do so, or Return if none do.
Ranges may be entered.
A list of objects which specify lines to be replaced, or / if
all objects do so, or Return if none do. Ranges may be entered.
Size of the border around the points in a patch, which contains the
points which will be fit to (/ for default of 2 pixels)
Order of polynomial (/ for default of 2, which includes terms in
x, y, x**2, y**2 and x*y)
0 to exclude or 1 to include points adjacent to the points being replaced
in the polynomial fit (/ for default of 1)
HISTORY
Written by David Mastronarde 11/10/98
Automatic X-ray removal and pioneer use of PIP input, 6/9/03