Smooth smooths (i.e., blurs) images.
This module allows you to smooth (blur) images, which can be helpful to remove artifacts of a particular size. Note that smoothing can be a time-consuming process.
Select smoothing method
This module smooths images using one of several filters.
Fitting a polynomial
is fastest but does not allow a very tight fit compared to the other methods:
- Fit Polynomial: This method treats the intensity of the image pixels
as a polynomial function of the x and y position of
each pixel. It fits the intensity to the polynomial,
A x2 + B y2 + C xy + D x + E y + F.
This will produce a smoothed image with a single peak or trough of intensity
that tapers off elsewhere in the image. For many microscopy images (where
the illumination of the lamp is brightest in the center of field of view),
this method will produce an image with a bright central region and dimmer
edges. But, in some cases the peak/trough of the polynomial may actually
occur outside of the image itself.
- Gaussian Filter: This method convolves the image with a Gaussian whose
full width at half maximum is the artifact diameter entered.
Its effect is to blur and obscure features
smaller than the artifact diameter and spread bright or
dim features larger than the artifact diameter.
- Median Filter: This method finds the median pixel value within the
artifact diameter you specify. It removes bright or dim features that are much smaller
than the artifact diameter.
- Smooth Keeping Edges: This method uses a bilateral filter which
limits Gaussian smoothing across an edge while
applying smoothing perpendicular to an edge. The effect
is to respect edges in an image while smoothing other
features. Smooth Keeping Edges will filter an image with reasonable
speed for artifact diameters greater than 10 and for
intensity differences greater than 0.1. The algorithm
will consume more memory and operate more slowly as
you lower these numbers.
- Circular Average Filter: This method convolves the image with
a uniform circular averaging filter whose size is the artifact diameter entered. This filter is
useful for re-creating an out-of-focus blur to an image.
- Smooth to Average: Creates a flat, smooth image where every pixel
of the image equals the average value of the original image.
Calculate artifact diameter automatically?
(Used only if "Gaussian Filter", "Median Filter", "Smooth Keeping Edges" or "Circular Average Filter" is selected)
to choose an artifact diameter based on
the size of the image. The minimum size it will choose is 30 pixels,
otherwise the size is 1/40 of the size of the image.
Select Yes to manually enter an artifact diameter.
Typical artifact diameter
(Used only if choosing the artifact diameter automatically is set to "No")
Enter the approximate diameter (in pixels) of the features to be blurred by
the smoothing algorithm. This value is used to calculate the size of
the spatial filter. To measure distances in an open image, use the "Measure
length" tool under Tools in the display window menu bar. If you click on an image
and drag, a line will appear between the two endpoints, and the distance between them shown at the right-most
portion of the bottom panel.
For most smoothing methods, selecting a
diameter over ~50 will take substantial amounts of time to process.
Edge intensity difference
(Used only if "Smooth Keeping Edges" is selected)
Enter the intensity step (which indicates an edge in an image) that you want to preserve.
Edges are locations where the intensity changes precipitously, so this
setting is used to adjust the rough magnitude of these changes. A lower
number will preserve weaker edges. A higher number will preserve only stronger edges.
Values should be between zero and one. To view pixel intensities in an open image, use the
pixel intensity tool which is available in any open display window. When you move
your mouse over the image, the pixel intensities will appear in the bottom bar of the display window.
Clip intensities to 0 and 1?
(Used only if Fit Polynomial is selected)
The Fit Polynomial
method is the only smoothing option that can yield
an output image whose values are outside of the values of the
input image. This setting controls whether to limit the image
intensity to the 0 - 1 range used by CellProfiler.
Select Yes to set all output image pixels less than zero to zero
and all pixels greater than one to one.
Select No to
allow values less than zero and greater than one in the output