Module: Smooth

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:

Calculate artifact diameter automatically?

(Used only if "Gaussian Filter", "Median Filter", "Smooth Keeping Edges" or "Circular Average Filter" is selected)
Select Yes 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 image.