Smoothing methods


#1

Hi,

In the SmoothOrEnhance module, can you explain what the advantage of the median filter method over the “smooth keeping edges” filter is, or vice versa? In what cases might you use one rather than the other? Thanks.

Greg


Measuring the length of tight junctions
#2

Hi Greg,

Median filtering in SmoothOrEnhance uses Matlab’s medfilt2 (two-dimensional median filter). Each output pixel contains the median value in the neighborhood specified by the filter size in the SmoothOrEnhance settings. Median filtering is recommended for smoothing illumination correction functions- it tends to preserve more intensity information than the Gaussian or FItPolynomial options, which smooth the image more.

SmoothKeepingEdges is an implementation of a bilateral filter. The image is smoothed while preserving edge information. This option is recommended if you want to smooth but preserve not just intensity but also edge information. Probably not the case in illumination correction functions, but maybe in brightfield images of yeast colonies or worms on agar, for example, where the background shadows need to be smoothed, but the foreground object edges need to be preserved for segmentation.

-Kate