Peak counts of a single surfactant protein D molecule (an AFM image): signal processing programs: PeakValleyDetectionTemplate-xlsx uses a program by Thomas O’Haver. I found that the best results for the plots of surfactant protein D were found using a smooth level of 11.  In the results below, 10 of the 12 image processing programs that I have used to determine the number of peaks along a segmented line drawn through the center of surfactant protein D (hexamer) arms were “peak counted” with this excel program.  The peaks counted at the value of smooth 11 was in line with counts made directly from the images, and with other signal processing programs.  This peak counting program was the easiest (in my opinion) to use and it exported a plot with valleys marked making it very easy to come up with a graphic identifying the position (width and height) of peaks.

Sample plot above, peak count from ImageJ plot and peak count using PeakValleyDetectionTemplate.xlsx smooth 11.

Below, examples of smooth 5,7,9,11 and 15.  Smooth 11 varations and combinations of the image processing plots were used.