If I count peaks along a segmented line in ImageJ and the the numbers are the same between two images but the plots show different results, what does that say about visual assessments about AFM images vs those which are digitally manipulated.

I understand the sensitivity of programs, some plots show every pixel, very noisy, but is this relevant information. It is possible to smooth out that noise, it is done in many different applications all the time. Is smoothing the noise helpful.  Here are two images, plotted in ImageJ, the one on the left enhanced with a color height map, the one on the right proccessed many times in three programs. Both image however present to the “eye” seven peaks.  The image on the right was processed thusly:

Original color-height map image where distortion was corrected in photoshop with edit>transform>skew, exported as a tiff, imported into gwyddion where an integral transform>CWT-5px-gaussian was performed, then in photoshop converted to grayscale, contrast enhanced and an additional 10px gaussian filter was applied as well as an unsharp mask at 50% amount, 50px radius, level of threshold=0.