dontcha love it —
” In our opinion, the problem is so vast and severe that the damage caused by the users’ processing of the data can easily over-shadow any measurement imperfections, ruining instrumentation improvements and rendering them potentially worthless.” This is a quote from a paper entitled “Study of user influence in routine SPM (scanning probe microscopy) data processing” D Nečas and P Klapetek, (I recognize the names and email addresses of these individuals from Gwyddion support groups and comments) in Measurement Science and Technology. “eye roll” I appreciate the sentiment, and I join the voices that comment. I know it is disappointing to have tools not used “properly”, and from my perspective however, coming from an interest in scientific diagramming, particularly  looking at the countless diagrams about  tissues, cells, cell structures, organelles, protein cascades, signaling pathways and all things relational. While the comments might need to be said, and I will say them as well, this doesn’t make what we attempt to do as we image TEMs AFMs and other images “worthless” but what it does do is make us vigilant.

Comparisons before and after processing are all that is needed here and that goes with common good practice in any branch of science.
One quote from this aper — “Finally, just selecting the right tools for the data analysis task also seems to be a key issue. Here, better SPM education, training and documentation would probably help;” comes to the main purpose of my looking at various software applications to examine countless images of, from various researchers, of SP-D and DMBT1. I have concluded that the processing is just an aid to the eye, not the reverse.

COMMENT:  After 8 more months of trying to produce an informative diagrammatic model  — using “image processing” of SP-D images produced with AFM, and beginning the use “signal processing of the plots” (another story) and having a much better understanding of Gwyddion software as a mechanism to do this, I would probably add emphasis to the value of up front “documentation” of every possible use and misuse of processing software.  Not everyone will spend the time to do this… and while doing this with Gwyddion i did find huge difficulties in creating a “line” through molecules to get grayscale plots along that line. In fact there was a gross misrepresentation of grayscale plots because if my inability (or perhaps it wasn’t easily found in their software) to draw a freehand or segmented line through the molecules.  In addition, and more seriously, the lines i drew vertically were grossly skewed when plotted.   So  one does need to be “awake” or in the current vernacular “woke” to such errors in processing.