After analyzing about 7 AFM images of SP-D dodecamers using the process of isolating the parallel arms, cutting into about 1.6 nm slices  (that is around 62 slices per 100 nm SP-D molecule) and exporting to tiff (below is a comparison of the LUT from export as tiff vs export as jpg as analyzed in ImageJ) the plots are nice and they seem to represent quite accurately the number of “hand counted” bright peaks in each of the dimer-arms but clearly the export to jpg includes the “slices” which doesn’t happen with export to tiff.

I have not figure out yet how to blend the four arms into a single value per dodecamer, but that might actually not be necessary.  At any rate, the next comparison will be with the shadowed SP-D dodecamers.  It works really well on curved molecules…  though It is required to expand the plots to a set 100nm this doesn’t change the number of peaks along each arm but will affect the distance measured for each bright spot (including the center).