1) The Y axes on these plots are what are generated by ImageJ…. so the y axis apparently depends upon what kind of raster file I have used to get the luminance plots that ImageJ can detect. All y axes can be (should be) normalized either to 0-100 % or to 0-255 grayscale. I don’t know if it matters, but I believe most of the existing hundreds of excel plots have 0-255 (sometimes 300) as their Y axes. THE HEIGHT depends upon all the image factors, including the brightness and ppi of the original image.

2) The X axis is variable as well, SP-D molecules just fall as they may when they are dropped onto the mica grid so there are short arms, twisted arms, touching arms, bent arms, stretched etc etc. Distance of the entire molecule i have measured as a “diameter” defined by any circle that touches three of the four edges of the cross shaped molecule. I would like the x axis to be a composite number (in nanometers) of every arm I have measured (for each microscopic technique). I haven’t gotten that final number yet, but it will be very close to 135nm with a few nm SD. So All the plots need to be adjusted to that X axis.

3) The MAIN goal here is to normalize all the plots that i have and determine mean number of peaks (with some statistical measure of likelihood) from one side of the dodecamer to the other….. and then a) find the width of each set of peaks…. b) the relative height of each set of peaks,