I use the extract profile option and draw a line on the image. I get line profile as y-x plot but I can't understand it. Shouldn't it be z-x plot for a horizontal line?
If you are willing to switch from Image Plus I would highly recommend downloading Gwyddion, it an excellent free AFM image post-processing software and makes it very simple to get height profiles/3d images/etc.
You can get it here:
http://gwyddion.net/
Gwyddion is really good. But You can also try WSxM from Nanotec which is free and powerful as well: http://www.nanotec.es/products/wsxm/
Dear followers
I used both Gwyddion and WSxM softwares. as I mentioned in my question Gwyddion gives a y-x plot for extracting a profile. is y height of data points vs. their positions (x)? However, WSxM gives z-x plot. is z here height vs. position (x)? Are the plots from Gwyddion and WSxM same?
Yes, they are the same: Z vs X (WSxM) and Y vs X (Gwyddion). You can easily distinguish it, by values you have on Y or Z axes I suppose.
How I can calculate the number of gold nanoparticles from AFM image accurately?
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