PC3193: Scanning Tunneling Microscope - Manipulating HOPG scans with Gwyddion for lattice dimensions.

If you have had the misfortune of using the Nanosurf STM, you would no doubt be struggling to achieve a clean atomic resolution scan with your terrible self cut Pt/Ir tips.

Fret not. A shitty scan is all you need.

Look at this ugly beast, blegh. Open it in Gwyddion and select the topology channel.

Choose a funkalicious colour gradient that gets your jive on. Here’s a personal favourite.

But since this doesn’t fly with THE MAN, choose Gwyddion.net.

1 - Median Line Correction

2 - Remove Scars

3 - Remove polynomial background

4 - Shift min. data value to zero

5 - Correct affine distortion

Choose 2D ACF & HOPG preset (NOTE: your integrity is tested here, more on this later)

Adjust the grid to fit as well as you can, then hit Refine to get it spot on. If refine fails to get it perfect, retry and do a better job fitting it.

Spank the OK button

6 – 2D auto correlate function

Colour it. Take a moment to notice that it is ugly as heck.

I’m sure you are thinking this:

“Wow, so ugly, why didn’t I just 2D ACF’ed the picture before doing that Affine distortion crap, YOU LYING FIEND!”

Fret not, see, without Affine Distortion, the 2D ACF would give a nice picture with bad results. Observe.

Gross... What about the corrected one?

Nice results, BUT the affine correction overwrites the original image's scale info if you have chosen the "Exactly as specified option" which was used in the example shown. Thus giving you perfect results, at the cost of your integrity.

So either get your scanning angle adjustment right when taking the scan, or just use the "Preserve X scale" option.

K bye.

Excerpt from Gwyddion's web manual:

It should be noted that the correction method described above causes all lateral scale information in the image to be lost because the new lateral scale is fully determined by the correct lattice vectors. This is usually the best option for STM images of known atomic lattices, however, for a general skew or affine correction it can be impractical. Therefore, the dialog offers three different scaling choices:

Exactly as specified

Lattice vectors in the corrected image will have the specified lengths and angle between them. Scale information of the original image is discarded completely.

Preserve area

Lattice vectors in the corrected image will have the specified ratio of lengths and angle between them. However, the overall scale is calculated as to make the affine transformation area-preserving.

Preserve X scale

Lattice vectors in the corrected image will have the specified ratio of lengths and angle between them. However, the overall scale is calculated as to make the affine transformation preserve the original x-axis scale. This is somewhat analogous to the scale treatment in Drift compensation.