The correction algorithm may make foults, for instance not distinguish two sublattices, especially if the difference in atoms intensity is not large.
It is a good idea to guide the algorithm by setting so called Sticking Points , points that are supposed to be same in both original and rotated images.
For example, you may correct the half-unit cell shift appearing in the example discussed in Processing Flow .
Go to the processing step before merging (square button — State ) and press .
Two red circles appear in the left and right images. They are supposed to mark the same structural motif, but they do not — brightest and weakest atoms are interchanged. This clearly shows the half-period shift.
To fix it, drag one circle to a recognizable pattern. The second circle moves synchronously, which is not desired. Uncouple the circles using the switch at the lower-left of the tool. Then place the second circle on the same motif and click .
Then press again and observe the improved result. The sublattices are now clearly recognized.
Such guiding sticking points can be set at different stages of processing:
Note that the size of red circles can be changed by up- and down- arrows in the sticking control panel. This not only improves the visibility of sticking points but also affects processing. You are not obliged to drag the sticking points with a pixel precision - the tool can tune it automatically. And the size of the red circles defines the size for cross-correlation in this fine alignment.
You can control few options related to the sticking points via:
Menu Setting → Reference → Stick → stick size.
Default (initial) size of the circles around the sticking point
Menu Setting → Reference → Stick → fine stick.
Enable or disable the cross-correlation to refine the position of the sticking point within the red circle. This switch should be typically on for atomic resolution images but should be disabled if there are no clearly recognizable structure inside the red circle.
Fine cross-correlation is useful for atomic-resolution images if there are few atoms inside the circle. However, not use fine correction if there are no recognizable features inside the circle. That would result in random shift of the manually set sticking point.
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