icon under the left image — this briefly switches between the two images. The linear correction is based on the evaluated shift between the two images, provided that the pause between the two acquisitions was minimal. The drift is assumed to be constant, therefore affecting equally both images in the original and rotated oriuentation. Then, the affine transformation is applied to correct for images shear and contraction / extension
It is very important to determine whether your images are atomically resolved before starting correction. The shift is evaluated differently for different resolutions. FFT analysis is used for atomic-resolution images, while cross-correlation is used for lower-resolution images. The FFT method does not work for low-resolution images, while cross-correlation for high-resolution images is reasonable only if a clearly recognizable pattern exists on top of the atomic lattice.
After choosing the appropriate method, press .
The corrected images are displayed at the left and right windows. You can visualize how they fit each other. Just click the small icon under the left image — this briefly switches between the two images.
The affine transformation changes the image size. Between the left and right windows, there is a "frames" icon 
that allows you to view the results in different frames.
Initially, the display retains the original image size, cutting off some edges. The first click shows the complete (largest) view of both images. The second click shows the minimal area, i.e. a rectangle with no out-of-image pixels. Further clicks cycle through these views.
The current image width and height (in pixels) are displayed in the bar between the windows.
There are few settings to control the linear correction that you can access via Menu:
Cross correlation might show several peaks, therefore offering several variants for aligning images. This is especially pronoinced for atomic resolution images. It is important to chooze the nearest to the origin peak, i.e. chooze the minimal shift. You limit a shift via
Menu Setting → Linear →Proceed → cross-C → shift limit.
The value should range from 0.0 to 1.0 defining the maximal shift in the fraction of the total image size.Menu Setting → Linear → Proceed → cross-C → show.
Whether to show or not the cross-correlation after performing linear correction.If you mostly operate with atomic-resolution images, you might set "use FFT" as default. Go to
Menu Setting → Proceed → Linear → use FFT.
Then you do not need to activate this switch at each new tool launch.
Menu Setting → Proceed → Linear → FFT → spot radius.
The position of a pseudo-diffraction spots in FFT is determined with the sub-pixel precision. This number defines the radius (in pixels) outlined around the spot rough position in order to calculate its center-of-mass.
Menu Setting → Proceed → Linear → FFT → show,
If this is activated, the FFTs for the left and right images will appear after the linear correction. Two major spots used for calculation are marked at both FFTs. Their positions is used to determine the mutual distortion between images, and therefore the direction and magnitude of the shift.
After the affine transforation, certain out-of-image areas will apear at the edges of both images. The value in Menu Setting → Proceed → Linear → fill value defines how to fill these areas. The value should range from 0.0 to 1.0 where 0 means filling with the minimal value of images, 1.0 - maximal value and 0.5 - the average value of the raw images.
The evaluated shift can sometimes appear unreasonably large. The warning message is issued if the shift exceeds the predefined fracture of the image size in Menu Setting → Proceed → Linear → warning shift. This message indicates that the user should probably change the method of correlating images, for instance, change a "use FFT" switch or set a stick points. The message is solely for your information and you can disable it by setting a large value in this field.
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