FFT Cross-Correlation
The FFT Method of image alignment is the fully automated method of image alignment. Using this method, you can align image data in a sequence of frames/images with the click of a button. This method is accessed from the FFT Method tab of the Align dialog box.
To use the FFT Method of image alignment:
- Add the images you want aligned to the Selected Images list box.
- Configure the auto-alignment routine by using the various FFT Method controls (described below).
- Click Calculate (to calculate the transform values without creating an image) or click Apply to create a new sequence file with the alignment-corrected frames.
The following controls can be used to 'tune' the auto-alignment routine:
Rotation: Check this box to have Image-Pro evaluate the images/frames for possible misalignment due to rotation and to calculate rotation values to correct for it. For example, if it is possible that an image/frame in the stack will have to be slightly rotated clockwise or counterclockwise in order to align it to the other images, then this option should be checked. If you do not check this box, Image-Pro will ignore rotation as a possible factor in the misalignment of image data.
- accuracy 1/: This control lets you choose how many angles to test. Rotation can be +/- 90 degrees. This range is divided by the number of angles to test. Higher numbers will require more computation and higher accuracy. Note that these must be power of 2 factors for the FFT algorithms.
Scaling: Check this box to have Image-Pro evaluate the images/frames for possible misalignment due to scaling and to calculate resize values to correct for it. For example, if it is possible that an image/frame will have to be slightly enlarged or reduced in order to align it to the other images, then this option should be checked. If you do not check this box, Image-Pro will ignore scaling as a possible factor in the misalignment of image data.
- accuracy 1/: This control lets you choose how many scales to test. Scaling is possible over a range of about 0.7x to 1.4x (1x being no scaling at all). This range is divided by the number of scales to test. Higher numbers will require more computation and higher accuracy. Note that these must be power of 2 factors for the FFT algorithms.
Translation: Check this box to have Image-Pro evaluate the images/frames for possible misalignment due to shifts on the X or Y plan and to calculate 'translation' values to correct for it. For example, if it is possible that an image/frame will have to be slightly shifted left, right, up, or down in order to align it to the other images, then this option should be checked. If you do not check this box, Image-Pro will ignore translation as a possible factor in the misalignment of image data.
The max size control defines the maximum size of cross-correlation area used for calculation of the alignment (in pixels). The alignment area is in the center of the image. Limiting this size can speed up the alignment.
Subpixel Accuracy: Check this box to calculate alignment between images with subpixel accuracy (default). Use this option when images have small shifts comparable with pixel size. The option can be used for drift correction. Note, that when this option is on, the output images are created with sub-pixel image shifts using affine transform with bi-linear approximation.
Full/Phase Correlation: Select one of these radio buttons to perform the FFT translation correlation as a full correlation or as a phase-only correlation. Full correlation works better for most images. Phase-only correlation ignores image intensity, and may be preferable if the overall image intensities vary while the patterns remain similar.
Calculate: Click the Calculate button to get transform values (the calculated offset, rotation, and scaling values needed for each image in order to align them) without creating an image. The transform values can then be adjusted or saved in the Manual Method tab.