Automatic stack alignment

The automatic alignment routine attempts to align images by cross-correlations using Fourier transforms. If you have lots of similarly-shaped features in your images, then you may want to align based only on a subregion of the image and limit alignment searches to some finite pixel shift from image to image (30 is a reasonable number). Remember that when you select a subregion, you have to allow for the fact that the borders of the subregion will be smoothed with a Gaussian of 4 pixels (i.e., make the subregion larger). The alignment widget is shown in Fig. 11. Two images are displayed:

• The left window shows each image after it has been aligned.
• The right window shows the cross-correlation image.

The options you have in the menu are:

• You can choose to edge-enhance each image before alignment using the IDL sobel or roberts routines. A good procedure seems to be to first align without edge-enhancement. You can then specify a sub-region of the image, limit the alignment shift to be no more than perhaps 5 pixels, and re-run the alignment with the sobel option.

• You can choose to align all images to a constant image (recommended; it's best to pick the highest contrast, sharpest image), or to the image which preceded them. The latter choice is likely to suffer from error accumulation.

• You can identify the cross correlation point either by finding the position of the peak value, or by calculating the center of mass in the region of the peak. The X-cor peak usually works best. Note that you are much more likely to get a good alignment if you select a small subregion in the reference image which has a well-recognizable, high resolution, high contrast feature, as is shown in the screen snapshot above.

• You can constrain the shift of the center point to be no more than $n$ pixels. This is useful for cross-correlation alignment when you have contrast reversals in the image.

• You can also skip alignment by clicking on the Skip alignment button.

As the alignment runs, it shows you a plot of the drift of the center position of the images. When alignment is complete, the Skip alignment changes to Complete; go to stack_analyze and all other buttons become insensitive.

Figure 11: The automatic alignment widget.