The Align function will match the positions of 4 to 20 star pairs between the two images to a small fraction of a pixel (typically). Align accounts for differences in scale, rotation (up to +/- 60 deg), row shift and column shift.
When invoked, Align asks for how many star pairs to use. Four is usually sufficient. Image A is shown and you must select your first star. Flip between the A and B images using the A and B keys to be sure you can identify the matching star in the B image. If there is a lot of difference between the two images, this can be tricky. Position the cursor box so that the target star is within the box and press P ('Point' or 'Position'). JIMSAIP will locate the centroid of the star's position. Press the N key ('Next') and JIMSAIP will switch to the B image. Locate the star in the B image that corresponds to the one selected in the previous step in the A image. Position the cursor box over the target star and press P. Press the N key to complete the pair measurement.
JIMSAIP will return you to the A image to repeat the process until you have completed the number of star pairs you selected in the beginning. If you get confused, or for any other reason, you can abort the process by pressing the Q key ('Quit') at any time before the accepting the last star.
Upon completing the last star pair, JIMSAIP will calculate the alignment factors in a fraction of a second and will display the errors between the measured and predicted positions of each star pair in the order in which they were taken. Typically you will see the errors are less than 0.05 pixel. If you see significantly greater errors, it probably means you mis-matched one or more star pairs.
Pressing any key will next show you the results of the calibration. The average error among the alignment stars will be shown as will the scale factor between the images, the rotation, the row and column shifts.
Pressing any key will cause JIMSAIP to resample the image in the A buffer to match the image in the B buffer. After the resampling, the new A image will be displayed and you can toggle between the A and B images using the A and B keys to see the effect. You can Escape from the Examine Image mode and select the Merge - Blink function to rapidly blink the two images automatically. You can also select the Merge - Sum function to sum the two images thereby achieving the equivalent of a longer exposure time.
Because JIMSAIP handles rotations, it is ideal for summing exposures taken with alt-az systems that have inherent rotation between images taken at different times.
If you got a bad alignment because of mis-matching one or more star pairs, you will have to re-load the A image and start over again.
If the two images are significantly different, the A image may be affected considerably by the rotation/row shift/column shift. If you are summing two or more images, you can 'clean up' the final image with the Crop function.
Generally speaking you will have little trouble with the Align function on typical images. Align's accuracy depends on the quality of the centering function for the star images and that depends upon the box size and background threshold settings. If you are summing a series of images such that the image in B contains the summation of several preceding images, the background threshold will be considerably different than that of the A image, and you will have to adjust the threshold value every time you switch images.