Manual stack alignment

Sometimes the automatic alignment routine just can't seem to get a stack to align. You may then want to resort to manual alignment with the Manual alignment button, which gives you a window like what is shown in Fig. 12. Each image is displayed at its full size at right. You should then click on an object in the image that is recognizable throughout the stack. A magnified view of that region will then show up in the window labeled This subimage. Now you should carefully click on a point in the object. The first time you do this, the same magnified view of the region, but now centered on the point you clicked in in This subimage, will appear in the Reference window to the left so you can remember exactly where it was that you clicked.

You now go through a sequence of steps:

1. Click on the alignment object in the large image to the right
2. Carefully click on your alignment feature in This subimage
3. Click on "Next" go get the next image in the stack.

You can monitor how well your aligment is going by playing the movie and seeing how badly it flickers. If one particular frame looks bad, you can go to the file name by selecting it from the list at bottom left, or go to the movie frame number by selecting it from the list at the bottom right. The shift of each frame is indicated in the list at bottom right.

Figure 12: The manual alignment screen.