In this step you perform the image alignment. Therefore simply click on the Start Alignment button. To cancel the alignment click on the Stop button.

Before you start the alignment, select one channel as reference channel (e.g. DAPI, because it stains the nucleus and the nucleus is a proper structure for performing alignment).

During alignment, a splitter view is visible. In the left container you can see the original images, in the right container you can see the aligned images.