There are a number of commands that can be chosen from the menus in the menu bar which are described below.
On the PhotoSmart scanner, this is primarily useful for the print mode. You need to make sure you run this before making any scans of photographs (i.e. 5x7 prints). It creates vuescan.s10 (original PhotoSmart) or vuescan.s20 (PhotoSmart S20), which contains the calibration data for each of the 2700 scanner elements. If your scans have streaks in the scan direction, you probably need to clean the dust out of the scanner and then recalibrate.
On the Canon FS4000, this command creates vuescan.fs1, vuescan.fs2, and vuescan.fs3. These files contain the calibration data for the negative, slide and APS adapters.