First start MATLAB. BakingTray uses ScanImage to acquire image data and this must be started first. BakingTray will detect if ScanImage is running and start it if necessary. So you simply need to run
BakingTrayat the command line. This will bring up the ScanImage start GUI. Click "Start ScanImage"
Note we are loading a USR file with custom settings for our system. Once started, the USR file configures ScanImage to look something like this (click for full-size version) once started:
After ScanImage has opened, BakingTray will start automatically.