I am suggesting an option for the scanner to have command line arguments that would allow you to start the application using a config file that starts logging automatically and having a user defined output format that has the time or something unique so you don't have to name the output files each time you save them.

I could go on with more parameters but this would be a start.

This way if you have a shortcut or hotkey to start the app it would just take 1 button or click to get it all going.