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The EyeX Tracker itself cannot be configured to operate over smaller areas as the size over which areas can be accurately tracked is a biological not a technological limitation.
However, there are a few possible workarounds you might consider such as using a magnifier windows alongside your application.
Additionally, you might be able to adjust the GUI settings of the application to display larger buttons.
You should bear in mind that the Tobii EyeX is not designed for complete replacement to traditional input methods (such as mice and keyboard) but rather to work in tandem with it. That being said, there are a number of application such as Project IRIS (http://iris.xcessity.at/) which might help you in using the EyeX for controlling windows applications.