The magnifier allows a user to invert the colors of the entire Desktop.
Does anyone know how to invert the colors of just an application, or a specific window?
There are only three modes that Magnifier works in, and the high contrast colour inversion only works in conjunction with these modes. These modes are listed in the Microsoft page Make items on the screen appear bigger (Magnifier):
There are three Magnifier modes:
Full-screen mode. In full-screen mode, your entire screen is magnified. Depending on the size of your screen and the zoom level you choose, you might not be able to see all of the screen at the same time.
Lens mode. In lens mode, the area around the mouse pointer is magnified. When you move the mouse pointer, the area of the screen that's magnified moves along with it.
Docked mode. In docked mode, only a portion of the screen is magnified, leaving the rest of your desktop unchanged. You can then control which area of the screen is magnified.
So to achieve what you require, you will have to use in Docked mode, specifying a region occupied by a window (adjust the window to your particular tastes beforehand). Unfortunately you can not thereafter move the window and expect the magnifier to follow it, but you can always "re-dock" the magnifier to the new window position. Not ideal, but better than nothing.
This is the manner in which I use it. Hope this helps.