Windows – Is there any way to change a specific window’s colors

Perhaps Stardock's Windowblinds can help you? I'm pretty sure that it can do window color adjustments (not just border and decoration). Although I was never actually able to use it (this was a long time ago on a very old computer), I do seem to remember options relating to individual window colors.

My workaround is to transform standard contrast of the entire screen into lower one. This way, window with inverted colors becomes more bearable.

1. get NegativeScreen open source freeware

2. open configuration file

3. using copy-paste, add the following matrices:

# Based on Smart Inversion
Low Contrast si1=win+shift+alt+F5
{  0.3333333, -0.6666667, -0.6666667,  0.0000000,  0.0000000 }
{ -0.6666667,  0.3333333, -0.6666667,  0.0000000,  0.0000000 }
{ -0.6666667, -0.6666667,  0.3333333,  0.0000000,  0.0000000 }
{  0.0000000,  0.0000000,  0.0000000,  1.0000000,  0.0000000 }
{  1.2000000,  1.2000000,  1.2000000,  0.0000000,  1.0000000 }

# Based on Smart Inversion Alt 1: High saturation, good pure colors.
Low Contrast si2 (×*60% +30%)=win+shift+alt+F6
{  0.6, -0.6, -0.6,  0.0,  0.0 }
{ -0.6,  0.6, -0.6,  0.0,  0.0 }
{ -0.6, -0.6,  0.6,  0.0,  0.0 }
{  0.0,  0.0,  0.0,  1.0,  0.0 }
{  0.9,  0.9,  0.9,  0.0,  1.0 }

4. you can play with them until brightness and sharpness adjustment fits your needs.
   UPDATE 2016-10-20: Now you can create and edit matrices interactively using ColorMatrix Viewer tool.

Based on what you actually need, this could help you, because these adjustments can go beyond color adjustments reachable on standard LCD panels.

FYI the NegativeScreen tool is using your favorite magnifier functionality, but it can supply it with more color transformations than default simple inversion.

If eyesight is your main reason for asking this, you can also search for some decent e-ink display solution or check how to reduce blue light which in my case helped me more than e-ink display. Blue light and flicker of LCD backlight are behind several types of eye problems.