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My eyes were bothering me as well. I do not know if my reason is the same for you but here is my story.
Some years back I bought a new MacbookPro with LED backlight. I did not have any issues at all at first but I noticed that I got headaches more and more the longer I sat in front of the screen. The worst was some months ago where I got very dizzy and had strong headaches. The feeling was still noticable even the next day.
Research on the internet showed me that I was not alone and that other people were experiencing problems as well - especially with LED backlit screens.
So it seemed that the problems I had were not because "I just got older". It seemed to be the display technology.
You can check out more on this site from Eizo here:
This shows that the main problem with LED backlit displays are two things:
- the PWM flickering
- the emission of blue light from the LEDs
To attack the problem I bought a PWM flickerfree screen. You do not need to buy one from Eizo. There are multiple vendors now that have those up their sleaves. You can also check out a list of flicker free screens here:
With the flicker free screen I had some relief but still had issues and could not work long hours.
The solution was to buy a blue light filter for my glasses.
If you have good eyes or contact lenses you could buy one of those "computer glasses" with yellowish lenses or if you wear glasses like I do you could buy a clip on. I found mine on Amazon. It really looks strange at first but it is worth the relief it gives me.
Being able to work in front of the screen for hours again is invaluable!
There is a good chance glare is causing your eyestrain problem. The first thing I would try is one of those anti-glare screen covers. They costs $30+, but if it solves your problem it would be worth it. If you wear glasses, make sure you get anti-glare coating on your lenses. A cheap thing to try is to simply reposition your display to change the glare that is on there now. That might not help if you are in an office brightly lit with overhead lights, but if you are beside a window in may do the trick. Another thing I do that sometimes helps a little is to change my focal distance regularly. Look up from your display, look at something in the distance, look at something a few feet away, etc. It's not a magic bullet, but it does seem to help for me.