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I've shot a video with my Canon EOS 1100D, but unfortunately forgot to turn the auto lighting optimizer off.

Now the video footage looks really bad because there are random changes of brightness every time the colours change, similar to the changes seen in this video, only that it's even worse for me.

Is there a way to repair the footage and adapt the brightness so that it is equally the same throughout the video? Or is my footage lost?

Keyframing and changing the brightness & contrast would be the last possible option, but it's certainly far from perfect and very much work.

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Without knowing the exact result of this, if I where you I would give the GBDeflicker a shot (plugin for AE Win/Mac and stand-alone application):
http://www.granitebaysoftware.com/products/productgbd.aspx

This is a software meant to solve time-lapse flickering by averaging the luminance of the scene over time. For the video you showed as an example this would also be the case, unstable luminance.

You can probably isolate your background or the problem area for this plugin to work on, to achieve even better result.

You might need to adjust end lightness but after running the scene through this I would think that's just a matter of matching the first and last frame setting the keyframes for both.

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