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I have some 640x360 videos I want to re-encode with Handbrake to make their file size smaller. When I choose automatic cropping it shows 2 pixel cropping at the top and left, so I chose custom cropping, with everything set to zero.

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Despite setting width to 640 and height to 360 Handbrake produces a 638x358 video, i.e. it still applies the cropping. Checking "Keep aspect ratio" doesn't help.

How can I let Handbrake keep my video resolution?

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Handbrake encoding is restricted to the actual resolution of the video, which can be different from the "display resolution" of the video. MediaInfo, for example, only shows the display resolution, which are the same numbers that Handbrake reports.

As a matter of fact, however, Handbrake does not allow to increase (upscale) the actual resolution of a video by re-encoding it, but only to decrease (downscale) the resolution. So this could be the reason why your encoded video displays a lower resolution without actually being cropped.

Since this is just a guess, you should also try the Strict anamorphic mode instead of Loose or None to keep the maximum source size as the output resolution.

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