The handling of deinterlaced video streams.I also add a few points for urgent improvement:

Using FFMpeg as a base is definitely the right way to go, but I agree that adding support for Avisynth should already be one of your priorities for future updates (and maybe adding bitrate selection for converting audio tracks and adding the QTGMC deinterlacing method).

This version 3 is a step forward in many respects, but 2 steps backward in many others. So there will be no longer a need to resize input videos with non-square pixel aspect ratios in another software from rectangular to square pixels beforehand to get a correct scaling result. I already posted the most common pixel aspect ratios in the beta thread. Or even better: Some presets for common aspect ratios and the option to enter a custom pixel aspect ratio manually if needed. Please add an option to manually interpret the footage (framerate, field order, pixel aspect ratio, etc.) at one single place, like in any other professional video software… this can also be used throughout the program (so there is no need to define the input field order again at the enhance page, etc.). There is also no option to set a specific input pixel aspect ratio for all formats, only original pixel type and square pixels, and only for formats that already carry pixel aspect ratio metadata within the files.

Where do I find the direct frame number input on the timeline as in 2.6.4 and earlier versions, that was promised for the release-version of v3?

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