AJA FS2 - Manual (Page 54)

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Achieving the Highest Output Quality
To achieve the highest quality FS2 video output from a computer input, two
processes must work together: (1) the computer display card must be set to
scale the computer video output to the highest possible resolution and image
size, and (2) the FS2 must be set to convert the computer video to the closest
matching resolution in a broadcast format. If the computer is set for a small
video output format, such as 640x480 VGA, and the FS2 converts that to 1080i,
the result is a scale down by the computer card followed by a scale up in the FS2,
causing a loss of resolution. Your results will be much better if you use a high
resolution computer output and a closely matching FS2 conversion format.