I've never used VisionLab, but I'd imagine it can import an image sequence.
If it can, you might be further ahead to render an image sequence to a format that supports 32bit, [PNG or TGA], as that will save with an embedded alpha channel, eliminating the need to chromakey out the "green screen." This way you don't have to worry about any imperfections in that process, and you'll be working with uncompressed or only slightly compressed images rather than what is likely a compressed video file.
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