I did some tracking in Adobe AE and then ran a script to import it into Blender. I set a background image in the N menu, but I can only see it in the viewport, I can't see it when I render. Any help would be appreciated. Blender 2.79b, cycles render.

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2The background images you setup in the viewport settings are only for reference in the viewport while modelling. This answer should provide your answer. – sambler Nov 05 '18 at 04:34