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If they require darkness, then yeah, just don't take pictures during that time. Honestly, plants don't grow all that much when they don't have light. I honestly doubt you will lose all that much growth time by not taking the darkness shots. The important part, is just making sure you have steady lighting for the duration that you are taking pictures. For this, natural light isn't all that great since anything can happen, such as a cloudy day, or the difference in tone from sunrise, to noon, to sunset. Artificial lighting for the duration of the photograhy will give you the best final results, with the least 'cleanup' needed while sequencing the frames into a movie.
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