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Hi Briana,
flickering is a potentially difficult thing to deal with.
I assume that you do not see the flickering outside the program, because it is generated by the codec used for the video. This is usually not visible to the naked eye, but when loaded into MEA, the frame-differencing algorithm picks up these slight changes.
If this is a strong noise, it will definitely have an effect on the validity of your data.
I suggest the following:
Try adjusting the threshold in MEA, and see how this has an effect on the frame-differenced video (the black-and-white screen).
When you do not see the flickering anymore, maybe you can still use your videos.
Just make sure to check the raw data of MEA for signs of anomalies.
Best, Fabian