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I am currently optimizing the acquisition time of an experimental Physics setup. To achieve our goal, we need to be able to properly estimate the error bars of each of the 200-time domain points of an interferometric signal obtained with a single-photon detector and then fit this signal to a model using non-linear least squares.

The problem is that, while I can now repeat the measurements hundreds or maybe even thousands (which would take us around 3 days at least) of times to study and get a proper estimate of the noise, in a 'real' experiment we would be able to only perform two quick measurements before changing the experimental conditions. What would be the proper way for me to tackle this problem?. Right now I have multiple 100-measurement samples that I can study, so I was thinking of maybe bootstrapping with N=2 to estimate the standard deviation of a two-measurements signal, but I am not sure if this will work. Any help or suggestion will be very appreciated. Apologies in advance for my rusty English and Statistics skills.

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