I measured again the noise of the photodetector. The chopper is off and the lockin trigger comes from a function generator set at 430Hz. In order to check if the noise could come from the function generator, I measured the noise with the probe laser ON and with the probe laser OFF.

The AC noise std with the Probe ON is 18microV as usual.

The AC noise std with the Probe OFF is 0.7microV. Very similar to the case Chopper ON - Probe OFF measured before (0.8microV).

This means that the noise doesn't come from the function generator.

Other possible noise sources could be the HeNe power fluctuation or jitter position fluctuation due to some vibrations.

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During many noise acquisitions I noticed that sometimes (one time in 3 or 4 minutes) there is a strong peak of noise, about 2  order of magnitude higher than the usual noise. The system manual speaks about them and give this explanation: "There are various sources of spiky noise including dust particles crossing the probe beam path."