The background noise is “normal” but is varying a lot

The easiest method is simply to do many measurements and average the result. To do the average, first make sure that Plot->Overlay… is checked. If you click in the STI plot and then click the  button, the mean value for the displayed measurements will be displayed in the green line as shown in the figure below. The STD is also displayed as the two dash-dotted lines.

A solution here may also be to increase the duration of the measurement, e.g. to 30 seconds. This will average out the variations of the background noise.