Signal analysis: selection of oscillatory parts
By looking at that graph, it seems that simple math (or rather statistics) can be used to solve this problem. I'd divide (segment) your data into equal time frames and then compute the mean and possibly variance (or standard deviation) for each time frame.

The idea here is that the parts you're interested in will have a greater mean (and a greater variance) from the rest of the data. You'll still need a threshold, yes, but this approach is much more robust than just trying to compare the individual data points against the threshold.

For best results, you'll probably need to experiment a bit with different time frame lengths as well as different threshold values.