@imagejan: I merged your changes; thanks for that!
@Buono: Indeed, It would be great to see your data.
In general, the algorithm is very noise sensitive!
To fight this, I added a new option called:
Only consider pixels with values larger than: 0
If you find a value in your images that clearly distinguishes background noise from the actual structures, you should put it here. It can help a lot!
Let me know how it goes!