Jasperdavid:
Is it really necessary to filter my signal, even if my only goal is to count rising/falling flanks? or would the offset voltages ruin my signal and make the arduino think it's a pulse?
If you want to simply read the signal via a digital pin, yes you do need proper conditioning. If you assign an analog pin you'll have to do the equivalent conditioning in software - and be aware that you'll be sampling at 10kHz at most in the default setup. Simple hardware low-pass noise filter will help either way.
For the analog pin route you need the signal to be in 0 to 5V range of course (the hardware conditioning could be made to work on the automotive 12V rail - so long as the comparator output pull-up stay at 5V)