I would like to use Arduino in the microlight plane (as a controller for electric flaps). I am dealing with interference on Arduino digital inputs when on board VHF radio (125 MHZ, 6W) is transmitting. Please see attached image - signal change is approximately +- 1,2V. I have tried to use external pul-up resisors (4,6k) but it has helped a little. Would ferrite toroids will help - what type? Any advice is appreciated.
Would ferrite toroids will help
Yes along with capacitors. You might want to look at a “feed through capacitor” and a screened box for the processor.
Even 100pF to ground will do a lot at those frequencies to bypass the RF from the Arduino. You really need a metal box and shielded cables though, 6W is enough to wreak havoc when in close proximity to unshielded circuits.
Is your wiring too close to the antenna ?
Since you say the "onboard radio", can we assume it is powered from the same source as the Arduino? Ferrite cores/beads are only effective if the ferrite mix will cause a high impedance at 125 mHz. Just any old core is a waste of effort.
Paul
If my understanding of a microLight plane is correct, there is a human aboard. So basically regardless of size this is an airplane.
As others have said you need a metal housing with feed-through capacitors, ferrite before the feed-through's could not hurt.
The only thing I can add is that ALL the inputs and outputs (including power) need to be filtered.
Then when you get it built and are testing I would determine how close to the source your wiring could ever be, cut that distance in half and verify operation.
I believe, most of the the interference comes from antenna when transmitting (antenna is about 60cm apart from arduino). Picture in the first post shows pin state before and during transmitting. Both arduino and radio are on the same power line. There are only buttons on inputs, so I am looking for some simple filtering - is on attached schematic correct wiring?
Roughly correct but you do need the inductors and a feed through capacitor. I am not sure you are taking the safety aspect as serious as you need to.
Based on the questions so far, can you say if this Microlight will be flying anywhere near me (UK) ?
srnet:
Based on the questions so far, can you say if this Microlight will be flying anywhere near me (UK) ?
Do not worry just testing it 
Since your radio is AM, amplitude modulation, you may be overmodulating. Doe the interference appear when you just press the PTT switch, or when you speak into the mike?
Paul