Can I run arduino on Windows Embedded Compact 2013? I'm actually working on a robotic project for which I'm planning to use arduino to drive the wheels.For this, I want to send signals from my Onboard embedded computer (which has Windows Embedded Compact 2013 OS) to arduino. Is this possible? If not possible, what are the other alternatives?
What OS is running on two different devices exchanging messages/signals, does not matter. What matters is the protocol. 

You can use a lot of different ones:


Wireless:


IR (infrared)
RF (radio), like 433 MHz, 2.4 GHz
WIFI (internet)
Bluetooth

Wired


SPI
'simple wires' / Wire library
Serial
USB (not on most Arduinos)



This list is not complete, just some examples.

Arduino supports all above (except USB fully), I don't know what Windows Embedded Compact OS supports.