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That should depend on compatible ports available on the 3E and aurduino board. It communication protocol can also depend on the volume and nature of data to be shared.
Serial communication should be available on both boards.
Hi, It depends on how the data is going to be shared between arudino board & SPARTAN 3E FPGA. Here the Arudino board has predefined I/Os & Bus timing protocols. Where as in FPGA you can configure the GPIOs as per your requirement. Make sure that whether you want to interface Data bus (Uni/Bi-Directional) of Arudino to FPGA, or simple i/o port of Arudino to FPGA. After confirming that, refer the timing specs of Arudino i/o and FPGA, create the timing events based signal for handshake between two devices. hope you understand what i mean,..