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Capturing the 100GbE traffic will be a challenge as @hugo.vanderkooij already mentioned. As for being able to analyze the data that is generated by the FPGA: as long as the FPGA generates packets that mimic protocols that Wireshark understands, then wireshark will fully dissect the packets. If the ethernet payload is random data or some protocol that wireshark does not understand, then the dissection will stop after the ethernet layer.