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FPGA photon counter low voltage

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Hi! I'm currently building a photon counter using the USB-7856R R series multi function rio. I have attached the labview program I'm using to count 1VPP square waves, and it works just fine. However, I eventually want to use it for photon counting, and our photon counter only outputs a signal of 200mV, which from what I understand is too low for any of the FPGA logic structures. Am I correct in this, and if so, is there any way to circumvent the issue?

 

Thank you!

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