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Line Noise caused by USB ground
Sometimes, the USB cable that connects the aq acquisition board to the PC (which is grounded to the building ground via the power supply) isnt isn't good enough -  grounding the external shield of the USB cable that connects the FPGA to the computer can help.

Line noise caused by different power circuits
Make  Make sure that all equipment, including the recording computer, is plugged into the same circuit and grounded to the same ground. This is especially crucial in buildings with separate building and earth grounds.
Be careful when bridging two ground circuits - sometimes they can carry a large potential difference. 

Dont use ungrounded laptops with no extra ground
If you're using the acquisition board with a laptop that's running off battery power, you will have a "floating" ground. This will cause your signals to look extremely noisy. To fix the issue, connect the ground of the acquisition board to whatever ground you're using for your experimental setup (perhaps a wall socket or a Faraday cage). You can either do this via the BNC connector (alligator clips work well for this), or by attaching a wire to one of the two dedicated screw terminals on the side of the board. The screw terminals are preferred because someday we may do something with the BNC. If you use the BNC, ground the shell of it to the wall, not the center pin. Connecting center pin of the BNC to ground will short your board and may fry the FPGA. 


Beware of bad power supplies
Sometimes, aftermarket power supplies, mostly for laptops, but also for LED lights, or any other power brick, can cause a lot of line noise - try individually turning off equipment to isolate the offending one. 

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