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Nice project.. The results are not perfect, but can give a reasonably good measurement of a cell's capacity. I found that powering the device with a 7V+ power supply on the VIN pin gave a more reliable 5V supply (mine was 4.98 as opposed to 4.5 from the USB). I also added time elapsed and power to the display. I didn't have a MOSFET so I just used a jumper to switch the load on and off. Obviously this requires that I pay attention to the voltage so I can turn it off at the right point!
DIY Arduino Battery Capacity Tester - V1.0