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You put the two inputs across your sensing resistor and have power supplies tto the amplifier that are high enough in voltage to keep the common mode voltage within the range of the amplifier. By common mode voltage I mean the absolute voltage at each end of the sensing resistor.
There are other methods of measuring current like Hall Effect sensors. These have elecctrically isolated outputs that can be connected to ordinar op amp stages. You can find them with a search engine and "hall effect current sensor" as the search term. Make sure you use one that measures DC.
how is the common mode effect taken care of in handheld multimeters with current measurement capability? My Fluke multimeter runs off of a 9V battery and yet I can measure current in series coming from sources much greater than that.
Anyway can a charge-pump be used for bias the instrumetation amp or does it introduce too much ripple, etc? If it can, could you recommend any good clean output charge pumps?