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I think that you can integrate the counts over the whole sensor size and not worry about the individual pixels for the measurements. Then you can work back (divide by pixel count) to get the per-pixel efficiencies.
1. Make sure that the lighting conditions are identical for the 2 cameras.
2. If the sensors don't have the same physical size the image from the camera with larger sensor must be cropped so that the two resulting images come from identical physical dimensions of the sensors. This will ensure that optical conditions are similar and hopefully identical.
And then repeat the measurement several times. With several cameras :-)
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