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Similar to luka's suggestion, could a comparison be done with another mono camera that has a known QE response . eg using a sub length that is within the linear range of both cameras,take a series of test shots, compare the resulting signal? if you combine with the narrowband filters, you would get relative QE at different wavelengths. Then use the known QE values for those wavelengths from the known camera to calculate the QE of the new mono DSLR.
Edit - if the pixel size of each camera is different, I suspect that this would also need to be taken into account.
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