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I'm not too sure. I think if you have enough data then transforming color spaces may not be needed, but if you only have a couple of data points then transforming might be nice to do.
It's also what you'd like the output of the matrix or LUT to be. If you transform before matching you'll need to also transform before you use the LUT or matrix values in another program.
Before matching, in addition to linearizing gamma, do we also need to uniformly transform the two sets of data into the same color space?
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