You might try making the selection area a little bigger than normal, making sure to include a bit of the sprocket holes (if it's 35mm). This added really light area might get you better shadow separation. Another idea would be to add an opaque mask around the negative and to include some of that. These two elements should be lighter and darker respectively than anything in the frame. That way, if the software automatically clips a little of both ends of the scale, you might get a less contrasty scan.
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