In general all "colour" coded look-up tables are based on the original 8- (or 16bit) greyscale reconstructions. So each colour you have in the 3D model equals one of the 256 values. Quite a good background reading: http://40two.info/barge/image_processing/Intro/PDF/Lookup_Tables.pdf

I don't know which piece of software you used - but in case it was ImageJ/Fiji you can easily find out the LUT values by just go for File > Open > luts (that's a folder in the progams folder). There's also the 'LUT editor' plugin that allows you to find it out (http://rsbweb.nih.gov/ij/plugins/lut-editor.html)

Any x-ray based imaging method that works with a polychromatic x-ray source (e.g. CT, CBCT, micro-CT) will give you a slightly different value each time you measure a sample. In most cases that's not a real problem, however one has to keep that in mind when aiming for precise measurements. Best thing to do would be to use a phantom to calibrate for it (e.g. Dipotassium phosphate liquid phantoms, or solid phantoms of known densities) rather than just relying on the internal calibration of the machine.

By the sound of it, you already scanned all your samples - what you could do is to make a phantom and scan this phantom with the same settings as you did for your samples. Using ImageJ you can create a calibration curve that gives you the values for the whole 8/16-bit region. If you need more information on how to do that, just let me know.

Thank you Michael and Julio for the insights. I'm looking into it now, and ImageJ will certainly do the trick. Thanks again.

@Paul: The Hounsfiled Unit (HU) is also derived from grey values - mostly it's an internal calibration already. One can easily do a rough calibration doing a scan (with the previously used settings) measuring just water and air values, but the calibration is not that good (only 2 points for a calibration). Moreover, HU values are mostly reported in (bio)medical literature, rarely in other fields.

Lorian, if you need any help with ImageJ, just drop a message- I've done it multiple times before..

I am using a Scanco vivaCT 40. Are you using a single pure color(red, green, or blue), or a group of colors? If it's a single color, any image program should show pixel values in a 0-1 or 0-255 range. In Scanco's software, those pixel values span the density range determined by my upper and lower thresholds. Any 3D or shadow effects should be taken out, though. I use MATLAB and freeware Photo Filtre for non-routine image work such as this.

If you have more than one color, I would not know how to interpret three different color indices. GE should be able to help.

I'm not sure if you can measure HU in cross section image. As long as I know your image need to have air and water values in order to calibrate HU . However , HU will accord density value.