I have recently started using an AFM machine, and have some issues with the way it saves the data. The people who maintain the machine haven't been very helpful with my concerns, so I'm hoping somebody here might be able to help me. I have been using Gwyddion to display the raw data images, which are in TIFF format. Apologies, by the way, if I put this in the wrong place; I'm not entirely sure where microscopy topics are meant to go. How is the data scaled? Presumably there is either a standard number of pixels per micron for all AFM images, or something within the image file header that tells the software how to treat it? I am even more unsure of the depth data; I know it uses colour to represent it, but it seems odd that it is in 3 channels rather than just one. I briefly had a look at the pallete in matlab, and it appears that the channels don't vary together (e.g. one channel only begins to vary halfway through the palette), so I am not sure whether I can rely on the depth values I can see when looking at the image using Gwyddion. Am I missing something?