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====== AFM Image Analysis ======

The raw data produced by the AFM goes through some significant process steps.

During imaging, the live traces of the height are automatically processed using "line-by-line first-order flattening". This means a linear regression was used to fit a straight line to the height data and the straight line was then subtracted.

After imaging, your IBW file contains this lightly processed height data (line-by-line first-order flattened). The image frequently needs further processing. For example, a "first-order plane fit". Before doing a first-order plane fit, you need to mask any parts of the image that are not in the flat plane.

When you are finished flattening, you should save the flattened version of the data as a new tab in your IBW file:

{{::flattening_ibw2.jpg|}}