Instructions:
This works for dimension 3100 software 0x0531000 anyway...
Open your afm data in imageJ. Draw a line and extract a cross section (i.e. Control K). Copy and paste the data to a spreadsheet. The intensity of the image is considered a z-coordinate now. Next we need to convert the x and z columns to realspace measurements. The x conversion is easiest: open the AFM file in a text editor (e.g. notepad). Then locate the image resolution and size (for example the image is 256 pixels by 256 pixels and the scan size is 40 000 nm). Then multiply each value by 40000/256 (the x scale factor) to convert to nm (the real space units).
The Z scale is conceptually the same, but slightly more complex to do. Again we wish to make a scale factor to convert our data. to do so we must locate the following lines in the header:
\@Sens. Zscan: V 14.30724 nm/V
\@2:Z scale: V [Sens. Zscan] (0.006713765 V/LSB) 334.2918 V
Note the numbers at the end will be different in each image, they are what we need to make the image specific conversion factor. In this case the conversion is 14.30724 x 334.2918 / 65535. The first two numbers are from the file (nm per volt and volts per digital value) and the last is the number of digital levels available to the scanner. Multiply your z column by this number and you are all set.
