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Exporting as TIF and processing of height images

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LizaW posted on Mon, Oct 5 2015 9:45 AM

Hi! I need some clarification on what is happening when I do the different methods to export my height channel for publication. 1) using Nanoscope software plane fit + flatten + export commands, versus, 2) using right-click on file then export-TIF. The second option is obviously not processing the data for bow, tilt, etc, so it has more height data in each pixel and it doesn't look as nice as the first option. One of our authors is concerned that when I process 4 different images using the first method, I have different file sizes even though all of the collection parameters are the same. Different file size for different height channel is acceptable right (because height represents Z distance which is also embedded in the pixel, and every sample will not be identical in the Z information)?? These are height 'maps', not a traditional digital picture.

Second part of my question is that, if raw AFM image is to be published (other than changing the dpi for publication requirements), how should one post-process height images, since they contain pixels with color inside them that represent Z ? If we export the images as TIF and process them in Photoshop to 'make prettier' (i.e, change pixel x pixel ratio, change contrast/brightness, etc) are we not altering the original height data map??

Thank you!

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Bruker Employee

Hi Lisa,

Just a quick answer, I am sure others could elaborate more. Yes, there are several export options exactly as you mention. In the end the kind of processing is a judgment call. It is very common to perform basic processing on AFM data and for good reasons. If you think about the height scale vs the XY scale, the height scale is commonly 1000x or more smaller. So the smallest sample tilt could dominate the Z data scale. And most of the time the sample tilt is meaningless, is the one thing you don't care about. So at the very least a first order plane fit is almost always done, and it is very common to do this and just state this. That is still close to raw data. You are really just fitting to a plane. You could even provide the extracted plane tilt parameters and then you basically give the instructions to reconstruct the original data. Also line-by-line 'flattening' is commonly done, and deemed acceptable if it is understood this operation has been performed. On the other hand you mention photoshopping the data to make it look prettier. Now that kind of operation, or any kind of filtering that averages adjacent points or frequency filters, there we are talking about serious data modification. That is definitely filtered data. This can also introduce real artifacts such as e.g. the appearance of a . That too is not uncommon and should be stated when performed.

Hope this helps,




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