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Peakforce QNM image analysis - guidelines for modifying the images

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LizaW posted on Thu, Nov 17 2016 1:44 PM

Hi all!

Two part question on how to handle images for viewing/export:

1) I am looking for a good reference that will help in better understanding the ways to 'post-process' our AFM images, ensuring that we are not artificially changing our displayed data maps (compared to raw data). The help guide really only focuses on height maps and doesn't delve into too much description about each channel. For example, while scanning in Peakforce QNM, all of our offline plane fit parameters [OL Planefit] are set to NONE, so that the raw data is collected as is, and no plane fits or offsets are applied. This is how you avoid negative range numbers (in the DMT Modulus data channel, offsetting can create negative values on the scale bar). For example in this channel, negative numbers make no sense. Before exporting my TIFF images, the only channel that I do flattening 2nd order command on is my height channel. All the rest of the channels are not processed, other than a '0' order plane fit. Is this the correct way to show the data? For any of the other QNM channels, can we do any other flattening, or will that affect the Z data in the images? And what is the explanation of the function of flattening when applying it to the other channels? What about bow/tilt adjustment of these channels?

2) Sometimes, the raw  dissipation channel or DMT Modulus channel for an image will have a negative data range (both in the color bar and when you look at a horizontal 'section' of the image), but a negative value would make no sense for these channels (ex: negative value for dissipation means that the tip gained energy!). What would be causing this? The set of images that I see this in, the fluid+ tip was not fully calibrated on glass (default tip settings were used). Is it as simple as not having a calibrated tip? If I calibrate and still see negative values, what else could be happening? 

Thank you!


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Top 10 Contributor
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Please check it out here for many online webinars:

There is one about "Advanced Functions of Nanoscope Software"

There are many detailed questions here. Addressing all these will need a very lengthy writing here. 

Please contact the Bruker Tech Support in your region. Ideally, please get a Service engineer to guide you through some basic software functions via remote demo, such as TeamViewer.




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