TT-AFM noise floor measurement

1. Place a clean silicon calibration sample on the scanner.
2. Place a new probe in the instrument.
3. For this comparison, use vibrating mode. Setup the optical  alignment and Tune frequency as normal.
4. Select parameters to test are listed below. note that for a fair comparison, you can use parameters relevant to your typical measurements. The parameters described here, will give you an “ideal” value, i.e the best result possible.

 

Suggested parameters 

Parameter

Suggested value

X Gain %

0

Y Gain %

0

XY HV Gain

Initially 1 (note it should be 0 for the actual measurement)

Z HV Gain

1

Image Add

Off

Z Feedback values

Values you typically  use, for example Gain 1.5, Proportional 150, Integral 1500

Lines

128

speed

1 Hz

Left Image

Z_DRIVE

Samples/Pixel

25

 

Note that you can use any different parameters you like for this, and they can and will alter the results that you get. Also, the instrument should be properly calibrated in z to allow comparison with any other values. Be aware that tip approach with Z HV gain at 1 will be very slow, and some post-approach adjustments might be necessary.(i.e Jog Down).

 

5. Go into feedback, and scan an image of a small area of the surface (XY HV Gain of 1). The image should be clean, with very few features visible. Ensure you end the scan with the probe on a flat part of the sample.

6. Withdraw probe.

7. Set scan size to 0, by using XY HV Gain = 0.

8. Approach surface again.

 

NOTE: It is important that you go into feedback on the surface in the same way as you did when you scanned an image. If you go into false feedback (probe almost but not quite, on the surface), you will not make a valid noise floor measurement.

9. Scan another image. No sample features should appear, as scan size is zero. The image may look something like the image below, or have some regular patterns in it.

noise-floor
1
0. Save the file, and open the Left image -  z piezo drive file (height image) in gwyddion.
11. Apply a 1st order polynomial levelling (fit linear).
12. Use “Statistical Quantities” and record the RMS average roughness (Sq). This is the noise floor

You should get a value of <1 angstrom (Gwyddion reports this in picometers, typically, so you expect to see a value of <100 pm).

If you do not get a satisfactory value, try removing sources of external vibration (other machinery, acoustic noise, unnecessary cables) from the instrument. Ensure probe and sample are grounded. Ensure that the vibration isolation system is setup properly.

Typical values found in a TT-AFM in an acoustically shielding box, with bungee-cord type isolation, in vibrating mode would be 0.3 to 0.6 angstrom.

You should be able to achieve at least the value specified by AFM workshop on the instrument specification sheet which was delivered with your instrument.


All materials on this website are copyright 2010-2018 Peter Eaton.

Introduction

This article contains a list of all the software freely available to manipulate data from Scanning Probe Microscopy (SPM), that is, Atomic Force Microscopy (AFM), and Scanning Tunnelling Microscopy (STM). It does not include software designed only to load one particular format, i.e. the software provided by the instrument manufacturers, unless they are able to open other formats. It is intended to summarise the third party software available. It does not compare the quality of the software, and the order is entirely arbitrary. If you know of other software available, let me know.  I do know there are two other lists of SPM software[This one and This one], although neither seem to be updated.

 

This list is an updated version of that which appeared in my book:"Atomic Force Microscopy", OUP, 2010, with Paul West.

 

List of Third Party SPM Software

Gwyddion

Freely available, open source software for manipulation of SPM files; supports very many formats, contains many analysis tools. Available for Linux, Windows and MAC OS. Frequently updated. Available here. (http://www.gwyddion.net)

 

SPIP (Scanning Probe Image Processor)

Commercial software for manipulation of SPM files; supports very many formats, contains many analysis tools. Also allows analysis of force curves in several formats. Has a purchase price, but a time-limited demonstration version is available. Frequently updated. Following acquisition of imagemet by digital surf, SPIP is being merged with the MountainsMap package (see below) . Details, purchase, and demo version here.  (http://www.imagemet.com)

 

MountainsMap SPM Image

This package loads all of the major formats of SPM files. I have recently tried this software, and it has most of the functions required, including an unusual "report" format of data analysis. Commercial software, but a downloadable demo version is available. Recently merged with SPIP into MountainsSPIP 8.
More details here. (https://www.digitalsurf.com/software-solutions/scanning-probe-microscopy/)

 

WSxM

Freely available software that supports many SPM file formats; and has many analysis tools. I personally like a lot the 3D rendering results from WSxM. It was originally developed by an AFM manufacturer for use with their instrument, but is now completely independent and supports very many other file formats. Unlike many third party programs, has support for force curves as well. Frequently updated. Available here. (http://wsxmsolutions.com/)

 

FemtoScan Online

Commercial software from a manufacturer, but loads lots of (about 20) other formats. 30-days trial has no functional limitations. English and Russian user interface. It seems to be quite capable software, if a little cryptic. Available here. (http://www.nanoscopy.net/en/Femtoscan-D.php)

 

PUNIAS (Protein Unfolding and Nanoindenation Analysis Software)

Commercial software, dedicated to analysis of force curves, supports several formats. Implements several of the common analysis techniques used for force spectroscopy, and nanoindentation data. Also supports force volume images. A licence must now be purchased to use it. Available here.  (http://punias.free.fr/)

 

AtomicJ

Freely available, open-source software, with versions for Windows, Mac and Linux. Like PUNIAs, this software concentrates on batch processing of force curves. Opens a small number of common file formats. Seems quite complete, and delivers thoroughly summarised results. Available here, and described in this paper.

 

Carpick Lab’s Software Toolbox

Some Matlab scripts to help with nanotribology research - i.e. friction measurements with the AFM. They are for Nanoscope files only. Available here. (http://nanoprobenetwork.org/software-library/welcome-to-the-carpick-labs-software-toolbox) (last time I checked this page had been "temporarily" taken down)


Image SXM

A version of NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Seems to be able to open lots of file formats, but only works on MAC, so I've never tried it. Available here. (http://www.liv.ac.uk/~sdb/ImageSXM/)


ImageJ

Cross-platform image analysis program, not specifically designed for SPM images, but there are plugins to load MI or Nanoscope files here. I don't find it's often very useful, but some people use it, and it does have some useful functions, for e.g. particle counting. Available here. (http://rsb.info.nih.gov/ij/)

 

GXSM

This is a cross-platform (Linux, with a Windows port) open-source package that not only analyses data, but runs hardware, too. I haven't tried it. More details here.

 

 TrueMap and TrueSurf

True Map is an analysis and display program. TrueSurf is a surface roughness analysis program. These are extensions of profiler software packages, now offering some AFM format support. Commercial software, a licence must be bought for extended use. More details here. (http://www.truegage.com)

 

OpenFovea

OpenFovea is a program for analysis of force-volume files, i.e. AFM files containing spatially-resolved force curves. It is a Linux-native program with a Windows verison also available. I have not tried this software. More details here. (http://www.freesbi.ch/en/openfovea)

 

Pycroscopy

New (2016) package that aims to allow analysis of data from a very wide range of different microscopy methods including AFM / SPM. The program is available as a package for the Pythn programming language, meaning it's necesssary to install a verison of Python before you can use it. More details here: (https://pycroscopy.github.io/pycroscopy/about.html)

 

 

Software that's no longer maintained

MIDAS 98

Program for deconvolution of AFM files. No longer updated. Appears to only open nanoscope files. Available here.

n-Surf

Freeware program to open display and manipulate SPM files. It seems to have most of the common functions, but opens Veeco and NT-MDT only, and appears to be still in beta, and last updated in 2005. The website is  available at www.n-surf.com.

 SPM Image Magic

This program seems to be no longer updated, it is designed for Windows95 or NT. Opens just a few SPM image formats, and has relatively few analysis options. At the same place is SPM Image Voyager, which seems to be an image browser utility. AFAIK, no longer available, since the old website at Geocities disappeared.

Note: I welcome comments/suggestions for these lists, please contact me via the "contact" page.

In this article, I’m going to talk about what not to do in AFM. I’ll list 4 mistakes that are common in AFM use, which if you avoid, will certainly improve your results!

 

  1. Using standard settings.This is possibly the worst mistake you can make. AFM imaging is a highly adaptable technique. It’s able to image very large samples of tens of microns with extremely rough topography, or make tiny image sof extremely smooth samples, with subnanometer features. There is no standard setting which will get good images of all samples. You need to be able to adapt the imaging settings based on the response from the instrument. Optimal AFM imaging is attained through an iterative process! If you don’t know how to optimise imaging of the AFM, I highly recommend revising chapter 4 of my book, “Atomic Force Microscopy”.

   

  1. Interpreting image artifacts as image features. It’s important to know which features in your image come from your sample, and which are image artifacts. Learning this can save you some major embarrassment, and a lot of time!

 

bad feedback imageExample of image showing imaging artifacts. being able to spot and correct these artifacts is a crucial skill for an AFM operator.
  1. Trying to image dirty or contaminated samples. Sample preparation is the first, and most important part of an AFM experiment. If your sample has a layer of contaminant covering the the part you are interested in imaging, it will make your job almost impossible. Prepare your sample so that it only contains things you want to image.

  

  1. “Optimising” your imaging for a nice-looking amplitude (or deflection) image. I was amazed to find people do this. Amplitude and deflection images are made up of the error signal in AFM. The less contrast here is in the error signal, the more accurate your height image is. So, if you optimise imaging to produce a nice-looking high-contrast image in amplitude, you are decreasing the accuracy of your height image!

 

Avoid these pitfalls and your AFM work should be hassle-free! For help avoiding them I recommend reading my book, “Atomic Force Microscopy”, soon to be released in paperback!

 


All text and images copyright 2018 Peter Eaton, AFMHelp.com

A couple of new details about my book, Atomic Force Microscopy. Firstly, I just found a new (to me) review (published in German in Physik Magazine), including this great quote:

 

"Atomic Force Microscopy by Peter Eaton and Paul West is the manual that should accompany any AFM."

Prof. Othmar Marti, University of Ulm 

 

Secondly, a new paperback edition of the book, was recently published. In addition to being approximately half the price of the hardback edition, this new edition has been updated and all (known) typos corrected, so this is the version to get if you can!

 

The paperback version can be found on amazon.com here.

Atomic force microscopy

 

My group recently published a paper in the journal Ultramicroscopy reporting on direct comparison we made between different techniques that can be used to characterise the size of nanoparticles.

 

There are a wide variety of technique available to make these kind of measurements nowadays, however, microscopy is often used, because it is a direct technique (some other techniques measure properties related to size), and because it’s also possible to measure shape at the same time. The size of nanoparticles is extremely important for their properties, and ideally a technique to measure nanoparticle size will have sub-nanometer resolution.

 

Apart from microscopy, light-scattering techniques are probably the most common techniques used. The method of dynamic light scattering, or DLS; is extremely popular and used in thousands of labs worldwide. A newer method based on laser light scattering, called nanoparticle tracking analysis, or NTA, is currently growing in popularity.

 

In our project, we prepared nine samples; these we made up of nanoparticles composed of three different, and commonly used materials, a metal, an oxide (silica), and a polymer. We examined each materials in two different sizes, and also tested the ability of each method to distinguish between different populations in mixed samples.

 

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