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 


Suggested value

X Gain %


Y Gain %


XY HV Gain

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

Z HV Gain


Image Add


Z Feedback values

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




1 Hz

Left Image





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.

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.

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 here.

Atomic force microscopy


Bart showing his results

Our atomic force microscopy training course for 2017 ran in April, between the 10th 
and the 13th. Once again, the course was a great success, and all the places were filled. In this post, I quote some of the the feedback we got from some of me of the attendees, as well as some of the images they produced. In this edition, the highlight (for me) was the talk from Prof. Bart Hoogenboom, from UCL.

Bart demonstrated some amazing results in AFM, and gave some real inspiration as to what AFM can achieve. 

Phase image of E. coli cells

Once again, we had a good mix of students. They came from Wales, Portugal, Switzerland, the Netherlands, and Germany. We had PhD students, AFM technicians, lecturers, post-doctoral fellows and industrial researchers. It's always great to have such a wide range of opinions and nationalities!

As usual, we began with the basics of AFM, including instrumentation, modes, and fundamental concepts. Then the more fun parts, how to prepare samples, tips and tricks for running the instruments, and how to process and analyse the data.Most of the students prepared samples, and they all ran the instruments and processed and analysed image files. Based on the feed back, the students thought the course very worthwhile.

"I liked the course a lot. I think it's well-adapted to people with no AFM experience, and it seems it works well also for experienced users"


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.



Atomic Force Microscopy (2010), 256 pp, OUP. ISBN: 9780199570454book cover new


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

Prof. Othmar Marti, University of Ulm 

Peter Eaton and Paul West share a common passion for atomic force microscopy. However, their involvement with atomic force microscopes are from very different perspectives. Over the past 10 years Peter used AFM's as the focal point of his research in a variety of scientific projects from materials science to biology. Paul, on the other hand, is an instrument builder and has spent the past 25 years creating microscopes for scientist and engineers. Together Peter and Paul have created an insightful book on the theory, practice and applications of atomic force microscopes. This book serves as an introduction to scientists and engineers that want to learn about these fascinating devices, and as a reference book for expert AFM users.


 The Oxford University Press page describing the book can be found here, although the contents listed there are out of date. A correct contents overview can be found here: Book Contents.

The book was published on the 25th March 2010. It can be found at and Noble, and all major book stores. Click the image on the right to go straight to the amazon page for the book. There is also a Kindle Versionalt of the book available. If you are affiliated to subscribing institution, then you may be able to access it via Oxford Scholarship Online