TT-AFM noise floor measurement


This procedure can also be applied to other AFMWorkshop instruments. For tip-scanning instruments such as the LS-AFM or NP-AFM, the results will show larger noise floors, while for the HR-AFM, extremely lownoise floors can be achieved. The TT2-AFM is practically identical to the first-gen TT-AFM in terms of noise floor.





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





* Z HV Gain is the most important parameter controlling the noise,  if the measurement is being made under low-noise conditions. Lower values will give lower values. However, lower values also decrease the overall z range of the scanner, making approaching problematic in non-ideal conditions. For a 17 microns scanner, decreasing this value may reduce noise further. Below a value of 3, it's unlikely to improve noise much. 

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 5 will be 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, would be 0.3 to 0.6 angstrom, 300 to 600 pm. Significant external noise will increase this.

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.

For an AFMWorkshop HR-AFM, achievable nosie floors can be less than 100 pm.

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

During July 2020, the AFMBiomed summer school series was supposed to take place in Marseille, France. Due to CoVID travel restrictions, the course took place online. However, since, there was no travel involved, and because the organizers kindly decided to make signup free, the school, had a record number of participants. At times 300 people were online, which is amazing for a specialized course like this, and showed just how many people around the world want to learn about and improve their AFM!

The lecturers were really great, and despite working in this field for 20 years, even I learned some things! Since I thought the material was so good, I am including links to the archived lectures below. The "tutorial" lectures were particularly good. Note that although the overall topic was "Biomedical Science", there are techniques here that could be useful for any AFM user.


This link contains the lectures in .pdf format:


Here You can find many of the lectures posted as videos on this site:


I highlight here some of the video tutorials that I found really useful: 





Please note that these video are published with a DOI record, therefore, it would be helpful to the authors if you cite them. I found this online class really great, and hope it returns!



  • Unfortunately, due to the coronavirus pandemic, we were unable to run the course on the proposed dates, so it's been postponed indefinitely.


Please click the image below to download the flyer with more details.

link to .pdf file of 2020 course flyer




 A blog with information and student feedback from the previous courses can be seen here:2017 course, 2014 course2013 course2011 course.

The course is supported by AFMWorkshop, The Faculty of Sciences of The University of Porto and my research institution, LAQV/Requimte

I recently wrote an application note on using AFM to characterize two-dimensional materials for AFMWorkshop. The full article can be found here. What follows is a brief extract.


Two dimensional materials are currently under development with potential to gain enormous importance in electronics, sensing, optics and other areas. Such materials, despite facile production methods in many cases, can display radically different properties compared to 3D or bulk materials. These new and enhanced properties come about due to nanoscale confinement effects, meaning they are generally accessible only when a material is limited to one, or at most to a few atomic layers. For this reason, research and development in 2D material and 2D materials-based devices relies crucially on the ability to characterise such materials at the nanoscale, including the observation of atomic steps. Atomic Force Microscopes are ideally suited for creating 3-D images and measurements on 2-D materials. This is because AFMs have extreme contrast on flat samples and can magnify surface heights by factors of millions to billions. AFM is unique in its ability to measure sample heights with resolution in excess of 0.1 nm. This explains why AFM has become a key tool in the arsenal of researchers studying 2D materials - for example, see the two images of layered materials below.




Figure 1a: Three dimensional color scaled image of SiC. The steps on this sample are 750 picometers.

Figure 1b: Colourscale image of HOPG, showing atomic steps.


Besides illustrating the power of an AFM, these types of samples serve as calibration samples for microscopes used for imaging 2-D materials.


Graphene is an extraordinary new two-dimensional material, consisting of single atomic layers of sp2 carbon. Although graphene is a single atom thick sheet, it is not typically found to be perfectly flat. Indeed, some nanometre scale corrugations, are commonly observed and may increase the stability of the 2D lattice. Despite its great strength, graphene is also a highly flexible material, and typically takes on the form of the underlying substrate. So, for example, on Si/SiO2 wafers, graphene can exhibit a considerable roughness due to the underlying substrate. Thus, a considerable texture, dependent on the SiO2 structure at the wafer surface, can be seen in the CVD graphene flakes shown in the left image in figure 2 below.



Figure 2. Examples of AFM images of CVD graphene deposited on Si/SiO2 wafers. Left: Single-layer graphene on a silicon wafer. In this example, the effect of the underlying texture on the graphene sheet is clearly seen. Right: Multilayer graphene of a silicon wafer. Arrows highlight some wrinkle-like defects, typical of CVD graphene.



To read more about AFM applications to two-dimensional materials, read the full application note here.

The last few years have seen quite a few changes in the AFM industry with some companies disappearing, and some others being acquired. presumably some caused by the financial crisis, which has certainly affected instrument spending.

Nanotec, a small Spanish company ceased trading in 2015. Nanotec were well-known for also producing their analysis software WSxM, which in addition to running their instruments, also opened almost all AFM image formats, and had a lot of great analysis features. Fortunately, WSxM is still available.

Keysight was a spin off of Agilent, and hosted the AFM division for a few years. unfortunately, they no longer make AFMs. Agilent had bought the IP of Molecular Imaging, which was one of the "big three" at one point. Agilent did continue to develop MI instruments for a number of years. Agilent had also bought the IP of Pacific Nanotechnology, but never did anything with it.

The biggest recent change is probably that Bruker bought JPK. JPK were early leaders in successful biological AFMs, and sold particularly well in Europe. As of now, Bruker are offering some of JPK's products and still exists. I kind of hope this continues as their Nanowizard AFMs are good products. Bruker also bought Anasys instruments, which make Nano-infrared microscopes, and are now offered under the Bruker brand.

Asylum Research was acquired by Oxford Instruments, and are still trading under the name Asylum Research - An Oxford Instruments company.

Of course, in addition, a few smaller companies came and went as usual! All these changes are reflected in the page "Where to Buy - AFM Instruments", linked below.

 link to instruments page

I also link below to an interesting Post on LinkedIn from Paul West on the history of the AFM business, for those who are interested!

Post about AFM Industry history