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


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. (



This package loads all of the major formats of SPM files. It is very complete,a and produces nice data analysis, including an unusual "report" format of data analysis. Commercial software, but a downloadable demo version is available. Recently merged with SPIP, which was itself extremely popular, into MountainsSPIP 8. DigitalSurf's "Mountains" package also analyses profiler and SEM data.
More details here. (



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. (


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. (



This is a nice-looking package for manipulaiton of NanoWizard force-distance data including force maps. Free to use, and available here. (


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.  (



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. ( (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. (


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. (



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. (



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 version also available. I have not tried this software. More details here. (



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 Python programming language, meaning it's necesssary to install a verison of Python before you can use it. More details here: (



Software that's no longer maintained

SPIP (Scanning Probe Image Processor)


Recently discontinued 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 has been merged with the MountainsMap package and now it's called MountainsSPIP.



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 No longer updated.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


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

 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.

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

In my job as a researcher using AFM, I often act as a scientific reviewer for papers describing AFM experiments. I also collaborate with many groups and spend a lot of time revising and correcting articles which contain AFM data. In this two part article, I’ll describe how you should go about preparing a scientific paper which contains AFM data.

NOTE: Some of this content is not really specific to AFM articles, but could be applied to any experimental scientific report. These parts should already be known to you if you are writing an scientific article, but many researchers are never taught how to correctly prepare a scientific article before they start writing them. For more general guides on preparing scientific articles, check here.


What are the overall requirements for an AFM paper?

  • Experimental conditions should be well described

  • Data should be presented in a useful format

  • Reproducibility should be addressed

  • Conclusions should be justified


These requirements may seem like “common sense”, but you might be surprised by the number of articles which are published but do not meet some, or even all of these criteria!


  • Experimental conditions:

    What should this include:

Imaging mode used. This is rather important, since the results can be different from mode to mode. It also helps to make your data reproducible. Note that not all instruments use the same terms to refer to specific modes :This is particularly the case for tapping mode. It can be useful to use both the manufacturer’s name, and the most commonly used name for example: Imaging was carried out in AC-AFM (Tapping) mode.”

Instrument used. You should name the instrument mode and the manufacturer. You can also include the version of the instrument model, if applicable. Some journals still request the location of the company, but this is becoming optional e.g., you might write “Bruker Multimode 8 (Bruker, Newhaven, CA)”.

Probe used. The type of probe used can determine the type of information available, as well as the interaction force. Since there are many probes available on the market, it’s also useful to say the (approximate) frequency of the probe, which gives some idea of the type of probe, without he use looking up the details. E.g. you might say “AppNano ACT probes with around 300 kHz frequency were used”.

Software used. All AFM images require image processing, or analysis before presentation. It is a good idea to describe the software used for processing of the AFM data. You might also describe the processes used for analysis and /or data processing. E.g. you might say “Gwyddion 2.49 software was used for processing the images, and Roughness was calculated with the Gwyddion 'Statistical Parameters' tool".

Amount of data collected, and statistical significance. This issue is addressed below. However, it's worth remembering, that the microscopy images you collect should be representative of the sample(s). A part of the “materials and methods” section should be explaining this. For example, you might write “At least six areas per sample were imaged, and representative images are shown here.” If you have a variety of different images, you could add additional images to a “supporting information” section.

  • Presenting data in a useful format

There are many different types of AFM images, and different ways to display them. Very often the instrument will produce several different image channels, such as height, phase, etc. The most commonly used channel is probably height, since this is the only one with three-dimensional data. However, sometimes, it’s hard to make out the sample details in height images. For this reason, other channels, such as deflection or phase are often used. I recommend that the height image, always come accompanied with a z scale (normally it’s a colour gradient), and they should have either an inset scale bar, distance markers on the outside, or the legend must state the scan size (x and y). Examples are shown below.


Different ways of showing scales. Left: a figure with distance marked on the figure frame. Middle: an image with an inset scale bar. Note how the length of the scale bar was chosen to highlight the repeat distance of the grid. Right: No lateral or vertical scale. I this case, the lateral scale should be described in the legend.


Does the colour I pick make any difference? No. You can choose which colours you like. For some reason, AFM images are “traditionally” shown in some shade of brown, but any colour scale is fine.

Should Amplitude/Deflection/Phase images have a z scale? No. The z scale on these channels is usually meaningless, as it might be in volts, or degrees, and in most conditions, is not needed. I recommend to remove it to avoid confusion.

Are the details you want to highlight easily visible? If not, the use of arrows to denote specific features in the image is recommended. The arrows should be referenced in the figure legend.

Talking of which, in part 2 of this article, I’ll talk about how a figure legend should be written, and how you should address reproducibility of the data, and draw appropriate conclusions from your results.

All images copyright peter Eaton 2019. Images produced with SPIP and Gwyddion software

This is the second part of this article about how to write an academic paper including AFM data. If you have not already, you should read the first part here.

NOTE: Some of this content is not really specific to AFM articles, but could be applied to any experimental scientific report. These parts should already be known to you if you are writing an scientific article, but many researchers are never taught how to correctly prepare a scientific article before they start writing them. For more general guides on preparing scientific articles, check here.


Figure legend. The figure legend is an important part of the figure. It should not be too brief, e.g. “Figure 1. AFM images of samples 1  and 2.”. But it should also not be too long. It should be concise, but has to have all the information needed to enable the reader to understand the figure. It should have a description of the type of data, if necessary explain the scale of the images, and clearly identify the samples shown. For example, a good figure legend might be: “Figure 1. Representative tapping mode AFM images of samples 1 and 2. A: Height image of sample 1; B: Phase image of sample 1; C: Height image of sample 2; D: Phase image of sample 2. All images show 1????m x 1????m areas, and the z scales are indicated next to the height images. The arrows show the location of anomalous nanoparticles discussed in the text.”

  • Reproducibility

All numeric values included in the results must be accompanied by standard errors, or standard deviation of the means. You must also say how many measurements were made. It is important to discuss how many areas were imaged, and how often the features discussed in the text occurred. It’s not acceptable to show only one image, with the assumption that it represents a whole sample!


  • Conclusions

It should go without saying that the conlcusions you make based on your AFM data must be justified. This often means that you should calculate the occurrence of specific features, so if you want to say that the surface got rougher, or features grew after treatment, you should measure this, and show means, and errors, or a histogram of results. Note that histograms can help a lot with non standard data distributions, i.e. where there are outliers.


Can lateral measurements be used in AFM? Yes - but with caution, and only sometimes. If you have samples that are small, comparable to an AFM probe tip, lateral measurements of them will be wildly erroneous with AFM. For this reason it’s nearly always preferable to use vertical measurements where possible. Lateral measurements typically only work well for features much larger than the AFM probe, so you must be careful with these. One way to reduce the effect of these errors is to deconvolve the probe shape from your images. See section 2.3.4 of Atomic Force Microscopy.


If your conclusions are based on certain small features in your images, you can present your images in a way so as to make these features clear. This can be done by:


  • Cropping. A nice way to highlight certain features is to show a large image as well as a cropped section magnifying the feature you wish to show.

  • Histogram control. Control the height range shown in your height images to highlight the part you are interested in showing. So for example, if you wish to show tiny 20 nm features, you cannot do it with a z-scale of microns in a height image.

  • Shading. Light shading is a routine available in all AFM processing packages (such as SPIP and Gwyddion), which can highlight small topographic differences

  • Including error signals or phase images. These channels are frequently better for showing small details.

  • Highlighting with arrows. As discussed above.

  • Using unusual colour schemes. In general complex colour schemes make for confusing images, but for some images they can be appropriate, and help to illustrate the different features at different heights.


Some examples of these schemes are shown below.

epithelial cell
In this image of an epithelial cell, the colour scale was adjusted with the histogram tool, to enhance contrast on the cell membrane
unusual colour scale
IN this height image with various features of different sizes, an unusual colour gradient was used to highlight different features.
In this image, a cropped image is used as an inset to highlight one particular cell.

Good luck with your AFM articles! If you have more questions, contact me here.

NB. All the images in these two articles were produced with SPIP 6.7.7 or Gwyddion 2.40

This article and all content is copyright Peter Eaton and 2019.


During our recent Porto AFM Training Workshop, we held a little competition, asking the students to produce and process the best images they could.

This year, the winner of the competition was Magdalena Scheibe, who produced this beautiful image of human hair. Well done, Magdalena!


Magdalena's winning image
Magdalena's winning image

However, we must also acknowledge two very inventive submissions, firstly this Game of Thrones-inspired one from Izabela (scanned with Anita), which actually shows a "wall" of nanoparticles, and nicely processed in SPIP.


Game of Thrones Nanofans
Game of Thrones Nanofans - Winter Is Coming

And finally, this "Moonlanding" on another hair surface from Sandra and Rita. Very nice!

Ana Rita and SandraExploring Hair at the Nanoscale with AFM

Thanks to everyone who entered the competition!


All images Copyright and their respective creators.