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.

 

 

HOPG
 

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.

 

Update

  • 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

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)

  

MountainsSPIP

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. (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://www.wsxm.es/)

 

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)

 

PyJibe

This is a nice-looking package for manipulaiton of NanoWizard force-distance data including force maps. Free to use, and available here. (https://github.com/AFM-analysis/PyJibe)

 

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 version 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 Python 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

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.

 

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.

AFM Manufacturer list

The following is a simple alphabetical list of, hopefully, all the AFM manufacturers in the world. If you have any additions to make, get in touch via the contact form. For AFM probes, look at the SPM Probes list, and for reference samples, see the SPM References list. Note: I have moved the companies that are no longer separate businesses to a new list, below.

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 www.jpk.com 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

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