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.

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

 

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 Amazon.comAmazon.co.ukaltBarnes 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

 

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