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. Probably the most comprehensive 3rd party AFM analysis package around. Details, purchase, and demo version here.  (http://www.imagemet.com)

 

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.

 

MountainsMap SPM Image

This package loads many 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.
More details here. (http://www.digitalsurf.fr/en/mntspm.html)

 

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.

This page has a list of corrections to the book "Atomic Force Microscopy".  If you notice any more mistakes, please let me know here. That way I can correct them in the next edition!

 

Important Note: All these errors will be corrected in the upcoming paperback edition. If you know of any more, let me know! 

Errors

  • Page 30 - Equation 2.6: Verr is used in place of Zerr in the first term.

 

  • Page 38 - The last paragraph erroneously refers to equations 2.5, 2.6 and 2.7, where it should be 2.7, 2.8 and 2.9, respectively.

 

  • page 53 - referring to the figure shown below:
Figure 3.4 - Canitlever and photodetector

In this figure, vertical bending is detected as "(A+B)-(C+D)", i.e. the difference of the top two and bottom two segments. On page 53 the book erroneously says "(A+B)-(C-D)".

 

  • Page 56 - Figure 3.6 Should read: "B-intermittent contact oscillation (large)".

 

  • Page 66 - Legend refers to colours in the image where there are none.

 

  • Page 114 - Section 5.2.4: Three-dimensional views. Should read: "...special glasses to differentiate the left eye's and right eye's views...".

 

  • Page 116 - Table 5.2. The Formula for skewness is incorect. The exponents should be 3, not 4. i.e., as shown below

Skewness formula

 

  • Page 164 - Misspelling of "fimbriae" as "fibriae".

 

Thanks very much to everyone who informed me of these errors!

Frequently Asked Questions about Atomic Force Microscopy

by Peter Eaton

This FAQ was originally created for clients of the AFM, i.e. those whose samples I scan.
However, it's grown a lot, and should also answer many questions of people planning to use the AFM themselves, or researching the technique. Its contents include a description of AFM suitability to various samples, sample preparation, tips for scanning and data processing, and a short bibliography. There is also a guide to recognising artifacts in AFM.

All the material here is discussed in greater detail in the book "Atomic Force Microscopy".

 

Afmhelp.com has just been published, it does not have much content right now, but it's coming soon.

The website will launch towards the end of 2009, for more information see "About AFMHelp.com".

About AFMHelp.com

 

  • What's this site about?

  This site is designed to offer help with atomic force microscopy (AFM). AFM is an amazing and powerful technique for measuring images, and making other measurements of a wide range of samples. However, it can be rather daunting to use, especially for the beginner. On this website, as well as in the accompanying book we've collected a lot of information that explains how AFM works, and howto use AFM, and to process and analyse the images.

 

  • What's AFM?

There's a lot of information about AFM all over this website,  but for an overview, take a look at the AFM: Beginner's Guide page, and for frequently asked questions check out the AFM FAQ.

 

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