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Atomic Force Microscopy$

Peter Eaton and Paul West

Print publication date: 2010

Print ISBN-13: 9780199570454

Published to Oxford Scholarship Online: May 2010

DOI: 10.1093/acprof:oso/9780199570454.001.0001

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(p.198) Appendix C Third party AFM software

(p.198) Appendix C Third party AFM software

Atomic Force Microscopy
Oxford University Press

(p.198) Appendix C

Third party AFM software

All commercial AFM instruments are supplied with image processing display and analysis software. In general, AFM image processing and analysis is usually best done with the software supplied with the instrument. The reason for this is that this is the only software that is sure to open the AFM data acquired by the instrument correctly. Due to the very broad range of available file formats that are constantly evolving to reflect new AFM capabilities, writing and maintaining a single program to open all these formats correctly is not trivial [737]. However, there will be cases where the user requires more capabilities than are available in the supplied software. Some of the manufacturer's packages are excellent and comprehensive, but others are rather limited, and some manufacturers even go as far as to supplement them by including one of the third party packages included in this section along with their own software. If the user decides to use a third party package, it must be done with caution, and even if the files can be opened the user must check that the data is scaled correctly. This can be quickly done by measuring a few points on an unprocessed image in both the original and the third party programs and checking they are identical. The following sections describe briefly the major third party software tools available for working with AFM data. Some of these packages are commercial projects; others are academic projects. All the packages described in this chapter are in current development at the time of writing. In the accompanying website at http://afmhelp.com some other abandoned or outdated packages are also listed, as well as details of how to get all the software described. The relative merits of these packages are not reviewed here, and their order is entirely arbitrary. It is worth noting that most of these packages are aimed at SPM rather than just AFM – so they also deal with STM or SNOM files. Except where otherwise described, these packages are designed for use in MS Windows operating systems.

Gwyddion – Free SPM (AFM, SNOM/NSOM, STM, MFM,…) data analysis software. Freely available, open source, cross‐platform software for manipulation of SPM files; this software reads many (>50) image file formats. The software is quite well documented, and as it is open source it is (in principle) possible to inspect the algorithms it uses. The package was developed by academics from the Czech metrology institute, and is updated quite regularly. Packages are available for MAC OS, Windows and Linux. All the procedures described in Chapter 5 can be carried out with Gwyddion.

Scanning Probe Image Processor – SPIP. Commercial software for manipulation of SPM files; it is probably the most comprehensive package available at the moment, but requires purchase of a license for extended use. A limited‐function demonstration version is available for free download. It supports a very large number (>70) of image formats, and in some cases also opens force‐curve data, and is updated quite regularly. All the procedures described in Chapter 5 can be carried out with SPIP.


Table C1. Some third party software for processing and analysis of AFM images.

Software Package








FemtoScan Online




Image SXM




WSxM – Windows Scanning x Microscope [738]. This is commercial but free software that enables control of the AFM instruments sold by the company that developed it, but which is also a processing and analysis software package. It opens many image file formats and also some force‐curve data, and it is updated regularly. All the procedures described in Chapter 5 can be carried out with WSxM.

FemtoScan Online. Commercial software from an instrument manufacturer, but which is also a processing and analysis software package that loads several other image file formats. A 30‐day trial version is available for free download.

PUNIAS (Protein Unfolding and Nanoindentation Analysis Software). This free software is dedicated to analysis of force curves, and force‐curve map files. It implements several of the common algorithms used for analysis of force spectroscopy and nanoindentation data. It is able to load force curve data from several of the most popular file formats. It is updated fairly regularly.

Image SXM and ImageJ. Both of these programs are versions of NIH Image, a public domain image processing and analysis program for the Macintosh. Image SXM is a Mac OS‐only version of NIH Image that has been extended to handle the loading, display and analysis of AFM images in several file formats. Image J is a cross‐platform image analysis program, again based on NIH Image. Packages are available for Mac OS, Linux and Windows. It is not specifically designed for SPM images, but there are plugins available to load a few file formats. These programs are rather limited in their applicability to AFM files, as they are not by default designed to work with three‐dimensional topographical data, but have many more ‘classical’ image analysis procedures, and so can be useful under some circumstances.

A list of urls linking to all the software described here is reproduced in Table C1. An updated listing is available at http://afmhelp.com. (p.200)