Biomedical Engineering Reference
In-Depth Information
Appendix C
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some other abandoned or outdated packages are also listed, as well as details of how to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.
