A very kind mention of our book has been made on the blog from the people at NuNano. This was in an article entitled "12 Brilliant Books on Atomic Force Microscopy". The post is well worth a read, as it covers a lot of the best general texts out there, and some of the more specialised ones as well. Nunano have also been doing quote a lot to create better community around AFM, and their blog is a must-read for me. There is alot of very useful material on their website for the AFM User. Thanks a lot for the kind words, guys!
"This classic text was the starting point from which the website afmhelp.com emerged, run and regularly updated by author Peter Eaton, with the explicit objective to contain all the AFM related material they couldn’t fit into the book! There’s a lot of love for the website from the AFM Community and wholesale agreement that the book behind it is a must-have too."
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Atomic Force Microscopy (2010), 256 pp, OUP. ISBN: 9780199570454
"Atomic Force Microscopy by Peter Eaton and Paul West is the manual that should accompany any AFM." - Prof. Othmar Marti, University of Ulm
"This classic text was the starting point from which the website afmhelp.com emerged, run and regularly updated by author Peter Eaton, with the explicit objective to contain all the AFM related material they couldn’t fit into the book! There’s a lot of love for the website from the AFM Community and wholesale agreement that the book behind it is a must-have too." - Nunano.com
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The Oxford University Press page describing the book can be found here, although the contents listed there are out of date.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. There is also a Kindle Version 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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I've recently updated the SPM software list, with a couple of new (to me) programs, after many years! The links to the programs can be found on the software page.
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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 of one other existing list of SPM software[This one], although I dont think it's being 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/)
TopoStats
TopoStats is Python package that is designed to batch process AFM images (topogrpahy), and extract statisitical information. Can do automated DNA contour tracing. Documentation is here and source code is here.
You need a Python environemnt to run it.
Software for AFM & SPM data analysis
A community hub for Atomic Force Microscopy and Scanning Probe Microscopy analysis code. Has a few different programs availble, source code only, rather than standalaone packages as far as I can tell. aintained, or at leat setup, by the AFM and SPM section of the RMS.
WSxM - Appears to be no longer availble
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. Was frequently updated and available here. (http://www.wsxm.es/) - This link is now dead, if anyone knows of a current website, please let me know.
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.
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
A 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
Note: I welcome comments/suggestions for these lists, please contact me via the "contact" page.
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A request for help!
I am currently looking for one manual, and one piece of AFM control software:
- Topometrix Discoverer manual
- Nanocockpit software disc (CD-ROM?) This is the software to control a Nano-R AFM or similar from Pacific Nanotechology.
If you haveeither of these, please get in touch at This email address is being protected from spambots. You need JavaScript enabled to view it.
This page is intended to act as a repository for manuals for atomic force microscopes. At this time, there is relatively little information here (basically, the manuals I have .pdf copies of), but I hope that over time it will grow. If you have a manual for your instrument that you think could be useful for other AFM users, please send it to me at This email address is being protected from spambots. You need JavaScript enabled to view it..
I hope that this page is useful for AFM users, especially those who inherited older instruments that have become spearated.
AFMWorkshop
- TT2-AFM manual v2.3 - This .pdf file is the user manual for AFMWorkshop's 2nd gen TT-AFM , i.e. "Table-Top AFM"
- LS-AFM Manual v1.1 - This user manual is for AFMWorkshop's "Life Sciences AFM". This covers the AFM instrument, there may be a separate manual for the optical microscope from AFM Workshop if you have a copy of that one, please send it to me
- HR-AFM Manual - This .pdf file is the user manual for AFMWorkshop's "High Resolution AFM" instrument. Unlike the TT2 manual, it covers use of the v4.x software
- B-AFM Manual v1.0 - This is the user maual for the B-AFM from AFMWorkshop
Asylum Research (now Oxford Instruments)
- MFP 3D User Guide V13 - This is the .pdf file of the user guide for the MFP 3D Bio-AFM from Asylum which was since aquired by Oxford Instruments
- Cypher User Guide - This is the User guide for the Cypher "small sample AFM", from Asylum
Nanonics
- NWS User guide - This is the .pdf file of the user g uide for the NWS (NanoWorkshop) softwar euse dby Nanonics
- MV4000 user guide - This is the user guide (pdf) for theNanonics multiview 4000 AFM/SPM system. These systems are very unusual in supporting multiple probes scanning the sample at the same time (up to four I think).
DI/Veeco/Bruker
- Nanoscope Software 6.13 User Guide - This .pdf file is the user manual for the nanoscope software interface for any microscope using a nanoscope controller, i.e. the popular multimode and dimension instruments. This version is compatible with Windows XP latest.
- Multimode Instruction Manual v4.31 - This is a .pdf version of the instruction manual for the multimode microscope. This is based on a rather old version of the software (in DOS windows). Note that for these DI instruments, the controller and microscope have spearate manuals.
JPK (now a part of Bruker)
- Nanowizard User Manual - This .pdf file is the user manual for JPK (now Bruker) Nanowizard bio-AFM instruments. THis covers the version 6.0 software. As far as I know this means instruments up to Nanowizard 4. Covers hardware, control software and analysis functions.
Molecular Imaging/Agilent/Keysight
- Agilent 5500 User Guide revB - This .pdf is the user guide for the Agilent 5500 microscope, which I think used to be called the PicoPlus before it becasme an Agilent instrument
Other Documents
A Practical Guide to Scanning Probe Microscopy - This is a .pdf file of the SPM practical guide, which I beleive was first made by TopoMetrix, this is the Thermomicroscopes version. This is a very old document, but contains a lot of helpful information for AFM users, still. Not an instrument manual, it's a simple guide to the general principles of how an AFM works. If you read this and want something more in-depth, I reccomend this book!
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