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.

 

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 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

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.
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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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We will be running a two-day AFM course at The Bridge, at the University of Lincoln in June. Details can be found on the page linked below. You can also email me directly with questions.

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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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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".

 

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  1. About the author
  2. How Does AFM compare to SEM?
  3. Noise measurements on the TT-AFM
  4. AFMBioMed 2020

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