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, 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 (topography), and extract statisitical information. Can do automated DNA contour tracing. Documentation is here and source code is here.

You need a Python environment 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. Maintained, or at leat setup, by the AFM and SPM section of the RMS.

WSxM - Appears to be no longer available

Freely available software that supports many SPM file formats; and has many analysis tools. I personally like the 3D rendering results from WSxM a lot. It was originally developed by an AFM manufacturer for use with their instrument, but later became 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.

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. Not very geared towards SPM data, 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.

 SPM Image Magic