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AFM and STM 3rd Party Software for Image Analysis

Image SXM (Mac) 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. A paper about Image SXM Software for SPM Paper
ImageJ NIH Image software
Carpick labs software toolbox Matlab scripts to help with nanotribology research - i.e. friction measurements with the AFM.
Gwyddion (PC & Mac) 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
WSxM Program Freely available software that supports many SPM file formats; and has many analysis tools. It was developed by an AFM manufacturer for use with their instrument, but also supports very many other file formats. Unlike many third party programs, has good support for force curves as well. Frequently updated.
True Map 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 license must be bought for extended use.
Scanning Probe Image Processor (Commercial) An image processing program designed with focus on characterization of SPM instruments and accurate quantification of image structures. Other instruments like interference microscopes, profilers and scanning electron microscopes are also supported.
MIDAS is deconvolution software made specifically for the Atomic Force Microscope. This Web site is designed to explain and promote the dilation/erosion process.
3D Surface View Software Scientific visualization software package for quick creation of professional images and animation from various 3D and 4D datasets.
MountainsMap SPM image Image analysis software for SPM
List of Software for SPM