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Gwyddion
Gwyddion 2.66   
... obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other height field and image analysis, for instance for analysis of profilometry ...
Open Source

JohanneumSTM
JohanneumSTM 20120512 Beta   
... accessible and useful tool for 2D and 3D STM viewing. This software is designed for DAQ systems by BMCM (we use the USB-AD16F), but it should not be too difficult ...
Freeware
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