GRASS GIS is one of the few vector topology engines out there, it can handle volumetric raster data ( Voxels), 3d vector data, works in a variety of ecosystems, GRASS functionality is accessible via a range of interfaces ... and completely free!

GRASS GIS https://grass.osgeo.org/ 

Thanks, Markus!

https://www.mundialis.de/

https://twitter.com/MarkusNeteler

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