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GeoScene3D is perfectly suited for groundwater and environmental use, providing visualization, interpreting, editing, and publishing of many different types of geological data, for example drill holes, geophysics, water chemistry, terrain and geological layers. Geographic Information Systems Stack Exchange is a question and answer site for cartographers, geographers and GIS professionals.
How can we create GIS based 3d application like below attachment using opensource softwares in GIS.

Not the answer you're looking for?Browse other questions tagged openlayers geoserver javascript web-mapping ext-js or ask your own question. A leading developer of environmental GIS solutions, I-GIS customers include the Danish Ministry of Environment, Geological Survey of Denmark and Greenland (GEUS), Danish Road Directorate, most Danish municipalities, and all Danish agencies for spatial and environmental planning. All data types can be edited directly in 3D views, in cross sections, or in maps with a large range of tools.

I-GIS projects often involve high resolution geological mapping data prepared by associated organizations SkyTem and Aarhus University (also TatukGIS customers).

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