By default Metashape Pro assumes that the altitude values loaded to the Reference pane are estimated from the corresponding ellipsoid, however, in case the height should be estimated from the geoid it is necessary to select the corresponding compound system from the EPSG list or create the coordinate system that includes the vertical datum.


The steps below shows how the compound coordinate system can be created and the geoid model can be loaded. 


1. Download the corresponding TIFF from the geoids page of Agisoft web-site if available and put to /Metashape Pro/geoids/ folder and re-start Metashape Pro:
https://www.agisoft.com/downloads/geoids/

Or have the prepared file with the undulation grid (offsets between the ellipsoid and geoid).


* In the example we are using "DVR90 geoid model (EPSG::5206)" -> dvr90.tif file.


2. Open coordinate system selection dialog (for example, in the Reference pane settings) and locate the horizontal system that requires vertical datum to be applied and press Edit button.


* In the example we are using "ETRS89 / DKTM3 (EPSG::4095)" coordinate system.



3. Modify the new name of the coordinate system that will be created and in the "Vertical CS" field select the required vertical datum (geoid):




4. Modified coordinate system will appear in the section of User-defined coordinate system and will be available for selection at any time (for example, during coordinate system conversion):