I am trying to produce plant height with a digital surface model "TIF" file that was obtained with a drone. I have clipped out the section with plants and then used "Gap Fill" to produce a digital terrain model. I then used the "Minus" function between the surface model and terrain model.

Does anyone have any other ideas on how to do this that are not so time consuming. The results I got were not very accurate either compared to the in field measurements.

The picture below is of sunflower plants that I would like to get the height of. I would need the height of an entire section. Not a single plant.

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1 Answer 1


Create a bunch of points in the green (flat field) portion of your surface. Add the elevation values to these points using SAGA tools or the Point Sampling Tool. Interpolate a new surface from these points. Subtract the interpolated raster from your drone surface. The areas that are flat field should be zero or close to zero and the areas that are sunflowers should have values above the field elevation.

Be forewarned. Drone surfaces of vegetation are quite suspect since the drone is capturing images of the plants from different angles/distances through the leaves. Consider the example below...The first image is a hillshade created by Structure from Motion (SfM) software of a river with the adjacent coniferous forest circled in red. The second image is a LiDAR derived surface of the same area. As you can see the SfM surface does not do a good job representing plant height since the SfM surface cannot properly model the plants.

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  • Nice solution. Works great. I just used "Regular Points" then manually deleted those points that were above the vegetation and "IDW Interpolation". The trick now is finding a way to automatically get to these points above vegetation with the "Graphical Modeler'. I was thinking of combing with NDVI or something. Thanks.
    – Dan Olson
    Feb 7, 2020 at 18:51

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