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At the moment I am processing an orthomosaic from a plantation and I would like to remove all pixels at ground level to just keep the plants captured on the image.

I would prefer to be using QGIS.

I created the orthomosaic in Agisoft Photoscan by using aerial multispectral imagery.

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You do not need the orthomosaic to do what you want to accomplish. What you need is to export from photoscan the pointcloud as a LAS file. This kind of file is for LIDAR data, but you can also use them from photogrametric point clouds.

After this you can install lastools (if you are using a QGIS version previous to 3) and

  1. Use lasground to identify ground points
  2. Use lasheight to normalize height above ground
  3. Use lasclassify to identify High vegetation and buildings
  4. Use las2las to filter the las/laz pointcloud to isolate vegetation
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