Detecting and measuring planting gaps (precision agriculture)

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After the great success of the Oil palm trees counting thread (Thanks Anna and others), I am here asking for another help with UAV imagery in precision agriculture.
Giving a proper orthomosaic of a plantation (RGB or NDVI), I want the software to detect and measure plantation lines and plantation gaps, I attach a picture to better explain but don’t consider the low quality, i still have to do the orthofoto.
Do you think is possible with ImageJ?
Thank you very much

Oil palm tree counting

Hi Lanzo,

what exactly would you like to measure, e.g. percentage of gaps per line?
In general you need two steps: 1) segment your trees and b) detect your plantation lines.

For segmentation of the trees I tried converting to HSB-stack, slight morphological closing (MorphoLibJ needed) and then thresholding:

run("HSB Stack");
run("Duplicate...", "title=Brightness duplicate range=3-3");
run("Morphological Filters", "operation=Closing element=Square radius=2");

I then searched for a solution to automatically identify the individual plantation lines. I automatically determined the median distance between lines (in this image around 38 pixels) and then was thinking to shift a user-drawn poly-line by this value. This does not work well because of non-regular distances between and unregular shape of the plantation lines in the image.

So for now I can only think of rather ugly manual approaches:
To get the percentage of gaps:

  1. Manually draw a poly-line along one plantation of linewidth 1 in the binary image.
  2. Measure Integrated Density and Area. Ratio of gap/plantation line is: Integrated Density/Area*255

To count the number of non-gaps:

  1. Manually draw a poly-line along one plantation of linewidth 25 in the binary image.
  2. run("Line to Area");
  3. run("Analyze Particles...", "size=5-Infinity summarize add");



Hello Lanzo,

Here is a paper that deals with your situation using QGIS and R. Still is not totally automatic but it gives good results:

I hope it helps. Best regards,


Sorry for no reply, I am far from home, as soon as possible I will check everything, thank you very much