3D Robotics

Misconceptions about UAV-collected NDVI imagery and the Agribotix experience in ground truthing these images for agriculture

Posted by Daniel McKinnon on June 10, 2014 at 3:47pm

Thanks to all of your for your great feedback on my last blog post on airframe selection. There has been a lot of interest and misinformation about NDVI images on here recently, so I thought the topic deserved its own post. Briefly, I explained a little bit of history, why NDVI may not be the best index for UAVs, and showed some ground-truthing we did with NDVI maps. It ended up being a little too long to summarize here, but check it out at http://agribotix.com/blog/2014/6/10/misconceptions-about-uav-collected-ndvi-imagery-and-the-agribotix-experience-in-ground-truthing-these-images-for-agriculture

I would encourage anyone interested in the topic to check out some of Compton Tucker's original papers on the subject as they are really illuminating as to how the index came about. There is a lot of home research on Public Labs dedicated to making NDVI work with different systems, but NDVI was never a golden standard and different equipment may require different image processing metrics.

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Replies

  • Antonio Vigoni June 19, 2014 at 2:39pm

    Canon sx260 + Event38

    Agribotix script and LUT

    Mais 

    mais1.jpg

    • James Slizewski > Antonio Vigoni June 19, 2014 at 3:14pm

      Hi Antonio, 

      If I may ask what image processing system are you using? Fiji (ImageJ)?

      Thanks,

      Jim

    • Antonio Vigoni > James Slizewski June 19, 2014 at 10:45pm

      I used ImageJ

      The same photo with AgPixel, nice program but too expensive

      mais1.Enhanced3.jpg

  • This reply was deleted.
    • 3D Robotics
      Daniel McKinnon June 19, 2014 at 10:20am

      Hi Richard,

      For a camera equipped with the Event38 filter, I believe green is a better choice than blue because the blue channel picks up quite a bit of NIR signal. Based on my fairly unscientific experiment of imaging a hot stove that was not emitting in the visible and quantifying pixel intensity, I saw that the blue channel picked up about 80% of the NIR of the red channel and the green channel only picked up a small fraction. I don't have the exact numbers handy, but you should do the experiment yourself if you're curious.

      That said, for both the Schott and Event38 filters, the channels are really blue + NIR, green, and NIR. A more or less intact green channel seemed valuable for calculating vegetation indices, but, if you play with my script, you'll see there is really no difference in between using the blue or the green as the visible channel, so it probably doesn't matter which one you choose.

      I haven't compared the two filters in detail, but I have done significant ground truthing with images taken using the Event38 filter and the NIR-VIS index and can say with confidence that we are getting solid results. I will show some of them off at DroneCon, if you'll be there, but if not I'll write up a blog post in the next week or so. I think you would likely get good results using the Schott as well.

      I would also be careful with plots like the one you attached. There are a lot of reflectance spectra out there that try to present the information too generally. What is a healthy plant? What is an unhealthy plant? The sensitivity of the detectors in different cameras are also not widely published and I think the solution to developing a reliable vegetation index is just going out and collecting a bunch of images and seeing which ones correlate to what's going on on the ground.

      Good luck with your imaging and let me know if I can answer any more questions!

      Best,

      Daniel

    • 3D Robotics
      Daniel McKinnon June 20, 2014 at 7:09am

      Hi Richard,

      This is the other common way to collect NIR images and there are a few posts on Public Lab about using this technique. You end up with NIR, green, and NIR+red channels. Before I figured out that DVI images were groundtruthing very well (I will post a bunch more examples in the next week or so), I was a little frustrated with NDVI and was planning on trying this out. Imaging is going very well now, so I'm sticking with our current setup, but I want to play with this this winter when things slow down to compare the two. I suspect they are equivalent, but it would be nice to know for sure.

      Best,
      Daniel

    • 3D Robotics
      Daniel McKinnon June 20, 2014 at 7:04am

      Hi Richard,

      Your reasoning is spot on. So much NIR light leaks through the blue channel that theoretically using the green should deliver better results. However, I just don't see that practically. Generating a DVI image using the blue yields an almost identical result to using the green. I believe its because there is a much greater difference between the NIR and either the blue or the green than the blue and the green.

      We use Fiji for the calculations. I don't think it makes much sense to buy Pix4D unless you also need it for the stitching. I've never used AgPixel.

      Best,

      Daniel

  • Moderator
    Jost Laznik June 15, 2014 at 9:28am

    Dear Daniel

    Congrats for good work (Ned you to, amazing job)

    Daniel i tried to run your script for DVI index and ran on this error. Enclosed it is an image with the error.

    thanks

    jl

    Untitled.jpg

    • 3D Robotics
      Daniel McKinnon > Jost Laznik June 15, 2014 at 4:48pm

      Hi Joscht

      I believe you are trying to select your image when prompted for a LUT (lookup table). Download the Agribotix_LUT from one of the previous posts on this thread or use any other LUT (they use .lut as an extension) and open that instead of the image. The script will ask you to select the folder containing your images after that step.

      Best,

      Daniel

    • Moderator
      Jost Laznik > Daniel McKinnon June 16, 2014 at 11:42am

      Works amazing

      thanks

  • John Stuart June 13, 2014 at 7:05am

    I'd like to add another mosaic. With more time on my hands, I tried two things based on the feedback earlier in the thread:

    • I played with the DVI scaling parameters in the plugin till I got a more realistic value (in this case 0 to 128) - this fixed the saturation problem and I now have an image that contains as much information as the NDVI version.
    • I removed the shadow parts from the NRG and ran the NDVI process on the 'de-shadowed' version.

    The result is two images that on the face of it contain very similar information and apparent usefulness. Daniel's original claim that DVI is very effective in dealing with false NDVI from shadow is completely backed up by these images. On the other hand, using a colour-replacer batch script on your images after defining the colour representing shadow and setting tolerances will also produce shadow-corrected NDVI images.

    NDVI vs DVI v2.jpg

This reply was deleted.