The NIR illumination is probably not needed because daylight is a very consistent source of lots of NIR (although using NIR illumination at night could work well). If your goal is to distinguish healthy plants (weeds) from bare soil, your task is fairly easy. Healthy foliage reflects many times more NIR than most bare soil.
Above: Pure NIR (>720 nm) photo of live dandelion surrounded by bare soil. It's easy to tell what is plant and what is not.
An index (e.g., NDVI) is not needed because a pure NIR photo probably produces more contrast between plants and soil. If you are using a good red filter which passes only wavelengths longer than 600 nm, then the blue channel of those photos could be a rather pure NIR photo. Exposure, focus, and processing might be easier with a pure NIR filter like Wratten 87.
If the soil is not bare, the task could be more difficult because old leaves reflect some NIR. In that case it could help to use an index which compares NIR with visible light.
Above: Pure NIR photo (>720 nm) of the same dandelion before I removed the old dead leaves covering the soil. The contrast is not so great here.
Above: NDVI image of the same dandelion on leaf-covered ground. This image was made from a single photo taken with a long pass filter at 620 nm (so the blue channel captured mostly NIR and the red channel captured both NIR and red).
Although an index like NDVI can be helpful, producing useful NDVI images requires a good filter, good exposure, custom white balance or calibration, and image processing. It has to be done carefully to get better results than you could get with pure NIR photos.
Thanks for the in depth answer Chris! If i needed to use this system in low light or night, do you think I would need to add NIR light, or is there some present in a regular led light? As I said above to William, by the looks of your examples above I might loose the weed in the image using NIR. I can play with both and see which one works best. Thanks again, Adam
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I don't know how much LEDs vary in their NIR emission. But it's easy to add some NIR LEDs to the mix. There is an advantage to using only artificial lighting (doing the whole thing at night) because then the spectral quality of the illumination is constant. That can make computing indices (e.g., NDVI) more reliable.
One problem with lamps is that they could cast shadows which will add distinct patterns to the photos and also might compute to erroneous NDVI values (a common issue). Ideally, the lamps should be in a wide array behind a diffuser to reduce shadowing.
If you use lamps at night, the proportion of red to NIR might not be similar to daylight so standard indices will not give typical results. That is, legacy NDVI is based on the assumption that the foliage is being illuminated by sunlight which has a particular proportion of red and NIR. If you change this proportion, NDVI values could change and be out of the expected range for NDVI of healthy foliage. That won't be a problem, but you will have to redefine the range of NDVI values which signify healthy foliage.