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Question:Feasibility-check: NDVI analysis of moss

zomb23 is asking a question about ndvi: Follow this topic

by zomb23 | November 15, 2019 16:20 | #21496

Dear Public Lab community,

first of all: I just stumbled upon this website and I am impressed by how extremely thorough the projects and works done in this context are.

I am a researcher myself, looking for a method to estimate the photosynthesis rate of moss. The images I work with are recorded under lab conditions, so I have control over the light setting. I would like to be able to see, how the photosynthesis of the moss is affected by changing different parameters (light, humidity, airflow, ...).

My question is: How sensitive is the algorythm in terms of color-gradients. If the color of my moss changes slightly, will I be able to detect it?

On the images, solely moss and substrate will be visible. I would like to grow the moss at the same time I am evaluating the photosynthesis rate. Will the change in plant/substrate ratio on the images alter the analysis?

I assume these questions are quite simple but I would like to know, if I can use this technique in my studies before I dive into it.




I think NDVI will provide some information about the photosynthetic rate of mosses. Moss leaves capable of rapid photosynthesis will probably be absorbing more red light than slower growing leaves. If NIR reflection from those leaves is a constant, the NDVI equation will provide a larger value when high photosynthesis allows more absorbance (and therefore less reflection) of red. In herbaceous and woody plants, reflection of NIR decreases as leaves are stressed, lowering the NDVI value. I don't know if this also happens in moss leaves. So the relationship between photosynthetic rate and NDVI might be different in mosses.

When the change in photosynthetic rate is subtle, NDVI can still reflect the change. The colors typically used to represent NDVI values are not suited to display subtle differences, because only a dozen or so easily discernible colors represent all the NDVI values between no photosynthesis (0.1) and maximum photosynthesis (0.8). The NDVI numerical values will be required to document subtle differences, or color gradients can be made for subsets of the NDVI range.

To determine the NDVI value for moss, an area of an NDVI image where there is only moss foliage can be used. NDVI values for non moss areas in the image can be ignored.

For more precise estimates of photosynthetic activity, chlorophyll fluorescence can be used. Chlorophyll emits light in a narrow band when excited by light of another narrow band. The level of fluorescence can be used to estimate photosynthetic potential. Devices are available to measure fluorescence but it can be done with LEDs and light sensors.


Hi Chris, thank you for the quick and comprehensive response. That sounds really promising. I will look into chlorophyll fluorescence and if/how I could utilize it in my setup.

Based on your insights I already found a very interesting development by MSU, the DEPI chamber (Dynamic Environmental Photosynthetic Imager).


Seems to be exactly what I was looking for.

Thanks again!


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Chris, please look at my image taken from modified camera using red filter bought from Public Lab. Is this the correct results or should I do some modification to get the standard results. Thanks

Picture_40.jpg Picture_40_NDVI.jpg

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