🎈 Public Lab: Raspberry + NoIR cam + Sensors to detect water stress of the plants during their growing

Raspberry + NoIR cam + Sensors to detect water stress of the plants during their growing

by LaPa | March 31, 2016 13:36 31 Mar 13:36 ... | #12900 | #12900

What I want to do

I'm an agronomist, I'm going to make a IR RaspiCam to do an IR Timelapse in greenhouse. I want add same sensors (temperature, moisture, soil moisture) at the IR Raspicam in order to link environmental condition to Health of the plant.

I wrote this previous research note https://publiclab.org/notes/LaPa/12-03-2015/how-do-i-set-a-costum-white-balance-of-the-noir-modulo-cam

My attempt and results

I built a IR camera + blue filter (# 2008) by Raspberry Pi in order to have the time lapse movies of growing plants in greenhouse. I would like especially to detect the water stress or the micro water stress during the stage of growing of the plant o during the day. So I placed the IR camera in a greenhouse at the first stage of growing of the plants of cucumber. The camera use a custom white balance according to https://publiclab.org/notes/LaPa/12-03-2015/how-do-i-set-a-costum-white-balance-of-the-noir-modulo-cam

I posted my first attempts with IR on youtube: the first one portrays 3 water stressed plants of primula just after water supply. Indeed you can see in the time lapse movie the leaves of the plants to increase their turgor as clear demonstration of the reduction of water stress.

Here is the movie by raw IR photo https://www.youtube.com/watch?v=545sW7hBGVM

I use "ImageJ (FiJi)" + "photo monitoring plugin" to elaborate raw IR photos into NDVI by using InfraBlue.lut that you can see here https://www.youtube.com/watch?v=DUKliCFogxA.

Here you can see the transformation into NDVI using VGYRM.lut https://www.youtube.com/watch?v=vs8DS24s9j4

Here the timelapse of the first 7 days of the cucumber plants in greenhouse resulting from raw IR photos https://www.youtube.com/watch?v=PdglYb19DmM

And here that timelapse transformed into NDVI using VGYRM.lut https://www.youtube.com/watch?v=EAuAU7f2NvE

Questions and next steps

Now I am keeping to shoot photos of the growing cucumber plants in greenhouse. I'm going to elaborate those into NDVI again.

Have that sense for my goals? Could this technique be proper for detecting the water stress of the plants?

Am I going in the right direction?

Any suggestions?

If is it necessary I can send some single photos that I used for my time-lapses

If you consider useful to use Raspberry pi for IR green plant analysis, where I can post some images that I shoot?

Thanks in advance

Best regards by LaPa

Why I'm interested

1) Learn more about IR Images of the plants; 2) to identify by IR Images of the plants best of growing condition or the moments of the worst health (water stress) of the plants during their growth; 3) to use IR Raspicam on aerostatic baloon; 4) To build DIY weather tools by Raspberry Pi

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26 Comments

Hi LaPa,

Your time-lapse videos are impressive. These are excellent teaching videos. You can clearly see that the NDVI values for the foliage of the plants changes dramatically through the day. It is likely that these changes are not due to physiological changes in the plant (stress, growth, productivity), but instead to changes in the ambient light and/or camera settings. There are probably also changes in the plant health during these periods of time, but they are too subtle to see. These changes in plant health might produce a change in NDVI of maybe 0.05 or 0.1 or so if the plant was stressed by heat or drought. The color gradients you used have approximately the same color for NDVI values of (e.g.) 0.4 and 0.45, so the color of a plant leaf might not change much if it was actually stressed.

To allow a video like these to show plant stress, a few things must happen:

the ambient light must be constant or nearly constant (brightness, color) for the entire video,
the camera must use the same settings when each frame is captured,
if numbers 1 and 2 are not true, then each frame must be calibrated,
the color gradient used (lut) must have different colors for NDVI values of stressed and unstressed foliage.

There are not enough colors to differentiate all the NDVI values between 0.2 and 0.8 with enough resolution to detect small changes in plant health. So a special lut could be used to differentiate changes in NDVI between (e.g.) 0.5 and 0.3 using all the obvious colors.

Chris

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Hi @LaPa, great to see your note! I'm tagging some other raspberry pi developers @rjstatic and @seankmcginnis

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Thank a lot all of you for the consideration and the suggestions!

Chris, sincerely I didn't understand from your reply if you consider my direction completely wrong or just that I have a long way ahead.

But, anyway I try to answer to your considerations:

1) I'm using my camera in operative greenhouse (in farm), so the light and color conditions vary widely. And I can't change this. But I can choose some photos where the conditions are similar, for example in same hours of the day but in different days, and work with those.

2) I shoot several hundreds of photos, and I am continuing to do so, to make those movies the white balance is fixed in every photos. The exposure I guess is automatic so I think that vary in each photo. I think it is possible to set fixed exposure for each photo, but I have to understand how to do that.

3) I don't know how to calibrate the photos

4) Is there any lut that I can use in Fiji Photo monitoring plug in. If there isn't how to get the the "special lut to differentiate changes in NDVI" using Fiji Photo monitoring plug in?

Best regards

LaPa

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NDVI is based solely on color (near infrared is one of the colors). If a camera records different colors for two leaves, the NDVI computed for those leaves will probably differ. The color captured by a camera depends on the surface properties (spectral reflection and absorption) of objects in the scene and also the color and angle of the light illuminating the surface. To detect differences in the reflective and absorptive properties of objects, the light illuminating the scene must be constant. If the light is not constant, the change must be accounted for. Accounting for changing light conditions is done by "calibrating" the process.

One process of calibration requires that special surfaces (calibration targets) of known spectral reflectivity be included in the photographs. The color of all pixels in a photograph is adjusted based on the color of pixels in those targets. Some research notes at Public Lab describe the development of a procedure for calibrating the process, and a plugin for Fiji automates the process. There are still issues with the procedure, and no tests have been described which demonstrate that NDVI derived from the calibration process is always robust. Without calibration, interpreting the meaning of NDVI values should be limited to very general patterns.

It is easy to make new color look up tables (luts) in Fiji. When an image with a lut applied is displayed in Fiji, open the lut editor (Image/Color/Edit lut). Below is a lut in the editor which shows color only for the NDVI values between 0.38 and 0.5.

Almost every color used can be distinguished, so leaves with NDVI values of 0.4 could be distinguished from leaves with values of 0.45. With a series of calibrated NDVI images, this lut could allow a visualization of plants becoming stressed (assuming NDVI of 0.5 is not stressed and NDVI of 0.4 is stressed, and that leaves in the scene have NDVI values in that range).

NDVI_38-5.lut

Chris

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