🎈 Public Lab: Horticultural Spectrometer Upgrade

Horticultural Spectrometer Upgrade - Planning

by jenjimah | April 07, 2019 01:50 07 Apr 01:50 ... | #18991 | #18991

Objective: To create a spectrometer that has a few optimized functionalities for horticultural lighting research. This puts the price point up a bit, but hopefully will stay no greater than $100 USD.

How will this spectrometer be used?

A calibrated spectrometer that measures ambient light is an important measurement tool for high quality horticultural lighting research. For many experiments, the goal is to evaluate various light treatments (e.g. with varying intensity or spectral quality) to see which produces desired outcomes in plant growth, flowering, or morphology (plant shape). A spectrometer is used to measure exactly how much light at which wavelengths will be received by the plants under each treatment. However, knowledge of just the lighting fixtures is not enough, because the intensity per m² changes with distance from the source roughly following the inverse square law, and also due to nearby reflective surfaces. Thus, the exact intensity has to be measured on a plane relevant to the plants, such as canopy height.

A practical method to characterize the light treatments is to take a series of measurements at pot-height or canopy-height after setting up the lights to get an average intensity and standard deviation, and to gauge the consistency of spectrum over the treatment area. Sometimes, if light intensity is substantially brighter in the center of the plot, this can be managed by periodically rotating the plants within a treatment (e.g. every few days) to reduce effects due to light variation.

Functionality Needed:

Extended range (at least 400 - 800 nm). UV would be great but technically too difficult to achieve
High resolution (1-2 nm)
Wavelength & Gain calibrated (using Spectral Workbench)
Live capture with a button to capture a "Dark spectrum" (noise subtraction), ability to set # of captures to average, and option for an output graph giving data in photon flux units (micromoles * m^-2 * s^-1)
Integration of light from 180 degrees (hemisphere) centered in the direction of the spectrometer opening, so the output represents the photon flux density on a horizontal plane.

Upgrades required to achieve above functionality (based on the lego spectrometer kit):

1. NoIR camera upgrade to achieve extended range into the Near Infrared (NIR). This requires the use of a Raspberry Pi Zero W

2. To improve resolution: In addition to the 8 MP camera, an upgraded diffraction grating and use of razor blades for the slit (target 0.1 mm) should maintain acceptable resolution. (Photos and Measurements from dhaffnersr explained why using razor blades is a good choice, and see Optimal Slit Width post by stoft about why 0.09 mm is desirable)

3. Calibration of wavelength can be done with a fluorescent light, gain can be calibrated using solar measurements or known light source (e.g. Solux)

4. Live capture and processing will be achieved by programming the Pi Zero to act as a webcam, so it plugs into the USB slot in the laptop and can be used to Live Capture on Spectral Workbench just like any other webcam, except we maintain more control over the exposure time and camera settings. The extra processing required may be programmed on the Spectral Workbench capture module using Scripts, and since it's being processed on the laptop, the processing speed should still be fast.

5. To enable light capture from 180 degrees centered on the direction of the spectrometer's opening, a cosine correcting diffusing material can be used, so that the light is collected from the entire horizontal surface of the spectrometer's tube opening rather than relying on the light being shone directly into the slit. I found a few candidates < $15 so far from ThorLabs.

Reference Professional Spectrometer:

STS-RAD from Ocean Optics

Range: 350-800 nm
Grating: 600 g/mm
Slit: 50 µm
Resolution: 3 nm
Sampling Optics: CC-3-DA direct-attach cosine corrector (diameter: 7140 µm)

Progress:

June 25, 2019 - Assembly III(Final Assembly)

June 12, 2019 - Described a Method for HDR Imaging

June 12, 2019 - DVD vs. Holographic Film grating comparison

June 2, 2019 - Assembly part II

May 30, 2019 - Assembly part I

May 26, 2019 - Raspberry pi running with IP Camera accessible over USB as an ethernet gadget using this tutorials:

April 13, 2019 - All materials sourced except razor blades

April 2019 - Currently, I'm sourcing all the parts for this project. I just wanted to lay out my ideas in case anyone has some feedback before it's built. I'll try to update here as it progresses.

20 Comments

This is really cool! We'd love to see build photos as you go. We're also really interested in lighting setups and would love to see more documentation online about how to properly control lighting! Thanks!

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Hi Warren, thanks! I'll definitely try to document my process well as it comes along. I have a lot of motivation to get this going because I want to start some home based horticultural research, and be set up before the end of the summer '19.

Just for clarification, what are you referring to regarding lighting control? I'm guessing you might be talking about calibration, but I the point of this spectrometer is to characterize lighting setups for plant experiments so I wasn't sure.

On Mon, Apr 8, 2019 at 1:51 PM \<notifications@publiclab.org> wrote:

Hi! There's been a response to your research note 'Horticultural Spectrometer Upgrade - Planning'. You can reply to this email or visit this link:

https://publiclab.org/notes/jenjimah/04-07-2019/horticultural-spectroscope-upgrade-planning#c23768

warren wrote:

This is really cool! We'd love to see build photos as you go. We're also really interested in lighting setups and would love to see more documentation online about how to properly control lighting! Thanks!

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Interesting project.

I did not readily find spectral response curves from Sony on the IMX219 sensor though others in that family of devices appear to have some sensitivity out to 800nm. Might be good to find real data.

On #2, 'good' diffraction gratings are expensive and I suspect for IR more so. For upgrades to the DVD material, I'd suggest focusing on 'true parallel' gratings on rigid material as the distortion from curved DVDs or from holographic film gratings are a bigger issue IMHO than line density. Just a thought. Agreed; a razor blade slit is best; totally opaque with very well defined slit opening edge - just keep them parallel.

On #3, yes CFL for wavelength is good as other choices get very expensive. For amplitude, I'd suggest the Solux 4700k halogen as there is data to 1100nm and the spectral output curve is 'smooth' and stable after warmup.

On #5, I may not be following your optics, but remember the slit provides light collimation and thus formation of a very narrow-angle ('beam' if you will) of photons orthogonal to the diffraction grating to produce the grating's interference pattern to produce the spectrum. Please pardon if I missed your point, but light 'shining directly into the slit 'at' a small # lines of the grating is want you need. Think of it as illuminating only limited number of grating lines - 20? 50? or such as opposed to the entire grating. The 'broader' the illumination of the grating, the greater the distortion (spreading) of the spectrum because the incident angle changes. If you are wanting to collect light from a larger physical area (to integrate the light collection perhaps) then I can understand collecting light by optics or reflection to a diffuser 'spot area' and then 'point' the spectrometer slit at that spot.

Hope these few thoughts are helpful. You could also browse here: [ https://publiclab.org/notes/author/stoft ] in case some of my past related observations provide some useful ideas for your project.

Cheers, Dave

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Hi Dave, I looked at some of your posts before writing this one, actually! Your work is super helpful.

I also couldn't find IR data from the Sony IMX219 sensor, but I just sent them a message so we'll see if they can give any information when they respond.

On (2) Did you or anyone try comparing the rigid grating (I think the upgrade kit from Public Lab has rigid gratings) vs. the holographic film ones? I tried searching but didn't find anything.

On (3) Solux 4700K seems like a good option for the relative gain. I still would probably want to use the sun for absolute intensity management - perhaps those two combined with CFL for wavelength calibration would give something really nice.

For (5) The diffuser is a common attachment on ambient light spectrometers like This STS-RAD from Ocean Optics. This is the type of spectrometer I'm used to using for characterizing LED or sunlight intensity at crop level, i.e. an ambient light spectrometer. The idea is that a leaf receives light from all angles, but not all angles equally (mostly from perpendicular direction to the leaf surface) so the diffuser integrates the light hitting the horizontal plain.

It's possible that the diffuser might negatively affect the resolution, but in the STS-VIS and other spectrometers I believe it really just is the diffusing material hovering a short distance above the slit. Since the lego model already has that tube sticking out, I figured if I put the diffuser over the tube it would be very similar.

Thanks for your comments! Jasmine

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Jasmin, glad my previous notes were helpful.

I did find one plot for the IMX219, but it was not from Sony and only covered to 700nm. The IMX265 curves do appear to better push the range out past 700. The reason I mention this is that as the response 'tails off' the sensitivity often drops quickly and noise swamps the measurements.

True, the solar spectra is fairly well characterized. However, there are a few practical difficulties. 1) The shear intensity of sunlight overloads the spectrometer. While neutral density filters can provide attenuation, those filters need their own calibration data (though good ones might be flat enough over 400-800nm -- but again, good response data would be required to know it). 2) Solar spectra changes with a) time of day, b) atmospheric water vapor, c) altitude, d) latitude, etc. so you'd need at least some good reference curves which match your measurement location and environment. The curve differences are significant -- which is why digital camera's have deg-K whit-balance settings ... just to get a simple approximation. Finally, the solar spectra isn't actually flat or smooth (though for a simple spectrometer one can average...) So, a local broadband source, which has spectral data, is rather convenient.

Ok, so you are just wanting to average the received light so the diffuser would both integrate the light and act like a distant source. However, the photons which reach the diffraction grating will still be those whose incident angle is inline with the slit and diffuser; all others will just be scattered in other directions. A typical result (for the PLab web-cam type spectrometers, is reflected-light (reflected off the subject[plant]) being very weak. This is quite different from the 'typical' PLab experiment of looking a absorption by a liquid of light from a direct source. From my own similar experiments, this will likely require a very bright light source and-or (can't use a 'slash' in this on-line editor) get quite close to the plants. This just means some preliminary proof-of-concept experiments for light level. After all, you are interested in only the reflected light, not the source light.

Of course, this raises the question: Could useful information be gleaned from simply extracting RGB hostogram data from a color photo of the plants (and doing the analysis in software...)?

Or, using the spectrometer but looking at a bright light source shining through leaf material -- and integrating many results from many leaf regions? Just other thoughts.

Dave

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Hi Dave, I just heard back from Sony regarding the IMX219 Sensor response. Here's the pdf and a screenshot: IMX219_Spectrum.pdf

Although it does trail off, it seems like it should still give usable data up to around 800 nm, from the way it looks. Once I get all the parts confirmed, maybe I'll make a post with as many datasheets as I can find for everything and just list them all together.

For the solar spectrum, I think you're right that a smooth spectrum emitter is better for relative intensity, since it won't be affected by the atmosphere. I'm really interested in getting a calibration for absolute intensity though (e.g. Watts per m²) and that's where the sun comes in handy.

For example, for an 8 month period I measured direct solar radiation with my lab's spectrometer and calculated its intensity, and found that when there are no visible clouds or haze over the sun, the intensity is quite consistent with solar elevation. I published the data recently in the last Appendix in my masters thesis (here). One thing I didn't get a chance to delve into is how closely my measured data corresponds with simulated data, for example solar simulators like MODTRAN, although I'm also looking for an open source version of a solar simulator that can take the atmosphere, water vapor, latitude, longitude etc. into account.

If the simulated data match closely with measured data, which I'm hoping it does, then it would be reasonable justification to use the sun as just a absolute intensity calibration. So the order would be 1) use CFL for wavelength calibration 2) use Solux for relative intensity correction and 3) use a few clear-day direct solar measurements for absolute intensity calibration. Maybe if I have the diffuser on, and use a very short integration time, the sensor won't be flooded, but I am not aware if there is a minimum integration time that can be used for the NoIR camera hooked up to the Raspberry Pi.

As for the plant measurements, I think I should add a paragraph in the research note describing how this will be used. It's not for looking at the plants, but just for characterizing the light sources that will shine on the plants. This is for lighting research in horticulture, where I want to design various light treatments to see how plants respond under different spectra. However, in order to have useful data, it is highly important that the light spectra and intensities are well characterized so if you compare two spectra a) it's controlled and repeatable and b) it's a fair comparison so one treatment is not giving more photons from 400-700 nm than the other so the differences will be attributable to spectral quality and not due to overall photons available for photosynthesis.

Definitely, looking at the RGB reflectance of the plants using photos would be another useful form of analysis, which I may do. I've seen other people get reasonable results by putting the leaves in a scanner as then the lighting is very consistent and you don't have to deal with shadows.

Sorry it seems this comment is a little long winded!

Jasmine

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Ah, I've seen the curve on the web but it was not attributed to the specific sensor. It's helpful to now have that information. It looks like the double response from B&G improves the sensitivity out near the IR.

It appears you want to use the sun as an absolute reference for W per M² and therefore "calibrate" another (eg LED) light source for intensity. However the sun's distance means that light is uniform over area. A local light source (plant lights) would be quite close so intensity follows the inverse-square law so would not be uniform....

I suspect the Sony sensor is made via an extremely repeatable process such that relative to any simple 'absolute power calibration' based on some known spectrum (eg. solar) a one-time measure (for a single given mechanical configuration of a spectrometer) is all that would be required. I suspect sensors would not vary by much in sensitivity -- though the data sheet should have numbers.

Ok, so your interest in only in the light sources ... so the plants are therefore not part of the measurement. That means you would just perform direct measurements of various light sources -- no reflectance measurements. Right? That simplifies some things.

Characterizing the light applied to the plants could take several forms. Eg: 1) Step-and-repeat the spectrometer over an area of light (for the plants) for a given source and map both average intensity and spectral content, 2) attempt to diffuse via collection of light from a broad area to find an average, 3) if the light is bright enough, place the source at a distance, measure the spectrum (rough diffusion via distance) and the average a few near-field measurements for average intensity.

I'm just guessing here as I'm not visualizing the full concept of your experimental hypothesis, clarity of the required results, the methods to acquire the data or the uncertainty of the measurements (to know the expected limits to the proposed methods). Perhaps these would be good thought experiments to design up-front as a proof of concept. Measurement uncertainties have a way of creeping in and having significant affect on final results.

Dave

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A few more thoughts...

On absolute 'average' intensity - You could use a Solux source (at fixed distance and known orientation) as a transfer standard. This would mean finding an attenuated solar measurement with close to the same measured level as a setup with a Solux lamp but then you would have a portable 'standard'.

On camera integration time: There are limits. If the source intensity is beyond some limit, the sensor will simply saturate no matter the exposure window. At lower intensities, there will be a trade-off with noise. Integration time is necessary to obtain sufficiently low measurement noise levels to not affect the collected data. SNR is really important with spectrometer measurements -- especially toward the IR where the sensitivity is dropping rapidly.

Dave

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Research note

Horticultural Spectrometer Upgrade - Planning

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