This is a really good collection of information about photosynthesis and spectral analysis.

My understanding was that NDVI has largely been used for wide area scanning, but it isn't so useful at a per-plant level. However, in a controlled environment (such as an indoor aeroponics station or a small garden at night), per plant analysis might be possible by trying controlled experiments to separately judge reflectance+transmittance, phosphorescence, and heat; that leaves photosynthesis as the free variable. It might take a bit more than a single camera and a single light source for such a battery of tests though. If we figure out how to do those tests by hand, the next step is to automate it.

Btw, some of the information and graphics have linked sources, others do not. It'd be great if all the sources could be filled in.

Woops I skipped the part at the top where it seems to suggest in advertisement language that the PhotosynQ gives you this and more!

Any chance you could remove the PhotosynQ advert or describe how PhotosynQ addresses all of the salient bits of information about photosynthesis contained in the majority of the note?

Thanks Bryan. You're right that NDVI rose to fame as a satellite and airborne tool, and has only recently been used more widely at close range. It can work well up close, but it's potential might have been overstated in some of our presentations. Distinguishing stressed from healthy plants requires a well tuned Infragram camera and driving it very precisely. It's far from plug and play. And NDVI might never be as effective as fluorescence at this. The MultispeQ makes a non-fluorescence measurement (SPAD) that is essentially NDVI using light transmitted through the leaf instead of reflected from it. So it will be enlightening to compare that with fluorescence based measurements. And in a development of great symmetry, there are plans to map chlorophyll fluorescence from space using sensors aboard the OCO-2 which were intended to map CO2.(Great early animations of CO2 generation and dispersal.) The only way they can see the tiny glow of plant fluorescence from space is to look at the wavelengths of Fraunhofer lines where little sunlight reaches Earth. Are scientists clever or what?

The images in the note that do not have links were scraped from behind pay walls.

I have added a link to the description of measurements which can be made by the MultispeQ. I am still coming up to speed on understanding how these work and what they are good for. This note was intended to organize some information about the background science related to just one type of measurement (fluorescence) made by the device. I am the wrong person to explain much more about this. I don't even know what wavelength the device measures to quantify fluorescence.

I think I am flattered that my attempt to describe the context of the MultispeQ struck you as an advertisement. No two ways about it, this is a once in a lifetime opportunity to hold the power of a Real Scientist in your own hand. Don't delay, become a beta tester today!

Good stuff. From my perspective NDVI is good for mapping vegetation and can provide some indication of overall health and is good at differentiating between vegetated and non-vegetated areas but fluorescence is a better indicator of plant function. The remote sensing community is optimistic that in the next couple years new satellite sensors and algorithms will be able to provide decent estimates of global gross primary productivity (GPP) based on fluorescence measurements. Currently different estimates of global GPP vary by a factor of two. Passive mapping of fluorescence (usually called solar induced chlorophyll fluorescence [SIF] in the remote sensing literature) is not easy since, as the image above illustrates, the signal from fluorescence is very weak and it's difficult to separate that from all of the reflected light.

NDVI can still be useful at close range but it is quite different from coarse resolution satellite images. At close range a single pixel might fall entirely on a leaf but from satellite the pixel is a mix of leaves, branches, soil, shadows.

Apologies if I was being pedantic. Now that I think about it, cleaning up the note isn't a great solution. Instead of changing this note, the pertinant information would be great fodder for a wiki which could be cultivated, watered, artificially selected, and spectroscopically analyzed.

I saw @liz email about a high level farming wiki. This sort of content might make a good offshoot of that. I'll take a look.

I agree that this material is more appropriate for a wiki than a note, but I wanted people to see it.

Such a wiki should be built by somebody at PhotosynQ who actually understands this stuff, and the wiki should live at PhotosynQ where lots of people will be looking for information on how and why the MultispeQ works.

Stripped out all the juicy plant bits and spectral mumbo jumbo. added it here: http://publiclab.org/wiki/multispectral-analysis-for-determining-plant-health

Formatting is ugly on the wiki page, but whatever.

If PhotosynQ people want to make their own wiki, they're free to grab the content from your note here or the wiki page I made from your note. Everyone has a right to reproduce info and try to understand it and share it, just as you did. :)