Do you have any information on your instrument, how you take the chlorophyll readings? I see a good bit on how you are wanting to automate the data capture, but I didn't see a description of the fluorometer. I volunteer with LMVP (Lakes of Missouri Volunteer Program), and they conduct water quality monitoring. Their algae sampling is quite formal, where filtered, freeze-dried samples have the chlorophyll extracted and fluorometry is used to measure the chlorophyll. While the collection and freeze-drying is done by the volunteers, the analysis is done at a lab. I am interested in seeing what can be done on a local basis, with simple equipment. Looking at commercial probes, I do not see that they are that far different from the desktop spectrometer. LEDs in the 420-470 nm wavelength are easy to obtain. Have you looked at anything in this direction?

We do have some information about the unit itself and the science behind it if you go to our project page at https://opendesignengine.net/projects/photosynq/documents. I try to put together the data and experimental results there as we go along, though I'm a little behind on that at the moment.

I think you are right that we don't explain the science very well... thanks for prompting me to do something about it! I just added the below bit to the "how does it work" part of our webpage:

Well, different techniques do this different ways. As you did in Missouri, the classic way is to take a sample, break up the cells, remove the chlorophyll, and measure chlorophyll concentration in a controlled lab environment. That's time consuming and difficult. We're doing that same measurement without killing the plant or algae.

Eventually the device will measure many different aspects of photosynthesis, but the base unit will focus on a technique called pulse modulated fluorescence. The goal is to measure how much infra-red light (in the 680-700nm range) is being emitted by the chlorophyll in plant and algal cells in response to absorbing visible light. This infra-red 'fluorescence' relates directly to the amount of energy being absorbed by the plant to do useful work!

(didn't know that plants fluoresce? Well they do! You can see how much by looking at pictures from an IR camera... and if you want an IR camera you can get an open source one from these guys)

The problem is there is a lot of similar infra-red light coming from other sources (like the sun). In order to separate those two sources, we apply short pulses of visible light (25 millions of a second long) to the surface of the plant. The plant gives off pulses of infra-red light in response to the visible light pulses without perturbing the plant (very much). A detector is placed in front of the plant/algae to pick up the infra-red emissions. This detector only measures infra-red light (it doesn't respond to visible light) and it uses AC filtering to pick up only the pulsed infra-red light from the plants, ignoring the constant infra-red sources coming from the sun and other stuff in the environment. From this, we can figure out how much light plants are absorbing to do useful work (like make sugars and build more plant)!

In the long term, we'd also like to measure absorbance at various wavelengths, CO2, temperature, humidity, and other stuff.

For a in-depth discussion of measuring different aspects of photosynthesis, please read this paper for details: https://opendesignengine.net/documents/17

I hope this is useful - let me know if it's not and maybe I can improve the explanation.